bpp-raa-2.2.0/bpp-raa.spec000664 001750 001750 00000011614 12407766541 016736 0ustar00jdutheiljdutheil000000 000000 %define _basename bpp-raa %define _version 2.2.0 %define _release 1 %define _prefix /usr URL: http://biopp.univ-montp2.fr/ Name: %{_basename} Version: %{_version} Release: %{_release} License: CECILL-2.0 Vendor: The Bio++ Project Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz Summary: Bio++ Remote Acnuc Access library Group: Development/Libraries/C and C++ Requires: bpp-core = %{_version} Requires: bpp-seq = %{_version} BuildRoot: %{_builddir}/%{_basename}-root BuildRequires: cmake >= 2.6.0 BuildRequires: gcc-c++ >= 4.0.0 BuildRequires: libbpp-core2 = %{_version} BuildRequires: libbpp-core-devel = %{_version} BuildRequires: libbpp-seq9 = %{_version} BuildRequires: libbpp-seq-devel = %{_version} BuildRequires: zlib >= 1.2.3 BuildRequires: zlib-devel >= 1.2.3 AutoReq: yes AutoProv: yes %description This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc. It is part of the Bio++ project. %package -n libbpp-raa1 Summary: Bio++ Remote Acnuc Access library Group: Development/Libraries/C and C++ %description -n libbpp-raa1 This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc. It is part of the Bio++ project. %package -n libbpp-raa-devel Summary: Libraries, includes to develop applications with %{_basename} Group: Development/Libraries/C and C++ Requires: libbpp-raa1 = %{_version} Requires: libbpp-seq9 = %{_version} Requires: libbpp-seq-devel = %{_version} Requires: libbpp-core2 = %{_version} Requires: libbpp-core-devel = %{_version} Requires: zlib >= 1.2.3 Requires: zlib-devel >= 1.2.3 %description -n libbpp-raa-devel The libbpp-raa-devel package contains the header files and static libraries for building applications which use %{_basename}. %prep %setup -q %build CFLAGS="$RPM_OPT_FLAGS" CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF" if [ %{_lib} == 'lib64' ] ; then CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64" fi cmake $CMAKE_FLAGS . make %install make DESTDIR=$RPM_BUILD_ROOT install %clean rm -rf $RPM_BUILD_ROOT %post -n libbpp-raa1 -p /sbin/ldconfig %post -n libbpp-raa-devel createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } # Actualize .all files createGeneric %{_prefix}/include/Bpp exit 0 %preun -n libbpp-raa-devel removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } # Actualize .all files removeGeneric %{_prefix}/include/Bpp exit 0 %postun -n libbpp-raa1 -p /sbin/ldconfig %postun -n libbpp-raa-devel createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } # Actualize .all files createGeneric %{_prefix}/include/Bpp exit 0 %files -n libbpp-raa1 %defattr(-,root,root) %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog %{_prefix}/%{_lib}/lib*.so.* %files -n libbpp-raa-devel %defattr(-,root,root) %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog %{_prefix}/%{_lib}/lib*.so %{_prefix}/%{_lib}/lib*.a %{_prefix}/include/* %changelog * Mon Sep 22 2014 Julien Dutheil 2.2.0-1 - Compatibility update. * Thu Mar 07 2013 Julien Dutheil 2.1.0-1 - Compatibility update. * Thu Feb 09 2012 Julien Dutheil 2.0.3-1 - Compatibility update. * Thu Jun 09 2011 Julien Dutheil 2.0.2-1 - Compatibility update. * Mon Feb 28 2011 Julien Dutheil 2.0.1-1 * Mon Feb 07 2011 Julien Dutheil 2.0.0-1 * Thu Mar 25 2010 Julien Dutheil 1.0.0-1 * Wed Jun 24 2009 Julien Dutheil 0.1.0-1 - First draft of the spec file bpp-raa-2.2.0/src/CMakeLists.txt000664 001750 001750 00000002433 12372454333 020060 0ustar00jdutheiljdutheil000000 000000 # CMake script for Bio++ Remote Acnuc Access # Author: Sylvain Gaillard and Julien Dutheil # Created: 11/09/2009 # File list set(C_FILES Bpp/Raa/md5.c Bpp/Raa/parser.c Bpp/Raa/zsockr.c Bpp/Raa/misc_acnuc.c Bpp/Raa/RAA_acnuc.c ) set(CPP_FILES Bpp/Raa/RAA.cpp Bpp/Raa/RaaList.cpp Bpp/Raa/RaaSpeciesTree.cpp ) set(H_FILES Bpp/Raa/parser.h Bpp/Raa/RAA.h Bpp/Raa/RaaSeqAttributes.h Bpp/Raa/RAA_acnuc.h Bpp/Raa/RaaList.h Bpp/Raa/RaaSpeciesTree.h ) # Build the static lib add_library(bppraa-static STATIC ${CPP_FILES} ${C_FILES}) set_target_properties(bppraa-static PROPERTIES OUTPUT_NAME bpp-raa CLEAN_DIRECT_OUTPUT 1 ) target_link_libraries(bppraa-static ${LIBS}) # Build the shared lib add_library(bppraa-shared SHARED ${CPP_FILES} ${C_FILES}) set_target_properties(bppraa-shared PROPERTIES OUTPUT_NAME bpp-raa CLEAN_DIRECT_OUTPUT 1 VERSION ${BPPRAA_VERSION} SOVERSION ${BPPRAA_VERSION_MAJOR} ) target_link_libraries(bppraa-shared ${LIBS}) # Install libs install(TARGETS bppraa-static bppraa-shared DESTINATION lib${LIB_SUFFIX}) # Install headers install(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h") # Generate generic include files (.all) INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)") bpp-raa-2.2.0/src/Bpp/Raa.all000664 001750 001750 00000000243 12372454333 017233 0ustar00jdutheiljdutheil000000 000000 #include "Raa/RaaSpeciesTree.h" #include "Raa/parser.h" #include "Raa/RaaList.h" #include "Raa/RaaSeqAttributes.h" #include "Raa/RAA_acnuc.h" #include "Raa/RAA.h" bpp-raa-2.2.0/src/Bpp/Raa/RAA_acnuc.h000664 001750 001750 00000023546 12372454333 020501 0ustar00jdutheiljdutheil000000 000000 #ifndef RAA_ACNUC_H #define RAA_ACNUC_H #include #include #include #include #if defined(WIN32) #define SOCKBUFS 8192 #include #endif #ifdef __alpha typedef long raa_long; #define RAA_LONG_FORMAT "%lu" #else typedef long long raa_long; #define RAA_LONG_FORMAT "%llu" #endif #ifndef TRUE #define FALSE 0 #define TRUE (!FALSE) #endif #ifndef ERREUR #define ERREUR 1 #endif struct rlng { /* LONGL series of linked records containing lists of SUBSEQ ranks */ int next; /* to LONGL for next element of the long list, or 0 when list is finished */ int sub[1]; /* array (length given by global SUBINLNG) of ranks of SUBSEQ records or of 0s */ }; #define RAA_GFRAG_BSIZE 10000 struct gfrag_aux { char buffer[RAA_GFRAG_BSIZE + 1]; int lbuf, nseq_buf, first_buf, l_nseq_buf; }; struct readsub_aux { char *name; int lname, previous, length, type, toext, lkey, locus, frame, gencode, div; raa_long addr; }; #define ANNOTCOUNT 40 struct annot_aux { char *annotline[ANNOTCOUNT + 1]; int annotcurrent, annotcount, annotdiv; raa_long annotaddr, annotaddrfirst, annotaddrlast; char annotsbuffer[ 300 ]; }; struct readsp_kw_aux { char name[150], libel[200]; int lsub, desc, syno, host, previous; }; #define BLOCK_ELTS_IN_LIST 500 struct nextelt_aux { int current_rank, previous, total; int tabnum[BLOCK_ELTS_IN_LIST]; char *tabname[BLOCK_ELTS_IN_LIST]; int tablength[BLOCK_ELTS_IN_LIST]; raa_long taboffset[BLOCK_ELTS_IN_LIST]; int tabdiv[BLOCK_ELTS_IN_LIST]; }; #define S_BUF_SHRT 5000 /* number of memorized SHORTL records */ struct readshrt_aux { unsigned shrt_buffer[S_BUF_SHRT][3]; /* [0]=SHORTL_rank [1]=val [2]=next */ int shrt_max, shrt_begin, total; }; struct readsmj_aux { int lastrec; char **names, **libels; unsigned *plongs; }; typedef struct raa_node { char *name; char *libel; char *libel_upcase; int rank; int tid; int count; struct raa_node *parent; struct raa_pair *list_desc; struct raa_node *syno; } raa_node; struct raa_pair { raa_node *value; struct raa_pair *next; }; typedef struct _raa_db_access { char *dbname; FILE *raa_sockfdr, *raa_sockfdw; int genbank, embl, swissprot, nbrf; int nseq, longa, maxa; int L_MNEMO, WIDTH_SP, WIDTH_KW, WIDTH_SMJ, WIDTH_AUT, WIDTH_BIB, ACC_LENGTH, SUBINLNG, lrtxt; raa_node **sp_tree; /* NULL or the full taxonomy tree */ int max_tid; /* largest correct taxon ID value */ int *tid_to_rank; /* NULL or tid-to-rank table */ struct rlng *rlng_buffer; struct gfrag_aux gfrag_data; struct readsub_aux readsub_data; int first_recs[20]; struct annot_aux annot_data; struct readsp_kw_aux readspec_data, readkey_data; struct nextelt_aux nextelt_data; struct readshrt_aux readshrt_data; struct readsmj_aux readsmj_data; void *matchkey_data; /* mostly for raa_query/raa_query_win usage */ int tot_key_annots; char **key_annots, **key_annots_min; unsigned char *want_key_annots; #ifdef WIN32 char sock_input[SOCKBUFS]; /* WIN32 socket input buffer */ char *sock_input_pos, *sock_input_end; char sock_output[SOCKBUFS]; /* WIN32 socket output buffer */ DWORD sock_output_lbuf; #endif } raa_db_access; #define WIDTH_MAX 150 typedef enum { raa_sub = 0, raa_loc, raa_key, raa_spec, raa_shrt, raa_lng, raa_ext, raa_smj, raa_aut, raa_bib, raa_txt, raa_acc } raa_file; typedef void (*raa_char_void_function)(raa_db_access *, char *); struct chain_void { void *data; struct chain_void *next; }; /* global variables */ extern raa_char_void_function raa_error_mess_proc;/*this function sd call raa_acnucclose*/ extern int raa_acnucopen (char *clientid, raa_db_access **psock) ; extern int raa_decode_address(char *url, char **p_ip_name, int *socket, char **p_remote_db); extern int raa_acnucopen_alt (char *serveurName, int port, char *db_name, char *clientid, raa_db_access **psock); extern int raa_open_socket(char *serveurName, int port, char *clientid, raa_db_access **psock); extern int raa_opendb(raa_db_access *raa_current_db, char *db_name); int raa_opendb_pw(raa_db_access *raa_current_db, char *db_name, void *ptr, char *(*getpasswordf)(void *) ); extern int raa_gfrag(raa_db_access *raa_current_db, int nsub, int first, int lfrag, char *dseq) ; extern void raa_acnucclose(raa_db_access *raa_current_db) ; extern int raa_prep_acnuc_query(raa_db_access *raa_current_db) ; extern int raa_proc_query(raa_db_access *raa_current_db, char *query, char **message, char *nomliste, int *numlist, int *count, int *locus, int *type) ; int raa_nexteltinlist(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength) ; int raa_nexteltinlist_annots(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength, raa_long *paddr, int *pdiv); raa_long scan_raa_long(char *txt); int raa_seq_to_annots(raa_db_access *raa_current_db, int numseq, raa_long *faddr, int *div); char *print_raa_long(raa_long val); char *raa_read_annots(raa_db_access *raa_current_db, raa_long faddr, int div); char *raa_next_annots(raa_db_access *raa_current_db, raa_long *faddr); char *raa_translate_cds(raa_db_access *raa_current_db, int seqnum); char raa_translate_init_codon(raa_db_access *raa_current_db, int numseq); int raa_iknum(raa_db_access *raa_current_db, char *name, raa_file cas); int raa_isenum(raa_db_access *raa_current_db, char *name); int raa_bcount(raa_db_access *raa_current_db, int lrank); void raa_bit1(raa_db_access *raa_current_db, int lrank, int num); void raa_bit0(raa_db_access *raa_current_db, int lrank, int num); int raa_btest(raa_db_access *raa_current_db, int lrank, int num); void raa_copylist(raa_db_access *raa_current_db, int from, int to); void raa_zerolist(raa_db_access *raa_current_db, int rank); void raa_setliststate(raa_db_access *raa_current_db, int lrank, int locus, int type); char *raa_getliststate(raa_db_access *raa_current_db, int lrank, int *locus, int *type, int *count); char *raa_residuecount(raa_db_access *raa_current_db, int lrank); int raa_getemptylist(raa_db_access *raa_current_db, char *name); int raa_setlistname(raa_db_access *raa_current_db, int lrank, char *name); int raa_getlistrank(raa_db_access *raa_current_db, char *name); int raa_releaselist(raa_db_access *raa_current_db, int lrank); int raa_countfilles(raa_db_access *raa_current_db, int lrank); int raa_alllistranks(raa_db_access *raa_current_db, int **pranks); int raa_fcode(raa_db_access *raa_current_db, raa_file cas, char *name); int raa_read_first_rec(raa_db_access *raa_current_db, raa_file cas); char *raa_readsub(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus, int *pframe, int *pgencode); char *raa_readsub_pannots(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus, int *pframe, int *pgencode, raa_long *paddr, int *pdiv); char *raa_readloc(raa_db_access *raa_current_db, int num, int *sub, int *pnuc, int *spec, int *host, int *plref, int *molec, int *placc, int *org); char *raa_readspec(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *desc, int *syno, int *plhost); char *raa_readkey(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *desc, int *syno); char *raa_readsmj(raa_db_access *raa_current_db, int num, char **plibel, int *plong); char *raa_readacc(raa_db_access *raa_current_db, int num, int *plsub); int raa_readext(raa_db_access *raa_current_db, int num, int *mere, int *deb, int *fin); int raa_readlng(raa_db_access *raa_current_db, int num); unsigned raa_readshrt(raa_db_access *raa_current_db, unsigned point, int *val); char *raa_ghelp(raa_db_access *raa_current_db, char *fname, char *topic); int raa_nextmatchkey(raa_db_access *raa_current_db, int num, char *pattern, char **matching); int raa_savelist(raa_db_access *raa_current_db, int lrank, FILE *out, int use_acc, char *prefix); int raa_modifylist(raa_db_access *raa_current_db, int lrank, char *type /* "length" or "date" */, char *operation /* ">2000" */, int *pnewlrank, int (*check_interrupt)(void) , int *p_processed); int raa_knowndbs(raa_db_access *raa_current_db, char ***pnames, char ***pdescriptions); char *raa_short_descr(raa_db_access *raa_current_db, int seqnum, char *text, int maxlen, raa_long pinf, int div, char *name); struct chain_void *raa_get_list_open_dbs(void); void *raa_prep_extract(raa_db_access *raa_current_db, char *format, FILE *outstream, char *choix, char *feature_name, char *bornes, char *min_bornes, char **message, int lrank); int raa_extract_1_seq(void *opaque); int raa_extract_interrupt(raa_db_access *raa_current_db, void *opaque); void *raa_prep_coordinates(raa_db_access *raa_current_db, int lrank, int seqnum, char *operation, /* "simple","fragment","feature","region" */ char *feature_name, char *bounds, char *min_bounds); int *raa_1_coordinate_set(void *); int raa_loadtaxonomy(raa_db_access *raa_current_db, char *rootname, int (*progress_function)(int, void *), void *progress_arg, int (*need_interrupt_f)(void *), void *interrupt_arg); char *raa_get_taxon_info(raa_db_access *raa_current_db, char *name, int rank, int tid, int *p_rank, int *p_tid, int *p_parent, struct raa_pair **p_desc_list); char *raa_getattributes(raa_db_access *raa_current_db, const char *id, int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq); char *raa_seqrank_attributes(raa_db_access *raa_current_db, int rank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq); int sock_fputs(raa_db_access *raa_current_db, char *line); int sock_flush(raa_db_access *raa_current_db); char *read_sock(raa_db_access *raa_current_db); int trim_key(char *name); /* remove trailing spaces */ void majuscules(char *name); int atoi_u(const char *p); char *protect_quotes(char *name); /* replace " by \" returns in static memory */ void compact(char *chaine); int strcmptrail(char *s1, int l1, char *s2, int l2); #endif /* RAA_ACNUC_H */ bpp-raa-2.2.0/src/Bpp/Raa/parser.c000664 001750 001750 00000005001 12372454333 020176 0ustar00jdutheiljdutheil000000 000000 #include "parser.h" char *unprotect_quotes(char *name); /** initialisation d'une réponse **/ Reponse * initreponse(void) { Reponse *rep; rep = (Reponse *) malloc (sizeof(Reponse)); rep->nbarguments = 0; rep->arg = NULL; return rep; } void clear_reponse(Reponse * rep) { int pti; for(pti=0; pti < rep->nbarguments; pti++) { free(rep->arg[pti]); } if(rep->arg != NULL) free(rep->arg); free(rep); } void ajout_reponse(Reponse *rep, char *pile, int len) { int pti; if (rep->nbarguments==0) rep->arg = (char **)malloc(1 * sizeof(char *)); else rep->arg= (char**) realloc(rep->arg,(rep->nbarguments+1)* sizeof(char *)) ; /* ici j'ai deja alloue donc realloc (plus de ligne) */ rep->arg[rep->nbarguments]=(char *) malloc(len + 1); /* j'alloue l'espace pour l'argument */ pti=rep->nbarguments; memcpy(rep->arg[pti], pile, len); /* je stocke l'argument */ rep->arg[pti][len] = 0; rep->nbarguments++; } /** le parseur qui rempli la structure Reponse **/ void parse(char *chaine, Reponse *rep) { char *ori; ori=chaine; while(*chaine != 0) { if (*chaine == '"' ) { do { /* chercher le prochain " en ignorant les \" sauf si en fin de partie entre " " */ chaine++; if(*chaine == 0) break; } while(*chaine != '"' || ( *(chaine-1) == '\\' && *(chaine+1) != '&' && *(chaine+1) != 0) ); if(*chaine == 0) break; chaine++; } if(*chaine == '&') { ajout_reponse(rep, ori, chaine-ori); ori=chaine+1; } chaine++; } ajout_reponse(rep, ori, chaine-ori); } /** pour rechercher la valeur d'un argument dans la structure **/ char *val(Reponse *Mono, char *argument) { int count, num, l, larg; char *retval = NULL, *debut, *p; count = Mono->nbarguments; larg = strlen(argument); for(num=0; num < count; num++) { debut = Mono->arg[num]; p = strchr(debut, '='); if(p == NULL || larg != p - debut) continue; p++; if(strncmp(argument, debut, larg) != 0) continue; l = strlen(p); retval = (char *)malloc(l+1); strcpy(retval, p); unprotect_quotes(retval); break; } return retval; } char *unprotect_quotes(char *name) /* enlever les " " encadrantes et decoder les \" internes en " */ { char *p; int l; l = strlen(name); if(*name == '"') { memmove(name, name+1, l--); /* enlever la " initiale */ if( *(name+l-1) == '"') *(name + --l) = 0; /* enlever la " terminale */ } while ((p = strstr(name, "\\\"" /* la chaine \" */ )) != NULL) { memmove(p, p+1, name + l - p); l--; } return name; } bpp-raa-2.2.0/src/Bpp/Raa/RaaSeqAttributes.h000664 001750 001750 00000002762 12372454333 022145 0ustar00jdutheiljdutheil000000 000000 #ifndef _RAASEQATTRIBUTES_H_ #define _RAASEQATTRIBUTES_H_ #include namespace bpp { /** * @brief Contains various attributes of a sequence (length, name, species name, genetic code, etc...). * */ class RaaSeqAttributes { friend class RAA; public: /** * @brief Returns the sequence name. */ std::string getName() {return name; }; /** * @brief Returns the sequence length. */ int getLength() {return length; }; /** * @brief Returns the sequence database rank. */ int getRank() {return rank; }; /** * @brief Returns the sequence's NCBI genetic code number (1 is universal). Meaningful only for CDS sequences. */ int getGeneticCode() {return ncbi_gc; }; /** * @brief Returns the sequence reading frame (0, 1, or 2). Meaningful only for CDS sequences. */ int getReadingFrame() {return frame; }; /** * @brief Returns the sequence species name. */ std::string getSpeciesName() {return species; }; /** * @brief Returns the sequence primary accession number. */ std::string getAccessionNumber() {return accno; }; /** * @brief Returns a one-line description of the sequence. */ std::string getDescription() {return description; }; protected: /** * @brief The database connection of this sequence. */ RAA *raa; private: std::string name; int rank; int length; int ncbi_gc; int frame; std::string species; std::string accno; std::string description; }; } // namespace bpp #endif //_RAASEQATTRIBUTES_H_ bpp-raa-2.2.0/src/Bpp/Raa/RAA.cpp000664 001750 001750 00000034002 12372454333 017650 0ustar00jdutheiljdutheil000000 000000 /* * RAA.cpp * * */ #include "RAA.h" extern "C" { int get_ncbi_gc_number(int gc); int sock_printf(raa_db_access *raa_current_db, const char *fmt, ...); } using namespace std; using namespace bpp; RAA::RAA(const string &dbname, int port, const string &server) throw (int) { kw_pattern = NULL; current_address.div = -1; int error = raa_acnucopen_alt((char *)server.c_str(), port, (char *)dbname.c_str(), (char *)"Bio++", &raa_data); if(error) { throw error; } } RAA::RAA(int port, const string &server) throw(int) { kw_pattern = NULL; int error = raa_open_socket((char *)server.c_str(), port, (char *)"Bio++", &raa_data); if(error) { throw error; } } RAA::~RAA() { if(raa_data != NULL) raa_acnucclose(raa_data); if(kw_pattern) delete kw_pattern; } Sequence *RAA::getSeq_both(const string &name_or_accno, int rank, int maxlength) { int length; char *name, *description; if(rank == 0) name = raa_getattributes(raa_data, name_or_accno.c_str(), &rank, &length, NULL, NULL, NULL, &description, NULL, NULL); else name = raa_seqrank_attributes(raa_data, rank, &length, NULL, NULL, NULL, &description, NULL, NULL); if(length > maxlength) return NULL; string sname = name; vector comment(1, string(description) ); string *cseq = new string(length + 1, ' '); if(cseq == NULL) return NULL; raa_gfrag(this->raa_data, rank, 1, length, (char *)cseq->data()); cseq->resize(length); const Alphabet *alphab; if(raa_data->swissprot || raa_data->nbrf) alphab = &AlphabetTools::PROTEIN_ALPHABET; else alphab = &AlphabetTools::DNA_ALPHABET; Sequence *seq = new BasicSequence(sname, *cseq, comment, alphab); delete cseq; return seq; } Sequence *RAA::getSeq(const string &name_or_accno, int maxlength) { return getSeq_both(name_or_accno, 0, maxlength); } Sequence *RAA::getSeq(int seqrank, int maxlength) { if(seqrank < 2 || seqrank > raa_data->nseq) return NULL; return getSeq_both(string(""), seqrank, maxlength); } int RAA::getSeqFrag(int seqrank, int first, int length, string &sequence) { if(seqrank < 2 || seqrank > raa_data->nseq) return 0; sequence = ""; char *p = (char *)malloc(length + 1); if(p == NULL) return 0; int l = raa_gfrag(this->raa_data, seqrank, first, length, p); if(l > 0) { majuscules(p); sequence = p; } free(p); return l; } int RAA::getSeqFrag(const string &name_or_accno, int first, int length, string &sequence) { int seqrank; raa_getattributes(raa_data, name_or_accno.c_str(), &seqrank, NULL, NULL, NULL, NULL, NULL, NULL, NULL); if(seqrank == 0) return 0; return getSeqFrag(seqrank, first, length, sequence); } RaaSeqAttributes *RAA::getAttributes(const string &name_or_accno) { char *description, *species, *access; int acnuc_gc; RaaSeqAttributes *myattr = new RaaSeqAttributes(); char *name = raa_getattributes(this->raa_data, name_or_accno.c_str(), &myattr->rank, &myattr->length, &myattr->frame, &acnuc_gc, &access, &description, &species, NULL); myattr->raa = this; myattr->name = name; myattr->description = description; myattr->accno = access; myattr->species = species; myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc); return myattr; } RaaSeqAttributes *RAA::getAttributes(int seqrank) { char *description, *species, *access; int acnuc_gc; if(seqrank < 2 || seqrank > raa_data->nseq) return NULL; RaaSeqAttributes *myattr = new RaaSeqAttributes(); char *name = raa_seqrank_attributes(this->raa_data, seqrank, &myattr->length, &myattr->frame, &acnuc_gc, &access, &description, &species, NULL); if(name == NULL) return NULL; myattr->rank =seqrank; myattr->raa = this; myattr->name= name; myattr->description = description; myattr->accno = access; myattr->species = species; myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc); return myattr; } int RAA::knownDatabases(vector &name, vector &description) { char **cname, **cdescription; int count = raa_knowndbs(raa_data, &cname, &cdescription); name.resize(count); description.resize(count); for(int i = 0; i < count; i++) { name[i] = cname[i]; free(cname[i]); description[i] = cdescription[i]; free(cdescription[i]); } if(count > 0) { free(cname); free(cdescription); } return count; } int RAA::openDatabase(const string &dbname, char *(*getpasswordf)(void *), void *p) { current_address.div = -1; return raa_opendb_pw(raa_data, (char *)dbname.c_str(), p, getpasswordf); } void RAA::closeDatabase() { sock_fputs(this->raa_data, (char *)"acnucclose\n"); read_sock(this->raa_data); } string RAA::getFirstAnnotLine(int seqrank) { if(seqrank < 2 || seqrank > raa_data->nseq) return ""; raa_seq_to_annots(raa_data, seqrank, ¤t_address.faddr, ¤t_address.div); char *p = raa_read_annots(raa_data, current_address.faddr, current_address.div); string retval(p); return retval; } string RAA::getNextAnnotLine() { if(current_address.div == -1) return NULL; char *p = raa_next_annots(raa_data, ¤t_address.faddr); if(p != NULL) { string retval(p); return retval; } else return NULL; } RaaAddress RAA::getCurrentAnnotAddress() { return current_address; } string RAA::getAnnotLineAtAddress(RaaAddress address) { current_address = address; char *p = raa_read_annots(raa_data, current_address.faddr, current_address.div); string retval(p); return retval; } Sequence *RAA::translateCDS(int seqrank) throw(BadCharException) { char *descript; if(seqrank < 2 || seqrank > raa_data->nseq) return NULL; char *prot = raa_translate_cds(raa_data, seqrank); if(prot == NULL) return NULL; int l = strlen(prot) - 1; if(l >= 0 && prot[l] == '*') prot[l] = 0; char *name = raa_seqrank_attributes(raa_data, seqrank, NULL, NULL, NULL, NULL, &descript, NULL, NULL); string *sname = new string(name); string *pstring = new string(prot); if(sname == NULL || pstring == NULL) return NULL; Sequence *Sprot; try { Sprot = new BasicSequence(*sname, *pstring, &AlphabetTools::PROTEIN_ALPHABET ); } catch (BadCharException e){ delete sname; delete pstring; throw e; } delete sname; delete pstring; vector comment(1, string(descript) ); Sprot->setComments(comment); return Sprot; } Sequence *RAA::translateCDS(const string &name) throw(BadCharException) { int rank; rank = raa_isenum(raa_data, (char *)name.c_str()); if(rank == 0) return NULL; Sequence *Sprot; try { Sprot = translateCDS(rank); } catch (BadCharException e){ throw e; } return Sprot; } char RAA::translateInitCodon(int seqrank) { if(seqrank < 2 || seqrank > raa_data->nseq) return 0; return raa_translate_init_codon(raa_data, seqrank); } RaaList *RAA::processQuery(const string &query, const string &listname) throw(string) { char *message; int type, rank; int err = raa_proc_query(raa_data, (char *)query.c_str(), &message, (char *)listname.c_str(), &rank, NULL, NULL, &type); if(err) { string errmess = message; free(message); throw errmess; } RaaList *mylist = new RaaList(); mylist->myraa = this; mylist->rank = rank; mylist->name = listname; if(type=='S') mylist->type = &RaaList::LIST_SEQUENCES; else if(type=='K') mylist->type = &RaaList::LIST_KEYWORDS; else mylist->type = &RaaList::LIST_SPECIES; return mylist; } RaaList *RAA::createEmptyList(const string &listname, const string &kind) throw(int) { int err, lrank; char type, *p, *q; sock_printf(raa_data, (char *)"getemptylist&name=%s\n", listname.c_str() ); char *reponse = read_sock(raa_data); p = strchr(reponse, '='); if(p) q = strchr(p+1, '='); sscanf(p+1, "%d", &err); if(err != 0) { throw err; } sscanf(q+1, "%d", &lrank); if(kind == RaaList::LIST_SEQUENCES) type='S'; else if(kind == RaaList::LIST_KEYWORDS) type='K'; else type='E'; sock_printf(raa_data, "setliststate&lrank=%d&type=%c\n", lrank, type); read_sock(raa_data); RaaList *mylist = new RaaList(); mylist->myraa = this; mylist->rank = lrank; mylist->name = listname; mylist->type = &kind; return mylist; } void RAA::deleteList(RaaList *list) { raa_releaselist(raa_data, list->rank); delete list; } int RAA::keywordPattern(const string &pattern) { current_kw_match = 2; if(kw_pattern) delete kw_pattern; kw_pattern = new string(pattern); return raa_data->WIDTH_KW; } int RAA::nextMatchingKeyword(string &matching) { char *keyword; if(current_kw_match==2) current_kw_match = raa_nextmatchkey(raa_data, 2, (char*)kw_pattern->c_str(), &keyword); else current_kw_match = raa_nextmatchkey(raa_data, current_kw_match, NULL, &keyword); if(current_kw_match) matching = keyword; return current_kw_match; } static int treeloadprogress(int percent, void *data) { bool *first =(bool *)data; if(*first) { cout << "Starting species tree download\n"; *first = false; } cout << '.'; fflush(stdout); return false; } RaaSpeciesTree *RAA::loadSpeciesTree(bool showprogress) { bool init_load_mess = true; int err = raa_loadtaxonomy(raa_data, (char *)"ROOT", showprogress ? treeloadprogress : NULL, &init_load_mess, NULL, NULL); if(err) return NULL; if( showprogress && (!init_load_mess) ) cout << "\nSpecies tree download completed\n"; RaaSpeciesTree *tree = new RaaSpeciesTree(); tree->raa_data = raa_data; tree->sp_tree = raa_data->sp_tree; tree->tid_to_rank = raa_data->tid_to_rank; tree->max_tid = raa_data->max_tid; tree->max_sp = raa_read_first_rec(raa_data, raa_spec); return tree; } void RAA::freeSpeciesTree(RaaSpeciesTree *tree) { int i; struct raa_pair *p, *q; for(i = 2; i <= tree->max_sp; i++) { if(raa_data->sp_tree[i] == NULL) continue; free(raa_data->sp_tree[i]->name); if(raa_data->sp_tree[i]->libel != NULL) free(raa_data->sp_tree[i]->libel); if(raa_data->sp_tree[i]->libel_upcase != NULL) free(raa_data->sp_tree[i]->libel_upcase); p = raa_data->sp_tree[i]->list_desc; while(p) { q = p->next; free(p); p = q; } free(raa_data->sp_tree[i]); } if(raa_data->tid_to_rank != NULL) free(raa_data->tid_to_rank); if(raa_data->sp_tree != NULL) free(raa_data->sp_tree); raa_data->sp_tree = NULL; raa_data->tid_to_rank = NULL; delete tree; } vector RAA::listDirectFeatureKeys() { int total, num; vector ftkeys; total = raa_read_first_rec(raa_data, raa_smj); for(num = 2; num <= total; num++) { char *name = raa_readsmj(raa_data, num, NULL, NULL); if(strncmp(name, "04", 2) != 0) continue; if(strcmp(name, "04ID") == 0) continue; if(strcmp(name, "04LOCUS") == 0) continue; ftkeys.push_back(name + 2); } return ftkeys; } static void godownkey(raa_db_access *raa_data, unsigned int p3, vector& ftkeys) { unsigned next; int value; char *name; next = raa_readshrt(raa_data, p3, &value); name = raa_readkey(raa_data, abs(value), NULL, NULL, NULL, NULL); ftkeys.push_back(name); while(next != 0) { next = raa_readshrt(raa_data, next, &value); godownkey(raa_data, value, ftkeys); } } vector RAA::listAllFeatureKeys() { vector ftkeys; int rank, pdesc; rank = raa_iknum(raa_data, (char *)"misc_feature", raa_key); raa_readkey(raa_data, rank, NULL, NULL, &pdesc, NULL); godownkey(raa_data, pdesc, ftkeys); return ftkeys; } RaaList *RAA::getDirectFeature(const string &seqname, const string &featurekey, const string &listname, const string &matching) { char query[80]; RaaList *list1; int matchinglist, err; sprintf(query, "n=%s and t=%s", seqname.c_str(), featurekey.c_str()); string squery = query; try { list1 = processQuery(squery, listname); } catch (string s) { return NULL; } if(matching.empty() || list1->getCount() == 0) return list1; sock_printf(raa_data, "prep_getannots&nl=1\n%s|%s\n", raa_data->embl ? "FT" : "FEATURES", featurekey.c_str()); char *p = read_sock(raa_data); if(strncmp(p, "code=0", 6) != 0) return NULL; err = raa_modifylist(raa_data, list1->getRank(), (char *)"scan", (char *)matching.c_str(), &matchinglist, NULL, NULL); if(err != 0 || raa_bcount(raa_data, matchinglist) == 0) { delete list1; if(err == 0) raa_releaselist(raa_data, matchinglist); return NULL; } raa_setlistname(raa_data, matchinglist, (char *)listname.c_str()); RaaList *list2 = new RaaList(); list2->rank = matchinglist; list2->myraa = this; list2->name = listname; list2->type = &RaaList::LIST_SEQUENCES; delete list1; return list2; } struct extract_data { char line[100]; }; void *RAA::prepareGetAnyFeature(int seqrank, const string &featurekey) throw(string) { char *p, *line; int l; if(seqrank < 2 || seqrank > raa_data->nseq) throw "Incorrect first argument"; struct extract_data *data = new struct extract_data; sock_printf(raa_data, "extractseqs&seqnum=%d&format=fasta&operation=feature&feature=%s&zlib=F\n", seqrank, featurekey.c_str()); line = read_sock(raa_data); if(strcmp(line, "code=0") == 0) { p = read_sock(raa_data); strcpy(data->line, p); return (void *)data; } delete data; p = strstr(line, "message="); if(p == NULL) return NULL; p += 8; if(*p == '"') p++; l = strlen(p); if(p[l-1] == '"') p[l-1] = 0; string message = p; throw message; } Sequence *RAA::getNextFeature(void *v) { char *p; Sequence *seq; string name; struct extract_data *data = (struct extract_data *)v; while( data->line[0] == 27 /* esc */ ) { p = read_sock(raa_data); strcpy(data->line, p); } if(strcmp(data->line, "extractseqs END.") == 0) { delete data; return NULL; } p = strchr(data->line, ' '); if(p != NULL)*p = 0; name = data->line + 1; p = read_sock(raa_data); string seqdata = ""; while( p != NULL && strcmp(p, "extractseqs END.") != 0 && *p != 27 /* esc */ && *p != '>') { seqdata += p; p = read_sock(raa_data); } if(p == NULL) strcpy(data->line, "extractseqs END."); else { if( *p == 27 /* esc */ ) p = read_sock(raa_data); strcpy(data->line, p); } seq = new BasicSequence(name, seqdata, &AlphabetTools::DNA_ALPHABET); return seq; } void RAA::interruptGetAnyFeature(void *v) { struct extract_data *data = (struct extract_data *)v; char *p; if(data == NULL) return; sock_fputs(raa_data, (char *)"\033" /* esc */); sock_flush(raa_data); p = data->line; while( strcmp(p, "extractseqs END.") != 0) { p = read_sock(raa_data); } delete data; /* just to consume ESC that may have arrived after extractseqs END. */ sock_fputs(raa_data, (char *)"null_command\n"); read_sock(raa_data); } bpp-raa-2.2.0/src/Bpp/Raa/zsockr.c000664 001750 001750 00000004731 12372454333 020226 0ustar00jdutheiljdutheil000000 000000 /* functions to handle zlib-compressed data read from socket */ #include #include #include #include #include #ifdef WIN32 #include #endif /* included functions */ void *prepare_sock_gz_r(FILE *sockr); int z_getc(void *v); char *z_gets(void *v, char *line, size_t len); char *z_read_sock(void *v); int close_sock_gz_r(void *v); #define ZBSIZE 100000 typedef struct { z_stream stream; char z_buffer[ZBSIZE]; /* compressed input buffer */ char text_buffer[4 * ZBSIZE]; /* decompressed buffer */ char *pos, *endbuf; #ifdef WIN32 SOCKET fd; #else int fd; #endif } sock_gz_r; void *prepare_sock_gz_r(FILE *sockr) { int err; sock_gz_r *big; big = (sock_gz_r *)malloc(sizeof(sock_gz_r)); if(big == NULL) return NULL; big->stream.next_in = Z_NULL; big->stream.avail_in = 0; big->stream.avail_out = 0; big->stream.zalloc = Z_NULL; big->stream.zfree = Z_NULL; big->stream.opaque = NULL; big->pos = big->text_buffer; big->endbuf = big->pos; #ifdef WIN32 big->fd = (SOCKET)sockr; #else big->fd = fileno(sockr); #endif err = inflateInit(&big->stream); return err == Z_OK ? (void *)big : NULL; } int z_getc(void *v) { int q; sock_gz_r *big = (sock_gz_r *)v; z_streamp zs; if(big->pos < big->endbuf) { return *(big->pos++); } zs = &(big->stream); zs->next_out = (Bytef *)big->text_buffer; zs->avail_out = sizeof(big->text_buffer); big->pos = (char *)zs->next_out; do { if(zs->avail_in == 0) { int lu; #ifdef WIN32 lu = recv( big->fd , big->z_buffer, ZBSIZE, 0 ); #else lu = read( big->fd , big->z_buffer, ZBSIZE ); #endif if(lu == -1) return EOF; zs->next_in = (Bytef *)big->z_buffer; zs->avail_in = lu; } q = inflate(zs, Z_NO_FLUSH); if(q == Z_STREAM_END) break; if(q != Z_OK) { break; } } while ( (char *)zs->next_out == big->pos); big->endbuf = (char *)zs->next_out; if(big->pos < big->endbuf) return *(big->pos++); else return EOF; } char *z_gets(void *v, char *line, size_t len) { int c; char *p; p = line; while(len > 1) { c = z_getc( v ); if(c == EOF) { if(p == line) return NULL; break; } *(p++) = c; if(c == '\n') break; len--; } *p = 0; return line; } char *z_read_sock(void *v) { static char line[500]; char *p; int l; p = z_gets(v, line, sizeof(line)); if(p == NULL) return NULL; l = strlen(line); if(l > 0 && line[l-1] == '\n') line[l-1] = 0; return line; } int close_sock_gz_r(void *v) { sock_gz_r *big = (sock_gz_r *)v; int val; val = inflateEnd(&(big->stream)); free(big); return val; } bpp-raa-2.2.0/src/Bpp/Raa/misc_acnuc.c000664 001750 001750 00000051625 12372454333 021023 0ustar00jdutheiljdutheil000000 000000 #include #include #include #include #if defined(WIN32) #include #elif defined(unix) || defined(__APPLE__) #define unixlike #include #endif /* included functions */ int trim_key(char* name); /* remove trailing spaces */ void padtosize(char* pname, char* name, int length); char* get_code_descr(int code); int calc_codon_number(char* codon); char codaa(char* codon, int code); int get_ncbi_gc_number(int gc); int get_acnuc_gc_number(int ncbi_gc); int strcmptrail(char *s1, int l1, char *s2, int l2); void majuscules(char *name); void compact(char *chaine); char complementer_base(char nucl); void complementer_seq(char* deb_ch, int l); char init_codon_to_aa(char* codon, int gc); int notrail2(char* chaine, int len); int prepch(char* chaine, char** posmot); int compch(char* cible, int lcible, char** posmot, int nbrmots); int chg_acnuc(char* acnucvar, char* gcgacnucvar); void gets_no_echo(char* password, size_t lpw); int trim_key(char* name) /* remove trailing spaces */ { char* p; int l = strlen(name); p = name + l - 1; while (p >= name && *p == ' ') *(p--) = 0; return (p + 1) - name; } void padtosize(char* pname, char* name, int length) { int i; strncpy(pname, name, length); pname[length] = 0; for (i = strlen(pname); i < length; i++) { pname[i] = ' '; } } #define TOTCODES 18 /* nbre total de codes definis, 0 inclus */ int totcodes = TOTCODES; char aminoacids[] = "RLSTPAGVKNQHEDYCFIMW*X"; struct genetic_code_libel /* definition d'un code genetique */ {char libel[61]; /* nom du code decrivant ses variants % code standard */ int code[65]; /* tableau codon->acide amine */ int ncbi_gc; /* numero NCBI du meme code */ int codon_init[64]; /* tableau codon initiateur -> acide amine */ }; /* les codons sont numerotes de 1 a 64 selon ordre alphabetique; le numero 65 est attribue a tout codon avec base hors AcCcGgTtUu les acides amines sont numerotes selon l'ordre de la variable aminoacids de un a 20 + * pour stop et X pour inconnu */ /* initialisation de tous les codes genetiques */ struct genetic_code_libel genetic_code[TOTCODES] = { { /* 0: universel */ {"Universal genetic code"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 21, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, /*ncbi*/ 1, /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */ } , { /* 1: yeast mt */ {"CUN=T AUA=M UGA=W"}, {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 19, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 3, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, 19, 0, /* AUA, AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 2: : MITOCHONDRIAL CODE OF VERTEBRATES */ {"AGR=* AUA=M UGA=W"}, {9, 10, 9, 10, 4, 4, 4, 4, 21, 3, 21, 3, 19, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 2, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 19, 19, 19, /* AUN */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 3: MITOCHONDRIAL CODE OF FILAMENTOUS FUNGI */ {"UGA=W"}, {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 4, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 19, 19, 19, /* AUN */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, 19, 0} /* UUR */ } , { /* 4: MITOCHONDRIAL CODE OF INSECT AND PLATYHELMINTHES */ {"AUA=M UGA=W AGR=S"}, {9, 10, 9, 10, 4, 4, 4, 4, 3, 3, 3, 3, 19, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 5, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 19, 19, 19, /* AUN */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */ } , { /* 5: Nuclear code of Candida cylindracea (see nature 341:164) */ {"CUG=S"}, {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, 12, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 6: NUCLEAR CODE OF CILIATA: UAR = Gln = Q */ {"UAR=Q"}, {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 11, 15, 11, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, 6, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 7: NUCLEAR CODE OF EUPLOTES */ {"UGA=C"}, {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 16, 16, 20, 16, 2, 17, 2, 17, 22}, 10, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 8: MITOCHONDRIAL CODE OF ECHINODERMS */ {"UGA=W AGR=S AAA=N"}, {10, 10, 9, 10, 4, 4, 4, 4, 3, 3, 3, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 9, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 9: MITOCHONDRIAL CODE OF ASCIDIACEA */ {"UGA=W AGR=G AUA=M"}, {9, 10, 9, 10, 4, 4, 4, 4, 7, 3, 7, 3, 19, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 13, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 10: MITOCHONDRIAL CODE OF PLATYHELMINTHES */ {"UGA=W AGR=S UAA=Y AAA=N"}, {10, 10, 9, 10, 4, 4, 4, 4, 3, 3, 3, 3, 18, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 15, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 14, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 11: NUCLEAR CODE OF BLEPHARISMA */ {"UAG=Q"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 11, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, 15, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 12: NUCLEAR CODE OF BACTERIA: differs only for initiation codons */ {"NUG=AUN=M when initiation codon"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 21, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, 11, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 19, 19, 19, /* AUN */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */ } , { /* 13: Chlorophycean Mitochondrial */ {"UAG=Leu"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 2, 15, 3, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, /*ncbi*/ 16, /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 14: MITOCHONDRIAL CODE OF TREMATODE */ {"AUA=M UGA=W AGR=S AAA=N"}, {10, 10, 9, 10, 4, 4, 4, 4, 3, 3, 3, 3, 19, 18, 19, 18, 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, 21, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 15: TAG-Leu,TCA-stop */ {"UAG=L UCA=*"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 2, 15, 21, 3, 3, 3, 21, 16, 20, 16, 2, 17, 2, 17, 22}, /*ncbi*/ 22, /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 16: Thraustochytrium-mt */ {"UUA=*"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 21, 15, 3, 3, 3, 3, 21, 16, 20, 16, 21, 17, 2, 17, 22}, /*ncbi*/ 23, /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 19, /* AUG AUU */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* GUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} } , { /* 17: MITOCHONDRIAL CODE OF Pterobranchia */ {"UGA=W AGA=S AGG=K"}, /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 3, 3, 9, 3, 18, 18, 19, 18, /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, /*TNN*/ 21, 15, 21, 15, 3, 3, 3, 3, 20, 16, 20, 16, 2, 17, 2, 17, 22}, /*ncbi*/ 24, /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */ } /* 1 2 1234567890123456789012 RLSTPAGVKNQHEDYCFIMW*X */ }; char* get_code_descr(int code) /* get a 60-letter (or less) description of a variant genetic code return value pointer to the description, not to be altered! */ { if (code >= 0 && code < totcodes) return genetic_code[code].libel; else return "Unknown genetic code. Standard code is used."; } int calc_codon_number(char* codon) { static char nucleotides[] = "AaCcGgTtUu"; static int nucnum[5] = {0, 1, 2, 3, 3}; int num, i, base; char* p; num = 0; for (i = 1; i <= 3; i++) { p = strchr(nucleotides, *codon); if (p == NULL) { num = 64; break; } else base = (p - nucleotides) / 2; num = num * 4 + nucnum[base]; codon++; } return num; } char codaa(char* codon, int code) /* amino acid translation: codon a 3-base string code the genetic code to be used return value the amino acid as 1 character */ { struct genetic_code_libel* pdata; int num; num = calc_codon_number(codon); if (code < 0 || code >= totcodes) code = 0; /*use regular code if unknown number */ pdata = &genetic_code[code]; /* ici ecriture plus compacte mal compilee sur PC*/ return aminoacids[ pdata->code[num] - 1 ]; } int get_ncbi_gc_number(int gc) { /* from acnuc to ncbi genetic code number */ return genetic_code[gc].ncbi_gc; } int get_acnuc_gc_number(int ncbi_gc) { /* from ncbi to acnuc genetic code number (returns 0 if not found) */ int num; for (num = 0; num < totcodes; num++) { if (genetic_code[num].ncbi_gc == ncbi_gc) return num; } return 0; } int strcmptrail(char* s1, int l1, char* s2, int l2) /* compare strings s1 and s2 of length l1 and l2 as done by strcmp but ignores all trailing spaces */ { char* fin; int l, flag = 1; if (l1 > 0) { if ( (fin = (char*)memchr(s1, 0, l1) ) != NULL) l1 = fin - s1; } if (l2 > 0) { if ( (fin = (char*)memchr(s2, 0, l2) ) != NULL) l2 = fin - s2; } if (l2 > l1) { flag = -1; fin = s1; s1 = s2; s2 = fin; l = l1; l1 = l2; l2 = l; } l = l2; fin = s2 + l; while (s2 < fin) { if (*s1 != *s2) return (*s1 - *s2) * flag; s1++; s2++; } fin = s1 + l1 - l2; while (s1 < fin) { if (*s1 != ' ') return flag; s1++; } return 0; } void majuscules(char* name) { name--; while (*(++name) != 0) *name = toupper(*name); } void compact(char* chaine) { int l; char* p, * q; l = strlen(chaine); p = chaine + l; while (*(--p) == ' ' && p >= chaine) *p = 0; while ((p = strchr(chaine, ' ')) != NULL) { q = p + 1; while (*q == ' ') q++; l = q - p; while (*q != 0) { *(q - l) = *q; q++; } *(q - l) = 0; } } char complementer_base(char nucl) { switch (nucl) { case 'a': case 'A': return 't'; case 'c': case 'C': return 'g'; case 'g': case 'G': return 'c'; case 'u': case 'U': case 't': case 'T': return 'a'; case 'r': case 'R': return 'y'; case 'y': case 'Y': return 'r'; default: return 'n'; } } /* ~~~~~~~~~~~~ retourne le complementaire d'une sequence ~~~~~~~~~~~ * recoit l'adresse du debut d'un tableau de caractere et sa longueur * inverse et complemente cette sequence * prend en compte si c'est un adn ou un arn * -------------------------------------------------------------------- */ void complementer_seq(char* deb_ch, int l) { int ii = 0; char compl1, compl2; for (ii = 0; ii <= (l - 1) / 2; ii++) { compl1 = complementer_base(*(deb_ch + ii)); compl2 = complementer_base(*(deb_ch + l - ii - 1)); *(deb_ch + ii) = compl2; *(deb_ch + l - ii - 1) = compl1; } } char init_codon_to_aa(char* codon, int gc) { int num, aa; struct genetic_code_libel* pdata; num = calc_codon_number(codon); if (num >= 64) return 'X'; /* use regular code if unknown number */ if (gc < 0 || gc >= totcodes) gc = 0; pdata = &genetic_code[gc]; aa = pdata->codon_init[num]; /* if not listed in expected init codons */ if (aa == 0) aa = pdata->code[num]; return aminoacids[aa - 1]; } int notrail2(char* chaine, int len) { len--; while (len >= 0 && chaine[len] == ' ') len--; return len + 1; } int prepch(char* chaine, char** posmot) { /* chaine: template a rechercher qui contient des wildcard @ posmot: tableau de pointeurs vers char au retour rempli avec des pointeurs adequats qui pointent dans chaine qui ne doit plus etre modifiee valeur rendue: nbre de pointeurs dans tableau posmot */ char* pos; int nbrmots; static char wildcard = '@'; if (strchr(chaine, '@') == NULL) return 0; nbrmots = -1; pos = chaine + strlen(chaine) - 1; while (pos >= chaine && *pos == ' ') pos--; *(pos + 1) = 0; pos = chaine; while (*pos != 0) { if (*pos == wildcard) { posmot[++nbrmots] = NULL; *pos = 0; while (*(pos + 1) == wildcard) pos++; } else { posmot[++nbrmots] = pos; while (*(pos + 1) != wildcard && *(pos + 1) != 0) pos++; } pos++; } return nbrmots + 1; } int compch(char* cible, int lcible, char** posmot, int nbrmots) { /* cible: chaine a tester pour presence du template lcible: long. de cible qui n'est pas forcement finie par \0 doit etre <= 150 posmot: tableau fabrique par prepch nbrmots: valeur rendue par prepch valeur rendue: 1 ssi template present dans cible, 0 si absent */ int num = 0, l, total; char* pos; static char vcible[151]; pos = cible + lcible - 1; while (pos >= cible && *pos == ' ') pos--; lcible = pos - cible + 1; memcpy(vcible, cible, lcible); vcible[lcible] = 0; cible = vcible; if (posmot[nbrmots - 1] == NULL) total = nbrmots - 1; else total = nbrmots - 2; if (posmot[0] != NULL) /* comparaison avec mot initial */ { l = strlen(posmot[0]); if (strncmp(cible, posmot[0], l) != 0) return 0; cible += l; num++; } while (num < total) /* recherche des mots internes */ { num++; pos = strstr(cible, posmot[num]); if (pos == NULL) return 0; l = strlen(posmot[num]); cible = pos + l; num++; } if (total == nbrmots - 1) return 1; /* template se termine par @ */ /* test si cible se termine par dernier mot du template */ l = strlen(posmot[nbrmots - 1]); if (strcmp(vcible + lcible - l, posmot[nbrmots - 1]) == 0) return 1; return 0; } int chg_acnuc(char* acnucvar, char* gcgacnucvar) /* Changing the values of variables acnuc and gcgacnuc : acnucvar the new value of acnuc (may be a variable, may be acnuc itself) gcgacnucvar the new value of gcgacnuc (may be a variable, may be gcgacnuc itself) returns TRUE if error, FALSE if ok */ { static char newacnuc[200], newgcgacnuc[200]; char* point; if (strcmp(acnucvar, "acnuc") != 0) { point = getenv(acnucvar); if (point != NULL) acnucvar = point; strcpy(newacnuc, "acnuc="); strcat(newacnuc, acnucvar); if (putenv(newacnuc) ) return 1; } if (strcmp(gcgacnucvar, "gcgacnuc") != 0) { point = getenv(gcgacnucvar); if (point != NULL) gcgacnucvar = point; strcpy(newgcgacnuc, "gcgacnuc="); strcat(newgcgacnuc, gcgacnucvar); if (putenv(newgcgacnuc) ) return 1; } return 0; } void gets_no_echo(char* password, size_t lpw) { char* p, c; #ifdef unixlike struct termios initialrsettings, newrsettings; int err; #elif defined(WIN32) DWORD mode, savemode, lu; HANDLE hconsole; int err; #endif #ifdef unixlike err = tcgetattr( fileno(stdin), &initialrsettings ); if (err == 0) { newrsettings = initialrsettings; newrsettings.c_lflag &= ~ECHO; newrsettings.c_lflag &= ~ICANON; tcsetattr( fileno(stdin), TCSAFLUSH, &newrsettings ); } #elif defined(WIN32) hconsole = GetStdHandle(STD_INPUT_HANDLE); err = GetConsoleMode(hconsole, &savemode); if (err != 0) { mode = savemode; mode &= ~ENABLE_ECHO_INPUT; mode &= ~ENABLE_LINE_INPUT; SetConsoleMode(hconsole, mode); FlushConsoleInputBuffer(hconsole); /* necessary */ } #endif p = password; do { #ifdef WIN32 ReadConsole(hconsole, &c, 1, &lu, NULL); #else c = getchar(); #endif if (c == EOF || c == '\n' || c == '\r') break; if (c != '\b' && c != '\x7F') { *(p++) = c; putchar('*'); } else { if (p > password) { p--; putchar('\b'); putchar(' '); putchar('\b'); } } } while (p - password < lpw); *p = 0; #ifdef unixlike if (err == 0) { tcsetattr( fileno(stdin), TCSANOW, &initialrsettings ); putchar('\n'); } #elif defined(WIN32) if (err != 0) { SetConsoleMode(hconsole, savemode); putchar('\n'); } #endif return; } bpp-raa-2.2.0/src/Bpp/Raa/RaaList.cpp000664 001750 001750 00000004614 12372454333 020612 0ustar00jdutheiljdutheil000000 000000 #include "RAA.h" using namespace std; using namespace bpp; RaaList::RaaList() { myraa = NULL; from = 1; } int RaaList::getCount(void) { return raa_bcount(myraa->raa_data, rank); } const string RaaList::LIST_SEQUENCES = "sequence list"; const string RaaList::LIST_KEYWORDS = "keyword list"; const string RaaList::LIST_SPECIES = "species list"; int RaaList::firstElement() { from = 1; return nextElement(); } int RaaList::nextElement() { char *sname; int seqrank = raa_nexteltinlist(myraa->raa_data, from, rank, &sname, &elementlength); if(seqrank) { elementname = sname; from = seqrank; } return seqrank; } void RaaList::setFrom(int element_rank) { from = element_rank; } string RaaList::residueCount() { char *count = raa_residuecount(myraa->raa_data, rank); string retval(count); return retval; } void RaaList::addElement(int elt_rank) { raa_bit1(myraa->raa_data, rank, elt_rank); } bool RaaList::parentsOnly(void) { if(*type == RaaList::LIST_SEQUENCES) return true; int isloc; raa_getliststate(myraa->raa_data, rank, &isloc, NULL, NULL); return (bool)isloc; } void RaaList::removeElement(int elt_rank) { raa_bit0(myraa->raa_data, rank, elt_rank); } void RaaList::zeroList(void) { raa_zerolist(myraa->raa_data, rank); } bool RaaList::isInList(int elt_rank) { return (bool)raa_btest(myraa->raa_data, rank, elt_rank); } RaaList *RaaList::modifyByLength(const string &criterion, const string &listname) { int err, newlistrank; if(getType() != RaaList::LIST_SEQUENCES) return NULL; err = raa_modifylist(myraa->raa_data, rank, (char *)"length", (char *)criterion.c_str(), &newlistrank, NULL, NULL); if(err) return NULL; raa_setlistname(myraa->raa_data, newlistrank, (char *)listname.c_str()); RaaList *list = new RaaList(); list->rank = newlistrank; list->myraa = myraa; list->name = listname; list->type = &RaaList::LIST_SEQUENCES; return list; } RaaList *RaaList::modifyByDate(const string &criterion, const string &listname) { int err, newlistrank; if(getType() != RaaList::LIST_SEQUENCES) return NULL; err = raa_modifylist(myraa->raa_data, rank, (char *)"date", (char *)criterion.c_str(), &newlistrank, NULL, NULL); if(err) return NULL; raa_setlistname(myraa->raa_data, newlistrank, (char *)listname.c_str()); RaaList *list = new RaaList(); list->rank = newlistrank; list->myraa = myraa; list->name = listname; list->type = &RaaList::LIST_SEQUENCES; return list; } bpp-raa-2.2.0/src/Bpp/Raa/RaaSpeciesTree.cpp000664 001750 001750 00000005070 12372454333 022107 0ustar00jdutheiljdutheil000000 000000 #include "RaaSpeciesTree.h" #include using namespace std; using namespace bpp; string RaaSpeciesTree::getName(int rank) { if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) { string name(sp_tree[rank]->name); return name; } else { string name(""); return name; } } int RaaSpeciesTree::parent(int rank) { if(!(rank > 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0; while(sp_tree[rank]->parent == NULL) rank = sp_tree[rank]->syno->rank; return sp_tree[rank]->parent->rank; } int RaaSpeciesTree::getTid(int rank) { if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->parent->tid; else return 0; } int RaaSpeciesTree::findNode(int tid) { if(tid >= 0 && tid <= max_tid) return tid_to_rank[tid]; else return 0; } int RaaSpeciesTree::findNode(const string &taxon, bool allowsynonym) { if(taxon == string("ROOT")) return 2; int num = raa_iknum(raa_data, (char*)taxon.c_str(), raa_spec); if(num != 0 && !allowsynonym) while(sp_tree[num]->parent == NULL) num = sp_tree[num]->syno->rank; return num; } int RaaSpeciesTree::count(int rank) { if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->count; else return 0; } string RaaSpeciesTree::label(int rank) { char *p; if(rank > 2 && rank <= max_sp && sp_tree[rank] != NULL && (p = sp_tree[rank]->libel) != NULL) { string retval(p); return retval; } else { string retval(""); return retval; } } int RaaSpeciesTree::firstChild(int rank) { if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->list_desc->value->rank; else return 0; } int RaaSpeciesTree::nextChild(int rank, int child) { if(!(rank >= 2 && rank <= max_sp && child > 2 && child <= max_sp && sp_tree[rank] != NULL && sp_tree[child] != NULL)) return 0; struct raa_pair *pair = sp_tree[rank]->list_desc; while(pair != NULL && pair->value->rank != child) { pair = pair->next; } return pair == NULL || pair->next == NULL ? 0 : pair->next->value->rank; } bool RaaSpeciesTree::isChild(int parent, int child) { while(child != parent) { child = this->parent(child); if(child == 0) return false; } return true; } int RaaSpeciesTree::nextSynonym(int rank) { if(!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0; struct raa_node *mynode = sp_tree[rank]->syno; if(mynode == NULL) return 0; else return mynode->rank; } int RaaSpeciesTree::getMajor(int rank) { if(!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0; while(sp_tree[rank]->parent == NULL) rank = sp_tree[rank]->syno->rank; return rank; } bpp-raa-2.2.0/src/Bpp/Raa/parser.h000664 001750 001750 00000000647 12372454333 020216 0ustar00jdutheiljdutheil000000 000000 #include #include typedef struct ThisReponse{ char **arg; /* je stocke les arguments */ int nbarguments; /* je stocke le nombre d'arguments */ } Reponse ; extern Reponse * initreponse(void) ; extern void clear_reponse(Reponse * rep) ; void ajout_reponse(Reponse *rep, char *pile, int len) ; extern void parse(char *chaine, Reponse *rep) ; extern char *val(Reponse *Mono, char *argument) ; bpp-raa-2.2.0/src/Bpp/Raa/RaaList.h000664 001750 001750 00000007767 12372454333 020273 0ustar00jdutheiljdutheil000000 000000 #ifndef _RAALIST_H_ #define _RAALIST_H_ #include namespace bpp { class RAA; /** * @brief List of sequences, keywords, or species returned by a database query. * * Instances of this class are created by database queries. Each instance contains * one or several elements that are often sequences, but can also be species or keywords. * Iteration through all elements of the list is possible. */ class RaaList { friend class RAA; RAA *myraa; int rank; std::string name; const std::string *type; int from; std::string elementname; int elementlength; public: /** * @brief Refers to a sequence list. */ static const std::string LIST_SEQUENCES; /** * @brief Refers to a keyword list. */ static const std::string LIST_KEYWORDS; /** * @brief Refers to a species list. */ static const std::string LIST_SPECIES; /** * @brief Gives the number of elements (often sequences) in the list. */ int getCount(); /** * @brief Gives the database rank of the first element of the list. */ int firstElement(); /** * @brief Gives the database rank of the list element following the last considered element. */ int nextElement(); /** * @brief Sets an element of the list from which nextElement() will start. * * @param element_rank The database rank of an element of the list, typically returned by * a previous nextElement() call. */ void setFrom(int element_rank); /** * @brief Gives the name of the last considered list element. */ std::string elementName() {return elementname; }; /** * @brief Gives the length of the last considered list element (meaningful only for sequence lists). */ int elementLength() {return elementlength; }; /** * @brief Returns the total # of residues in all sequences of list (meaningful only for sequence lists). * * Because this count can exceed a long integer, it is returned as a string. */ std::string residueCount(); /** * @brief Adds an element identified by its database rank to the list. */ void addElement(int rank); /** * @brief Removes an element identified by its database rank from the list. */ void removeElement(int rank); /** * @brief Tests whether an element identified by its database rank belongs to the list. */ bool isInList(int rank); /** * @brief Removes all elements from the list. */ void zeroList(); /** * @brief Gives the rank of the list. */ int getRank() {return rank; }; /** * @brief true means that list contains only parent sequences (does not contain any subsequence). */ bool parentsOnly(); /** * @brief Indicates whether the list contains sequences, species or keywords. * * @return can be "sequence list", "species list", or "keyword list" */ std::string getType() {return *type; }; /** * @brief Gives the list name. */ std::string getName() {return name; }; /** * @brief Modifies a sequence list by a length criterion. * * @param criterion Length criterion such as "> 1000" or "<5000". * @param listname Name to be given to created list of sequences matching the length criterion. * @return A new list of sequences matching the length criterion, or NULL if error. */ RaaList *modifyByLength(const std::string &criterion, const std::string &listname); /** * @brief Modifies a sequence list by a database insertion date criterion. * * The database insertion date of each sequence is that of the last DT record for the embl/swissprot format, * or that of the LOCUS record for the GenBank format. * * @param criterion Date criterion such as "> 1/jun/98" or "<10/DEC/2004". Year can be expressed with 2 or 4 digits. * Case is not significant. * @param listname Name to be given to the created list of sequences matching the date criterion. * @return A new list of sequences matching the date criterion, or NULL if error. */ RaaList *modifyByDate(const std::string &criterion, const std::string &listname); private: RaaList(); }; } //end of namespace bpp. #endif //_RAALIST_H_ bpp-raa-2.2.0/src/Bpp/Raa/RAA.h000664 001750 001750 00000047567 12372454333 017341 0ustar00jdutheiljdutheil000000 000000 /* * RAA.H */ #ifndef _RAA_H_ #define _RAA_H_ /** * @mainpage * * Network access to sequence databases (embl, genbank, swissprot, and others). * * These classes provides network access to several nucleotide and protein sequence databases * structured for multi-criteria retrieval under the ACNUC system as described in * Remote access to ACNUC nucleotide * and protein sequence databases at PBIL. * * The list of available databases is here. * EMBL and GenBank are daily updated; SwissProt (it is in fact UniProt and includes SwissProt and trEMBL) * is updated at each partial release; EMBLwgs is updated at each full release (that is, quarterly). * * */ extern "C" { #include "RAA_acnuc.h" } #include #include #include #include "RaaList.h" #include "RaaSpeciesTree.h" #include "RaaSeqAttributes.h" namespace bpp { /** * @brief Identifies an annotation line in a database. */ class RaaAddress { friend class RAA; int div; raa_long faddr; public: /** * @brief Gives the rank of the database file containing this annotation line. */ int getDiv() {return div; }; /** * @brief Gives, as a 64-bit int value, the offset of this annotation line within its database file. */ raa_long getAddr() {return faddr; }; }; /** * @brief Network access to sequence databases (embl, genbank, swissprot, and others). * * The list of available databases is here. * * Access can be done to single sequences from their name or accession number * or to lists of sequences matching a query combining several retrieval criteria. * Any fragment of any sequence defined by coordinates or by feature table entries * can be retrieved. Access to sequence annotations is possible. Concurrent access * to several databases is possible. * * Access is possible to database entries and also to subsequences, i.e., one or more fragments * of one or more parent sequences defined by a feature table entry. * Subsequences are named by adding an extension (e.g., .PE1) to the name of their parent sequence. */ class RAA { friend class RaaList; public: /** * @name Opening/closing database connections. * * @{ */ /** * @brief Direct constructor: opens a network connection to a database. * * @param dbname The database name (e.g., "embl", "genbank", "swissprot"). * @param port The IP port number of the server (the default value is a safe choice; make sure that no * firewall blocks outbound connections on this port). * @param server The IP name of the server (the default value is a safe choice). * @throw int An error code as follows:\n * 1: incorrect server name\n * 2: cannot create connection with server\n * 3: unknown database name\n * 4: database is currently not available for remote connection\n * 7: not enough memory */ RAA(const std::string &dbname, int port = 5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int); /** * @brief Direct constructor: opens a network connection to a database server, without specifying a database. * * Typical usage is to ask with knownDatabases() for the list of served databases, and then to open the chosen * database with openDatabase(). * * @param port The IP port number of the server (the default value is a safe choice; make sure that no * firewall blocks outbound connections on this port). * @param server The IP name of the server (the default value is a safe choice). * @throw int An error code as follows:\n * 1: incorrect server name\n * 2: cannot create connection with server\n * 7: not enough memory */ RAA(int port=5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int); /** * @brief Destructor: closes both the database access, if any, and the network connection. */ ~RAA(); /** * @brief Opens a database from its name. * * @param dbname The database name (e.g., "embl", "genbank", "swissprot"). * @param getpasswordf NULL, or, for a password-protected database, pointer to a password-providing function * that returns the password as a writable static char string. * @param p NULL, or pointer to data transmitted as argument of getpasswordf. * @return 0 if OK, or an error code as follows:\n * 3: unknown database name\n * 4: database is currently not available for remote connection\n * 5: a database was previously opened on this RAA object and not closed\n * 6: incorrect password for password-protected database\n * 7: not enough memory */ int openDatabase(const std::string &dbname, char *(*getpasswordf)(void *) = NULL, void *p = NULL); /** * @brief Closes a database connection. * Allows to later open another database with openDatabase() using the same RAA object. */ void closeDatabase(); /** * @brief Computes the list of names and descriptions of databases served by the server. * Typically used after creation of an RAA object without database and before openDatabase() call. * * @return The number of served databases. * @param name Vector of database names. Any of these names can be used * in openDatabase() calls. * @param description Vector of database descriptions. A description can * begin with "(offline)" to mean the database is currently not available. */ int knownDatabases(std::vector &name, std::vector &description); /** @} */ /** * @name Access to sequence data and annotations. * * @{ */ /** * @brief Returns several attributes of a sequence from its name or accession number. * * @param name_or_accno A sequence name or accession number. Case is not significant. * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence. */ RaaSeqAttributes *getAttributes(const std::string &name_or_accno); /** * @brief Returns several attributes of a sequence from its database rank. * * @param seqrank The database rank of a sequence. * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence, * or NULL if seqrank is not a valid database sequence rank. */ RaaSeqAttributes *getAttributes(int seqrank); /** * @brief Returns a database sequence identified by name or accession number. * * Because nucleotide database sequences can be several megabases in length, the maxlength argument * avoids unexpected huge sequence downloads. * * @param name_or_accno A sequence name or accession number. Case is not significant. * @param maxlength The maximum sequence length beyond which the function returns NULL. * @return The database sequence including a one-line comment, or NULL if name_or_accno * does not match any sequence or if the sequence length exceeds maxlength. */ Sequence *getSeq(const std::string &name_or_accno, int maxlength=100000); /** * @brief Returns a sequence identified by its database rank. * * Because nucleotide database sequences can be several megabases in length, the maxlength argument * avoids unexpected huge sequence downloads. * * @param seqrank The database rank of a sequence. * @param maxlength The maximum sequence length beyond which the function returns NULL. * @return The database sequence including a one-line comment, or NULL if seqrank * does not match any sequence or if the sequence length exceeds maxlength. */ Sequence *getSeq(int seqrank, int maxlength=100000); /** * @brief Returns any part of a sequence identified by its database rank. * * @param seqrank The database rank of a sequence. * @param first The first desired position within the sequence (1 is the smallest valid value). * @param length The desired number of residues (can be larger than what exists in the sequence). * @param sequence Filled upon return with requested sequence data. * @return The length of returned sequence data, or 0 if impossible. */ int getSeqFrag(int seqrank, int first, int length, std::string &sequence); /** * @brief Returns any part of a sequence identified by its name or accession number. * * @param name_or_accno The name or accession number of a sequence. Case is not significant. * @param first The first desired position within the sequence (1 is the smallest valid value). * @param length The desired number of residues (can be larger than what exists in the sequence). * @param sequence Filled upon return with requested sequence data. * @return The length of returned sequence data, or 0 if impossible. */ int getSeqFrag(const std::string &name_or_accno, int first, int length, std::string &sequence); /** * @brief Returns the first annotation line of the sequence of given database rank. * * @param seqrank Database rank of a sequence. * @return The first annotation line of this sequence (without terminal \\n). */ std::string getFirstAnnotLine(int seqrank); /** * @brief Returns the next annotation line after that previously read, or NULL if the end of the * database file was reached. * * @return The next annotation line after that previously read (without terminal \\n). */ std::string getNextAnnotLine(); /** * @brief Returns information identifying the position of the last read annotation line. * * @return Information identifying the position of the last read annotation line. */ RaaAddress getCurrentAnnotAddress(); /** * @brief Returns the annotation line at the given address. * * @param address Information identifying the position of an annotation line * typically obtained from a previous call to getCurrentAnnotAddress(). * @return The annotation line at that position (in static memory, without terminal \\n). */ std::string getAnnotLineAtAddress(RaaAddress address); /** * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence. * * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS. * @return The complete protein translation of this CDS, using the genetic code suggested * by the sequence annotations and with a one-line comment, or NULL if seqrank does not match a CDS * or if not enough memory. * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an * exception when translated to protein. */ Sequence *translateCDS(int seqrank) throw(BadCharException);//TODO add comment to Sequence /** * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence. * * @param name The name of a protein-coding sequence. It can be either a subsequence * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS. * @return The complete protein translation of this CDS, using the genetic code suggested * by the sequence annotations and with a one-line comment, or NULL if name does not match a CDS or * if not enough memory. * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an * exception when translated to protein. */ Sequence *translateCDS(const std::string &name) throw(BadCharException); /** * @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence. * * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS. * @return The amino acid corresponding to the start codon of this sequence, using the * adequate initiation-codon-specific genetic code. */ char translateInitCodon(int seqrank); /** @} */ /** * @name Creation of lists of sequences, species or keywords. * * @{ */ /** * @brief Returns the list of database elements (often sequences) matching a query. * * Query examples:\n k=ribosomal protein L14 \n sp=felis catus and t=cds * @param query A retrieval query following the syntax described * here. * @param listname A name to be given to the resulting list. Case is not significant. If a list with same * name already exists, it is replaced by the new list. * @return The resulting list of matching database elements. * @throw string If error, the string is a message describing the error cause. */ RaaList *processQuery(const std::string &query, const std::string &listname) throw(std::string); /** * @brief Creates an empty list with specified name. * * @param listname A name to be given to the resulting list. Case is not significant. * @param kind Nature of the resulting list. One of RaaList::LIST_SEQUENCES, RaaList::LIST_KEYWORDS, * RaaList::LIST_SPECIES. * @return The resulting list, unless an exception was raised. * @throw int 3: a list with same name already existed; it is left unchanged.\n * 4: the server cannot create more lists. */ RaaList *createEmptyList(const std::string &listname, const std::string &kind=RaaList::LIST_SEQUENCES) throw(int); /** * @brief Deletes a list and calls its destructor. * * @param list An RaaList object. */ void deleteList(RaaList *list); /** @} */ /** * @name Access to feature table-defined sequences (nucleotide databases only). * * @{ */ /** * @brief Computes the list of subsequences of a given sequence corresponding to a given feature key with * optional annotation string matching. * * This function allows to retrieve all features of the given sequence corresponding to a given feature key * and whose annotation optionally contains a given string. \n * Example:\n * getDirectFeature("AE005174", "tRNA", "mytrnas", "anticodon: TTG")\n * retrieves all tRNA features present in the feature table of sequence AE005174 that contain the string * "anticodon: TTG" in their annotations, and puts that in a sequence list called "mytrnas". This function is * meaningful with nucleotide sequence databases only (not with protein databases). * * @param seqname The name of a database sequence. Case is not significant. * @param featurekey A feature key (e.g., CDS, tRNA, ncRNA) that must be directly accessible, that is, one of those * returned by listDirectFeatureKeys(). Case is not significant. * @param listname The name to give to the resulting sequence list. * @param matching An optional string required to be present in the feature's annotations. Case is not significant. * @return The list of subsequences of seqname that correspond to the specified feature key and, optionally, whose * annotation contains the matching string, or NULL if no matching sequence exists. */ RaaList *getDirectFeature(const std::string &seqname, const std::string &featurekey, const std::string &listname, const std::string &matching = ""); /** * @brief Gives all feature keys of the database that can be directly accessed. * * These feature keys (e.g., CDS, rRNA, tRNA) can be used with function getDirectFeature(). This function is * meaningful with nucleotide sequence databases only (not with protein databases). * * @return A string vector listing all feature keys of the database that can be directly accessed. */ std::vector listDirectFeatureKeys(); /** * @brief Gives all feature keys of the database. * * These feature keys (e.g., CDS, conflict, misc_feature) can be used with function prepareGetAnyFeature(). This function is * meaningful with nucleotide sequence databases only (not with protein databases). * * @return A string vector listing all feature keys of the database. */ std::vector listAllFeatureKeys(); /** * @brief Starts extraction of all features of a specified key present in the feature table of a database sequence. * * A database sequence can contain many instances of a given feature key in its feature table. Thus, feature extraction * is done by first preparing the desired feature extraction, and by then successively extracting features * by getNextFeature() calls until no more exist in the feature table or until a call to interruptGetAnyFeature() is done. * Any successful prepareGetAnyFeature() call must be followed by getNextFeature() calls until * it returns NULL or by a call to interruptGetAnyFeature(); any call to other RAA member functions in between is prohibited. * * @param seqrank The database rank of a sequence. * @param featurekey Any feature key (direct or not) defined in * EMBL/GenBank/DDBJ feature tables. These are also returned by listAllFeatureKeys(). * @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature(). * @throw string A message indicating the cause of the error. */ void *prepareGetAnyFeature(int seqrank, const std::string &featurekey) throw(std::string); /** * @brief Successively returns features specified in a previous prepareGetAnyFeature() call. * * This function must be called repetitively until it returns NULL or until function interruptGetAnyFeature() is called. * Features are processed in their order of appearance in the feature table. * @param opaque A pointer returned by a previous prepareGetAnyFeature() call. * @return A sequence corresponding to one of the features specified in the prepareGetAnyFeature() call, or NULL * if no more such feature exists. */ Sequence *getNextFeature(void *opaque); /** * @brief Terminates a features extraction session initiated by a prepareGetAnyFeature() call before getNextFeature() call * returned NULL. * * @param opaque A pointer returned by a previous prepareGetAnyFeature() call. */ void interruptGetAnyFeature(void *opaque); /** @} */ /** * @name Browsing database species and keywords. * * @{ */ /** * @brief Loads the database's full species tree classification. * * This call takes a few seconds to run on large databases because much data get downloaded from the server. * * @param showprogress If true, progress information gets sent to stdout. * @return An object allowing work with the full species tree (see RaaSpeciesTree), or NULL if error. */ RaaSpeciesTree *loadSpeciesTree(bool showprogress=true); /** * @brief Frees the memory occupied by the species tree classification. * * @param tree An object previously returned by a loadSpeciesTree() call. It is deleted upon return. */ void freeSpeciesTree(RaaSpeciesTree *tree); /** * @brief Initializes pattern-matching in database keywords. Matching keywords are then returned by successive nextMatchingKeyword() calls. * * @param pattern A pattern-matching string using @ as wildcard (example: RNA\@polymerase\@). * Case is not significant. * @return The maximum length of any database keyword. */ int keywordPattern(const std::string &pattern); /** * @brief Finds next matching keyword in database. * * @param matching Set to the next matching keyword upon return. * @return The database rank of the next matching keyword, or 0 if no more matching keyword. */ int nextMatchingKeyword(std::string &matching); /** @} */ protected: raa_db_access *raa_data; private: RaaAddress current_address; int current_kw_match; std::string *kw_pattern; Sequence *getSeq_both(const std::string &name_or_accno, int rank, int maxlength); }; } //end of namespace bpp. #endif // _RAA_H_ bpp-raa-2.2.0/src/Bpp/Raa/RaaSpeciesTree.h000664 001750 001750 00000010242 12372454333 021551 0ustar00jdutheiljdutheil000000 000000 #ifndef _RAASPECIESTREE_H_ #define _RAASPECIESTREE_H_ extern "C" { #include "RAA_acnuc.h" } #include namespace bpp { /** * @brief To work with the species tree classification of the database. * * The tree can be walked up or down starting from a string, a database species rank, * or an NCBI taxonID (TID) value. The species tree also contains synonymous names. * The root of the tree is named "ROOT" and has database rank 2. */ class RaaSpeciesTree { friend class RAA; public: /** * @brief Returns the database rank of a taxon identified by its name. * * @param taxon A taxon name. Case is not significant. * @param allowsynonym If true, the return value will give the synonym's rank rather than the rank of its * major taxon. * @return The database rank of this taxon, or 0 if no such taxon exists in tree. */ int findNode(const std::string &taxon, bool allowsynonym = false); /** * @brief Returns the database rank of a taxon identified by a TID. * * @param tid A TID value. * @return The database rank of this taxon, or 0 if no such taxon exists in tree. */ int findNode(int tid); /** * @brief Returns the name of a taxon identified by its database rank. * * @param rank The database rank of a taxon. * @return The name of this taxon. */ std::string getName(int rank); /** * @brief Returns the database rank of the parent of a taxon in the tree. * * @param rank The database rank of a taxon. * @return The database rank of the parent of this taxon in the tree, or 0 if no such taxon exists in tree. */ int parent(int rank); /** * @brief Returns the TID of a taxon. * * @param rank The database rank of a taxon. * @return The TID of this taxon, or 0 if no such taxon exists in tree. */ int getTid(int rank); /** * @brief Returns the number of sequences attached to a taxon or to taxa below it in the species tree. * * @param rank The database rank of a taxon. * @return The number of sequences attached to this taxon or to taxa below it, or 0 if no such taxon exists in tree. */ int count(int rank); /** * @brief Returns the label of a taxon of given rank. * * Labels may contain taxon common names, genetic code information, TID values, and taxonomic * level information (e.g., genus, order). * @param rank The database rank of a taxon. * @return The label of this taxon, or "" if no such taxon or label exists in tree. */ std::string label(int rank); /** * @brief Returns the rank of the first child taxon of a given taxon. * * @param rank The database rank of a taxon. * @return The rank of its first child taxon, or 0 if no child taxon exists in tree. */ int firstChild(int rank); /** * @brief Allows to loop around all child taxa of a given taxon. * * @param parent The database rank of a taxon. * @param child The database rank of a child of taxon of rank parent. * @return The rank of the next child taxon of parent after taxon child, or 0 if no more child taxon exists in tree. */ int nextChild(int parent, int child); /** * @brief Tells whether there is a downward path from taxon parent to taxon child in the species tree. * * @param parent The database rank of a taxon. * @param child The database rank of another taxon. * @return true iff child is below parent (possibly with intermediate nodes) in the species tree. */ bool isChild(int parent, int child); /** * @brief Allows to loop around all synonymous taxa of a given taxon. * * Synonymous taxa of a taxon are chained in a closed loop, among which only one, the major taxon, * has a parent taxon. * * @param rank The database rank of a taxon. * @return The rank of the next synonymous taxon, or 0 if taxon rank has no synonymous taxon. */ int nextSynonym(int rank); /** * @brief Gives the major taxon among all synonyms of a given taxon. * * @param rank The database rank of a taxon. * @return The rank of the major taxon of taxon rank (can be itself). */ int getMajor(int rank); private: raa_db_access *raa_data; raa_node **sp_tree; int *tid_to_rank; int max_tid; int max_sp; }; } //namespace bpp. #endif // _RAASPECIESTREE_H_ bpp-raa-2.2.0/src/Bpp/Raa/RAA_acnuc.c000664 001750 001750 00000247052 12372454333 020474 0ustar00jdutheiljdutheil000000 000000 #include "RAA_acnuc.h" #include "parser.h" #include #include #include #include #include #if defined(unix) || defined(__APPLE__) #include #include #include #include #include #include #elif defined(WIN32) #include #include #endif #define SERVER_UPDATE_MESSAGE "acnuc stop for update\n" /* seules fctions utilisables hors de ce fichier pour ecrire sur socket */ int sock_fputs(raa_db_access *f, char *l); int sock_flush(raa_db_access *f); /* some prototypes */ void raa_acnucclose(raa_db_access *raa_current_db); void list_open_dbs_remove(raa_db_access *raa_current_db); /* needed functions */ extern char init_codon_to_aa(char *codon, int gc); char codaa(char *codon, int code); void *prepare_sock_gz_r(FILE *sockr); char *z_read_sock(void *v); int close_sock_gz_r(void *v); char *unprotect_quotes(char *name); /* global variables */ void (*raa_error_mess_proc)(raa_db_access *, char *) = NULL; #define MAX_RDSHRT 50 /* max short list length read in one time */ static raa_db_access *init_raa_db_access(void); static struct chain_void *raa_list_open_dbs = NULL; #if defined(WIN32) static int socket_getc(raa_db_access *raa_current_db, SOCKET f) { int q; if(raa_current_db->sock_input_pos < raa_current_db->sock_input_end) { return *(raa_current_db->sock_input_pos++); } q = recv(f, raa_current_db->sock_input, SOCKBUFS, 0); if(q == 0 || q == SOCKET_ERROR) return EOF; raa_current_db->sock_input_end = raa_current_db->sock_input + q; raa_current_db->sock_input_pos = raa_current_db->sock_input; return *(raa_current_db->sock_input_pos++); } static char *sock_fgets(raa_db_access *raa_current_db, char *line, int len) { int c; char *p; p = line; while(len > 1) { c = socket_getc(raa_current_db, (SOCKET)(raa_current_db->raa_sockfdr) ); if(c == EOF) { if(p == line) return NULL; break; } *(p++) = c; if(c == '\n') break; len--; } *p = 0; return line; } static int mswin_sock_flush(raa_db_access *raa_current_db) { int w; char *p; p = raa_current_db->sock_output; while(raa_current_db->sock_output_lbuf > 0) { w = send((SOCKET)raa_current_db->raa_sockfdw, p, raa_current_db->sock_output_lbuf, 0); raa_current_db->sock_output_lbuf -= w; p += w; } return 0; } int sock_flush(raa_db_access *raa_current_db) { if(raa_current_db == NULL) return 0; return mswin_sock_flush(raa_current_db); } int sock_fputs(raa_db_access *raa_current_db, char *s) { int l, r; if(raa_current_db == NULL) return 0; l = strlen(s); while(raa_current_db->sock_output_lbuf + l > SOCKBUFS) { r = SOCKBUFS - raa_current_db->sock_output_lbuf; memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, r); raa_current_db->sock_output_lbuf += r; l -= r; s += r; mswin_sock_flush(raa_current_db); } if(l > 0) { memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, l); raa_current_db->sock_output_lbuf += l; } return 0; } #else int sock_fputs(raa_db_access *raa_current_db, char *s) { if(raa_current_db == NULL) return EOF; return fputs(s, raa_current_db->raa_sockfdw); } int sock_flush(raa_db_access *raa_current_db) { if(raa_current_db == NULL) return EOF; return fflush(raa_current_db->raa_sockfdw); } #endif /* WIN32 */ int sock_printf(raa_db_access *raa_current_db, const char *fmt, ...) { va_list ap; int retval; static char buffer[1000]; va_start(ap, fmt); vsprintf(buffer, fmt, ap); retval = sock_fputs(raa_current_db, buffer); va_end(ap); return retval; } /******************************************************************/ /* lit une ligne au plus de la socket et transfere le resultat dans une chaine char * */ static char *read_sock_tell(raa_db_access *raa_current_db, int *wascompleteline) { #define RSOCKBUFS 5000 int lnbuf, isfull; char *p ; static char buffer[RSOCKBUFS]; static int was_here = FALSE; if(raa_current_db == NULL || was_here) return NULL; sock_flush(raa_current_db); /* tres important */ isfull = FALSE; #if defined(WIN32) p = sock_fgets(raa_current_db, buffer, RSOCKBUFS); #else p = fgets(buffer, RSOCKBUFS, raa_current_db->raa_sockfdr); #endif if(p == NULL || strcmp(p, SERVER_UPDATE_MESSAGE) == 0) { if(!was_here) { was_here = TRUE; *buffer = 0; if(raa_current_db != NULL && raa_current_db->dbname != NULL) { sprintf(buffer, "%s: ", raa_current_db->dbname); } strcat(buffer, ( p == NULL ? "Error: connection to acnuc server is down. Please try again." : "Error: acnuc server is down for database update. Please try again later." ) ); if(raa_error_mess_proc == NULL) { fprintf(stderr, "%s: %s\n", raa_current_db->dbname, buffer); /*raa_acnucclose(raa_current_db); exit(ERREUR);*/ return NULL; } else (*raa_error_mess_proc)(raa_current_db, buffer);/*this function sd call raa_acnucclose*/ was_here = FALSE; } return NULL; } was_here = FALSE; lnbuf = strlen(buffer); p = buffer + lnbuf - 1; if(*p == '\n') isfull = TRUE; while(p >= buffer && (*p == '\n' || *p == '\r') ) *(p--) = 0; if(wascompleteline != NULL) *wascompleteline = isfull; return buffer; } char *read_sock(raa_db_access *raa_current_db) /* lit une ligne entiere, rend ligne dans memoire privee */ { int wasfull, l2, l = 0; char *p; static char *reponse = NULL; static int lr = 0; do { p = read_sock_tell(raa_current_db, &wasfull); if(p == NULL) return NULL; l2 = strlen(p); if(l + l2 + 1 > lr) { lr = l + l2 + 1; reponse = (char *)realloc(reponse, lr); } memcpy(reponse + l, p, l2); l += l2; } while(! wasfull); reponse[l] = 0; return reponse; } char *read_sock_timeout(raa_db_access *raa_current_db, int timeout_ms) { fd_set readfds; struct timeval tout; int err; #if defined(WIN32) SOCKET fd; if(raa_current_db == NULL) return NULL; fd = (SOCKET)(raa_current_db->raa_sockfdr); #else int fd; if(raa_current_db == NULL) return NULL; fd = fileno(raa_current_db->raa_sockfdr); #endif FD_ZERO(&readfds); FD_SET(fd, &readfds); tout.tv_sec = timeout_ms / 1000; tout.tv_usec = 1000*(timeout_ms % 1000); err = select(fd + 1, &readfds, NULL, NULL, &tout); if(err > 0 && FD_ISSET(fd, &readfds) ) { return read_sock(raa_current_db); } return NULL; } enum {errservname=1, /* bad server name */ cantopensocket, /* 2 error opening socket */ unknowndb, /* 3 not in list of known dbs */ unavailabledb, /* 4 db is currently unavailable */ dbisopen, /* 5 a db is already open and was not closed */ badpsswd, /* 6 bad password for protected db */ nomemory, /* 7 not enough memory */ badracnuc, /* 8 enviroment variables racnuc or acnuc undefined or inadequate */ nosocket /* 9 no socket was opened yet */ }; int raa_acnucopen (char *clientid, raa_db_access **psock) /* opens the acnuc db using the environment variable racnuc, or, if undefined, acnuc, that should be defined to an url of the form raa://pbil.univ-lyon1.fr:5558/embl clientid: NULL or a string identifying the client */ { char *serveurName, *db_name, *p; int port, err; if( (p = getenv("racnuc")) == NULL) p = getenv("acnuc"); if(p == NULL) return badracnuc; err = raa_decode_address(p, &serveurName, &port, &db_name); if(err) return badracnuc; err = raa_acnucopen_alt (serveurName, port, db_name, clientid, psock); return err; } int raa_acnucopen_alt (char *serveurName, int port, char *db_name, char *clientid, raa_db_access **p) /* clientid: NULL or a string identifying the client */ { int err; err = raa_open_socket(serveurName, port, clientid, p); if(err != 0) return err; err = raa_opendb(*p, db_name); if(err != 0) { list_open_dbs_remove(*p); } return err; } int raa_open_socket(char *serveurName, int port, char *clientid, raa_db_access **psock) /* clientid: NULL or a string identifying the client */ { raa_db_access *raa_current_db; struct addrinfo *ai; char *reponse, portstring[10]; int err; #ifdef WIN32 WSADATA mywsadata; SOCKET raa_snum; #else int raa_snum; #endif raa_current_db = init_raa_db_access(); if(raa_current_db == NULL) return nomemory; /* not enough memory */ /* création de la socket */ #ifdef WIN32 err = WSAStartup(MAKEWORD(2,2), &mywsadata); /* indispensable avant utilisation socket */ if (err == 0) raa_snum = WSASocket(AF_INET, SOCK_STREAM, IPPROTO_TCP, NULL, (GROUP)0, 0); if (err != 0 || raa_snum == INVALID_SOCKET) { list_open_dbs_remove(raa_current_db); return cantopensocket; } #else raa_snum = socket(AF_INET, SOCK_STREAM, 0); if (raa_snum == -1) { list_open_dbs_remove(raa_current_db); return cantopensocket; } #endif /* création de deux flux type FILE * */ #if defined(WIN32) raa_current_db->raa_sockfdr = (FILE *)raa_snum; raa_current_db->raa_sockfdw = (FILE *)raa_snum; #else raa_current_db->raa_sockfdr = fdopen(raa_snum,"r"); raa_current_db->raa_sockfdw = fdopen(raa_snum,"a"); #endif sprintf(portstring, "%d", port); err = getaddrinfo(serveurName, portstring, NULL, &ai); if (err) { list_open_dbs_remove(raa_current_db); return errservname; } err = connect(raa_snum, ai->ai_addr, ai->ai_addrlen); freeaddrinfo(ai); if (err != 0) { list_open_dbs_remove(raa_current_db); return cantopensocket; } // read first reply from the server reponse = read_sock_timeout(raa_current_db, 1000*60 /* 1 min */); if(reponse == NULL || strcmp(reponse, "OK acnuc socket started") != 0) { list_open_dbs_remove(raa_current_db); return cantopensocket; } if(clientid != NULL) { sock_printf(raa_current_db, "clientid&id=\"%s\"\n", clientid); reponse=read_sock(raa_current_db); if(reponse == NULL) { list_open_dbs_remove(raa_current_db); return cantopensocket; } } *psock = raa_current_db; return 0; } extern void raa_MD5String (char *in_string, char out_digest[33]); int raa_opendb_pw(raa_db_access *raa_current_db, char *db_name, void *ptr, char *(*getpasswordf)(void *) ) /* getpasswordf: pointer to function that gets called if a password is needed ptr: pointer to data passed to the getpasswordf function return values : 3 not in list of known dbs 4 db is unavailable 5 a db is already open 6 failed password-based authorization */ { Reponse *rep; char *reponse, *code, *p, *challenge; int codret, totspecs, totkeys; if(raa_current_db == NULL) return nosocket; sock_printf(raa_current_db, "acnucopen&db=%s\n", db_name); reponse=read_sock(raa_current_db); if(reponse == NULL) return nosocket; rep=initreponse(); parse(reponse,rep); code=val(rep,"code"); codret=atoi(code); free(code); if(codret == 6) { static char reply[33], tmp[300]; char *password = NULL; clear_reponse(rep); if(getpasswordf != NULL) password = getpasswordf(ptr); if(password == NULL) return badpsswd; challenge = reponse + 17; /* reply = MD5 of challenge:db_name:MD5(password) */ raa_MD5String(password, reply); memset(password, 0, strlen(password)); sprintf(tmp, "%s:%s:%s", challenge, db_name, reply); raa_MD5String(tmp, reply); memset(tmp, 0, strlen(tmp)); sock_printf(raa_current_db, "reply=%s\n", reply); reponse = read_sock(raa_current_db); rep=initreponse(); parse(reponse,rep); code=val(rep,"code"); codret=atoi(code); free(code); } if (codret != 0) { clear_reponse(rep); return codret; } p = val(rep,"type"); raa_current_db->dbname = strdup(db_name); raa_current_db->genbank = raa_current_db->embl = raa_current_db->swissprot = raa_current_db->nbrf = FALSE; if(p != NULL) { if(strcmp(p, "GENBANK") == 0) raa_current_db->genbank = TRUE; else if(strcmp(p, "EMBL") == 0) raa_current_db->embl = TRUE; else if(strcmp(p, "SWISSPROT") == 0) raa_current_db->swissprot = TRUE; else if(strcmp(p, "NBRF") == 0) raa_current_db->nbrf = TRUE; free(p); } p = val(rep,"totseqs"); raa_current_db->nseq = atoi(p); free(p); p = val(rep,"totspecs"); totspecs = atoi(p); free(p); p = val(rep,"totkeys"); totkeys = atoi(p); free(p); raa_current_db->maxa=(totspecs > totkeys ? totspecs : totkeys); raa_current_db->longa=(raa_current_db->maxa-1)/(8 * sizeof(int))+1; /* default values useful if talking to old server */ raa_current_db->WIDTH_SMJ = 20; raa_current_db->L_MNEMO = 16; raa_current_db->WIDTH_BIB = 40; raa_current_db->WIDTH_AUT = 20; raa_current_db->WIDTH_SP = 40; raa_current_db->WIDTH_KW = 40; raa_current_db->lrtxt = 60; raa_current_db->SUBINLNG=63; raa_current_db->ACC_LENGTH=13; /* conservative value */ p = val(rep,"L_MNEMO"); if(p != NULL) { raa_current_db->L_MNEMO = atoi(p); free(p); } p = val(rep,"WIDTH_SP"); if(p != NULL) { raa_current_db->WIDTH_SP = atoi(p); free(p); } p = val(rep,"WIDTH_KW"); if(p != NULL) { raa_current_db->WIDTH_KW = atoi(p); free(p); } p = val(rep,"WIDTH_AUT"); if(p != NULL) { raa_current_db->WIDTH_AUT = atoi(p); free(p); } p = val(rep,"WIDTH_BIB"); if(p != NULL) { raa_current_db->WIDTH_BIB = atoi(p); free(p); } p = val(rep,"WIDTH_SMJ"); if(p != NULL) { raa_current_db->WIDTH_SMJ = atoi(p); free(p); } p = val(rep,"ACC_LENGTH"); if(p != NULL) { raa_current_db->ACC_LENGTH = atoi(p); free(p); } p = val(rep,"lrtxt"); if(p != NULL) { raa_current_db->lrtxt = atoi(p); free(p); } p = val(rep,"SUBINLNG"); if(p != NULL) { raa_current_db->SUBINLNG = atoi(p); free(p); raa_current_db->rlng_buffer = (struct rlng *)realloc(raa_current_db->rlng_buffer, (raa_current_db->SUBINLNG + 1) * sizeof(int)); } clear_reponse(rep); return 0; } int raa_opendb(raa_db_access *raa_current_db, char *db_name) { return raa_opendb_pw(raa_current_db, db_name, NULL, NULL); } int raa_decode_address(char *url, char **p_ip_name, int *socket, char **p_remote_db) /* decode syntax such as raa://pbil.univ-lyon1.fr:5557/embl return !=0 if error */ { char *p, *q; static char ip_name[200]; static char remote_db[100]; p = url; if(p == NULL) return 1; if( (q = strstr(url, "://") ) != NULL ) p = q + 3; q = strchr(p, ':'); if(q == NULL) return 1; memcpy(ip_name, p, q - p); ip_name[q - p] = 0; if(p_ip_name != NULL) *p_ip_name = ip_name; if(socket != NULL) *socket = atoi(q+1); if(p_remote_db == NULL) return 0; q = strchr(p, '/'); if(q != NULL) { q++; while(*q == ' ') q++; if(*q == 0) *p_remote_db = NULL; else { strcpy(remote_db, q); *p_remote_db = remote_db; } } else *p_remote_db = NULL; return 0; } #define maxSUBINLNG 512 static raa_db_access *init_raa_db_access(void) { raa_db_access *data; struct chain_void *elt; data = (raa_db_access *)calloc(1, sizeof(raa_db_access)); elt = (struct chain_void *)malloc(sizeof(struct chain_void)); if(data == NULL || elt == NULL) return NULL; data->rlng_buffer = (struct rlng *)malloc((maxSUBINLNG+1)*sizeof(int)); if(data->rlng_buffer == NULL) return NULL; /* ajouter un elt a liste ds db ouvertes */ elt->data = data; elt->next = raa_list_open_dbs; raa_list_open_dbs = elt; /* initialiser les champs non nuls */ data->gfrag_data.l_nseq_buf = INT_MAX; data->nextelt_data.current_rank = -1; data->nextelt_data.previous = -2; data->readshrt_data.shrt_begin = S_BUF_SHRT - 1; #ifdef WIN32 data->sock_input_pos = data->sock_input; data->sock_input_end = data->sock_input; #endif return data; } static int fill_gfrag_buf(raa_db_access *raa_current_db, int nsub, int first) { char *p, *line; int lu, l, length, wasfull; sock_printf(raa_current_db,"gfrag&number=%d&start=%d&length=%d\n", nsub, first, RAA_GFRAG_BSIZE); /* retour: length=xx&...the seq...\n */ line = read_sock_tell(raa_current_db, &wasfull); if(line == NULL) return 0; if(strncmp(line, "length=", 7) != 0 || (p = strchr(line, '&')) == NULL ) { return 0; } length = atoi(line + 7); lu = strlen(++p); memcpy(raa_current_db->gfrag_data.buffer, p, lu); while(! wasfull) { line = read_sock_tell(raa_current_db, &wasfull); if(line == NULL) break; l = strlen(line); if(lu+l <= RAA_GFRAG_BSIZE) memcpy(raa_current_db->gfrag_data.buffer + lu, line, l); lu += l; } raa_current_db->gfrag_data.buffer[lu] = 0; return lu; } int raa_gfrag(raa_db_access *raa_current_db, int nsub, int first, int lfrag, char *dseq) { int lu, piece; char *debut; if(raa_current_db == NULL) return 0; if(raa_current_db->gfrag_data.lbuf == 0 || nsub != raa_current_db->gfrag_data.nseq_buf || first >= raa_current_db->gfrag_data.first_buf + raa_current_db->gfrag_data.lbuf || first < raa_current_db->gfrag_data.first_buf) { if( nsub == raa_current_db->gfrag_data.nseq_buf && first > raa_current_db->gfrag_data.l_nseq_buf) lu = 0; else lu = fill_gfrag_buf(raa_current_db, nsub, first); if(lu == 0) return 0; raa_current_db->gfrag_data.lbuf = lu; if(raa_current_db->gfrag_data.lbuf < RAA_GFRAG_BSIZE) raa_current_db->gfrag_data.l_nseq_buf = first + raa_current_db->gfrag_data.lbuf - 1; else raa_current_db->gfrag_data.l_nseq_buf = INT_MAX; raa_current_db->gfrag_data.first_buf = first; raa_current_db->gfrag_data.nseq_buf = nsub; } debut = raa_current_db->gfrag_data.buffer + (first - raa_current_db->gfrag_data.first_buf); lu = raa_current_db->gfrag_data.lbuf + raa_current_db->gfrag_data.first_buf-1 - first+1; if( lu > lfrag) lu = lfrag; memcpy(dseq, debut, lu); while(lfrag > lu) { piece = raa_gfrag(raa_current_db, nsub, first + lu, lfrag - lu, dseq + lu); if(piece == 0) break; lu += piece; } dseq[lu] = 0; return lu; } void list_open_dbs_remove(raa_db_access *raa_current_db) /* enlever de liste des db ouvertes */ { struct chain_void *elt, *elt2; int i; if(raa_current_db == NULL) return; /* should not happen */ if(raa_current_db->dbname != NULL) free(raa_current_db->dbname); if(raa_current_db->rlng_buffer != NULL) free(raa_current_db->rlng_buffer); if(raa_current_db->readsub_data.name != NULL) free(raa_current_db->readsub_data.name); for(i = 0; i < raa_current_db->annot_data.annotcount; i++) free(raa_current_db->annot_data.annotline[i]); for(i = 0; i < BLOCK_ELTS_IN_LIST; i++) if(raa_current_db->nextelt_data.tabname[i] != NULL) free(raa_current_db->nextelt_data.tabname[i]); if(raa_current_db->readsmj_data.lastrec > 0) { free(raa_current_db->readsmj_data.plongs); for(i=2; i <= raa_current_db->readsmj_data.lastrec; i++) { if(raa_current_db->readsmj_data.names[i] != NULL) free(raa_current_db->readsmj_data.names[i]); if(raa_current_db->readsmj_data.libels[i] != NULL) free(raa_current_db->readsmj_data.libels[i]); } free(raa_current_db->readsmj_data.names); free(raa_current_db->readsmj_data.libels); raa_current_db->readsmj_data.lastrec = 0; } if(raa_list_open_dbs == NULL) return; /* should not happen */ if(raa_list_open_dbs->data == raa_current_db) { elt = raa_list_open_dbs; raa_list_open_dbs = raa_list_open_dbs->next; free(elt); } else { elt = raa_list_open_dbs; while(elt->next != NULL) { if(elt->next->data == raa_current_db) { elt2 = elt->next; elt->next = elt2->next; free(elt2); break; } elt = elt->next; } } free(raa_current_db); } static void raa_free_sp_tree(raa_node *pere) { raa_node *next, *tmp_n; struct raa_pair *liste, *tmp_p; liste = pere->list_desc; while(liste != NULL) { tmp_p = liste->next; raa_free_sp_tree(liste->value); free(liste); liste = tmp_p; } next = pere->syno; while(next != NULL && next != pere) { tmp_n = next->syno; free(next->name); free(next); next = tmp_n; } free(pere->name); if(pere->libel != NULL) free(pere->libel); if(pere->libel_upcase != NULL) free(pere->libel_upcase); free(pere); } void raa_acnucclose(raa_db_access *raa_current_db) { char *reponse; int i; if(raa_current_db == NULL) return; sock_fputs(raa_current_db, "acnucclose\n"); reponse=read_sock(raa_current_db); if(reponse != NULL) { sock_fputs(raa_current_db, "quit\n"); sock_flush(raa_current_db); } #ifdef WIN32 closesocket( (SOCKET) (raa_current_db->raa_sockfdw) ); #else fclose(raa_current_db->raa_sockfdr); fclose(raa_current_db->raa_sockfdw); #endif if(raa_current_db->tot_key_annots > 0) { for(i = 0; i < raa_current_db->tot_key_annots; i++) { free(raa_current_db->key_annots[i]); free(raa_current_db->key_annots_min[i]); } free(raa_current_db->key_annots); free(raa_current_db->key_annots_min); free(raa_current_db->want_key_annots); raa_current_db->tot_key_annots = 0; } if(raa_current_db->tid_to_rank != NULL) free(raa_current_db->tid_to_rank); if(raa_current_db->sp_tree != NULL) { raa_free_sp_tree(raa_current_db->sp_tree[2]); free(raa_current_db->sp_tree); } list_open_dbs_remove(raa_current_db); } int raa_prep_acnuc_query(raa_db_access *raa_current_db) { /* returns -1 if error or number of free bit lists */ char *reponse, *p, *q, *annotlines; int codret, i; Reponse *rep; if(raa_current_db == NULL) return -1; rep = initreponse(); sock_fputs(raa_current_db, "countfreelists\n"); reponse=read_sock(raa_current_db); if(reponse == NULL) return -1; parse(reponse,rep); reponse=val(rep,"code"); if(reponse == NULL) return -1; codret=atoi(reponse); free(reponse); if(codret != 0) return -1; reponse=val(rep,"free"); if(reponse != NULL) { codret = atoi(reponse); free(reponse); } annotlines = val(rep, "annotlines"); raa_current_db->tot_key_annots = 0; if(annotlines != NULL) { p = annotlines - 1; do { p++; raa_current_db->tot_key_annots++; } while((p = strchr(p, '|')) != NULL); raa_current_db->want_key_annots = (unsigned char *)malloc(raa_current_db->tot_key_annots * sizeof(unsigned char)); raa_current_db->key_annots = (char **)malloc(raa_current_db->tot_key_annots * sizeof(char *)); raa_current_db->key_annots_min = (char **)malloc(raa_current_db->tot_key_annots * sizeof(char *)); p = annotlines; for(i = 0; i < raa_current_db->tot_key_annots; i++) { q = strchr(p, '|'); if(q == NULL) q = p + strlen(p); raa_current_db->key_annots[i] = malloc(q - p + 1); raa_current_db->key_annots_min[i] = malloc(q - p + 1); memcpy(raa_current_db->key_annots_min[i], p, q - p); raa_current_db->key_annots_min[i][q - p] = 0; strcpy(raa_current_db->key_annots[i], raa_current_db->key_annots_min[i]); majuscules(raa_current_db->key_annots[i]); compact(raa_current_db->key_annots[i]); p = q + 1; } free(annotlines); } else codret = -1; clear_reponse(rep); return codret; } static char *raa_requete_remote_file(raa_db_access *raa_current_db, char *oldrequete, int **plist, char **); int raa_proc_query(raa_db_access *raa_current_db, char *requete, char **message, char *nomliste, int *numlist, int *count, int *locus, int *type) { char *reponse, *code, *numlistchr, *countchr, *locuschr, *typechr, *badfname; int codret, *tmp_blists; Reponse *rep; if(raa_current_db == NULL) return -1; requete = raa_requete_remote_file(raa_current_db, requete, &tmp_blists, &badfname); if(requete == NULL) { if(message != NULL) { static char fmt[] = "problem accessing file: %s"; *message = (char *)malloc(strlen(fmt) + strlen(badfname) + 1); sprintf(*message, fmt, badfname); } return 1; } sock_printf(raa_current_db,"proc_query&query=\"%s\"&name=\"%s\"\n", protect_quotes(requete), nomliste); free(requete); reponse=read_sock(raa_current_db); if(reponse == NULL) { if(message != NULL) *message = strdup("connection with server is down"); return -1; } rep=initreponse(); parse(reponse,rep); code=val(rep,"code"); codret=atoi(code); if(codret == 0) { numlistchr=val(rep,"lrank"); *numlist=atoi(numlistchr); countchr=val(rep,"count"); if(count != NULL) *count=atoi(countchr); typechr=val(rep,"type"); locuschr=val(rep,"locus"); if(type != NULL) { if (strcmp(typechr,"SQ")==0) *type='S'; else if (strcmp(typechr,"KW")==0) *type='K'; else if (strcmp(typechr,"SP")==0) *type='E'; } if(locus != NULL) *locus = strcmp(locuschr,"T") == 0; free(countchr); free(locuschr); free(typechr); free(numlistchr); } else if(message != NULL) { *message = val(rep, "message"); } free(code); clear_reponse(rep); if(tmp_blists != NULL) { while(*tmp_blists != 0) raa_releaselist(raa_current_db, *(tmp_blists++) ); } return codret; } int raa_nexteltinlist(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength) { return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, NULL, NULL); } int raa_nexteltinlist_annots(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength, raa_long *paddr, int *pdiv) { int num, next, count; char *p; Reponse *rep; if(raa_current_db == NULL) return 0; if(lrank == raa_current_db->nextelt_data.current_rank && raa_current_db->nextelt_data.previous < raa_current_db->nextelt_data.total - 1 && (raa_current_db->nextelt_data.previous == -1 || first == raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous] ) ) { raa_current_db->nextelt_data.previous++; next = raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous]; if(next != 0) { if(pname != NULL) *pname = raa_current_db->nextelt_data.tabname[raa_current_db->nextelt_data.previous]; if(plength != NULL) *plength = raa_current_db->nextelt_data.tablength[raa_current_db->nextelt_data.previous]; if(paddr != NULL) *paddr = raa_current_db->nextelt_data.taboffset[raa_current_db->nextelt_data.previous]; if(pdiv != NULL) *pdiv = raa_current_db->nextelt_data.tabdiv[raa_current_db->nextelt_data.previous]; } return next; } count = BLOCK_ELTS_IN_LIST; for(num = 0; num < count; num++) { if(raa_current_db->nextelt_data.tabname[num] != NULL) free(raa_current_db->nextelt_data.tabname[num]); } memset(raa_current_db->nextelt_data.tabname, 0, count * sizeof(char *)); sock_printf(raa_current_db,"nexteltinlist&lrank=%d&first=%d&count=%d\n",lrank,first, count); num = 0; raa_current_db->nextelt_data.current_rank = lrank; raa_current_db->nextelt_data.total = 0; do { p = read_sock(raa_current_db); if(p == NULL) return 0; rep = initreponse(); parse(p, rep); p = val(rep,"next"); if(p == NULL) { clear_reponse(rep); return 0; } next = atoi(p); free(p); raa_current_db->nextelt_data.total++; raa_current_db->nextelt_data.tabnum[num] = next; if(next != 0) { raa_current_db->nextelt_data.tabname[num] = val(rep, "name"); if( (p= val(rep, "length")) != NULL) { raa_current_db->nextelt_data.tablength[num] = atoi(p); free(p); } if((p= val(rep, "offset")) != NULL) { raa_current_db->nextelt_data.taboffset[num] = scan_raa_long(p); free(p); } if((p= val(rep, "div")) != NULL) { raa_current_db->nextelt_data.tabdiv[num] = atoi(p); free(p); } } clear_reponse(rep); num++; } while(next != 0 && --count > 0); raa_current_db->nextelt_data.previous = -1; return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, paddr, pdiv); } raa_long scan_raa_long(char *txt) { raa_long val; sscanf(txt, RAA_LONG_FORMAT, &val); return val; } char *print_raa_long(raa_long val) { static char buffer[50]; sprintf(buffer, RAA_LONG_FORMAT, val); return buffer; } static char *load_annots_buf(raa_db_access *raa_current_db, raa_long faddr, int div, int was_nextannots) /* appeler juste aprčs avoir envoye sur socket read_annots&... ou next_annots&... : retour attendu sur socket : nl=xx[&offset=xx]&...nl lines each with \n */ { int i, nl; char *firstline, *p, *q; if(raa_current_db == NULL) return NULL; for(i=0; i < raa_current_db->annot_data.annotcount; i++) free(raa_current_db->annot_data.annotline[i]); raa_current_db->annot_data.annotcount = 0; raa_current_db->annot_data.annotaddrlast = faddr; firstline = read_sock(raa_current_db); if(firstline == NULL) return NULL; if(strncmp(firstline, "nl=", 3) != 0 || (p = strchr(firstline, '&')) == NULL ) return NULL; nl = atoi(firstline + 3); if(nl == 0) return NULL; p++; if(was_nextannots && strncmp(p, "offset=", 7) == 0) { p = strchr(p, '&'); if(p == NULL) return NULL; p++; } i = strlen(p); raa_current_db->annot_data.annotline[0] = (char *)malloc(i+1); strcpy(raa_current_db->annot_data.annotline[0], p); raa_current_db->annot_data.annotaddrlast += strlen(raa_current_db->annot_data.annotline[0]) + 1; for(i = 1; i < nl; i++) { q = read_sock(raa_current_db); if(q == NULL) return NULL; raa_current_db->annot_data.annotline[i] = strdup( q ); raa_current_db->annot_data.annotaddrlast += strlen(raa_current_db->annot_data.annotline[i]) + 1; } raa_current_db->annot_data.annotcurrent = 1; raa_current_db->annot_data.annotcount = nl; raa_current_db->annot_data.annotaddr = faddr; raa_current_db->annot_data.annotdiv = div; raa_current_db->annot_data.annotaddrfirst = faddr; strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[0]); return raa_current_db->annot_data.annotsbuffer; } char *raa_read_annots(raa_db_access *raa_current_db, raa_long faddr, int div) { int i; raa_long debut; char *p; if(raa_current_db == NULL) return NULL; if(raa_current_db->annot_data.annotcount > 0 && div == raa_current_db->annot_data.annotdiv && faddr >= raa_current_db->annot_data.annotaddrfirst && faddr < raa_current_db->annot_data.annotaddrlast ) { debut = raa_current_db->annot_data.annotaddrfirst; for(i = 1; i <= raa_current_db->annot_data.annotcount; i++) { if(debut == faddr) { raa_current_db->annot_data.annotcurrent = i; raa_current_db->annot_data.annotaddr = debut; strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]); return raa_current_db->annot_data.annotsbuffer; } debut += strlen(raa_current_db->annot_data.annotline[i - 1]) + 1; } } sock_printf(raa_current_db,"read_annots&offset=%s&div=%d&nl=%d\n", print_raa_long(faddr), div, ANNOTCOUNT); p = load_annots_buf(raa_current_db, faddr, div, FALSE); return p; } char *raa_next_annots(raa_db_access *raa_current_db, raa_long *paddr) { raa_long faddr; char *p; if(raa_current_db == NULL) return NULL; if(raa_current_db->annot_data.annotcurrent < raa_current_db->annot_data.annotcount) { raa_current_db->annot_data.annotaddr += strlen(raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]) + 1; if(paddr != NULL) *paddr = raa_current_db->annot_data.annotaddr; raa_current_db->annot_data.annotcurrent++; strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]); return raa_current_db->annot_data.annotsbuffer; } faddr = raa_current_db->annot_data.annotaddrlast; if(paddr != NULL) *paddr = faddr; sock_printf(raa_current_db, "next_annots&nl=%d\n", ANNOTCOUNT); p = load_annots_buf(raa_current_db, faddr, raa_current_db->annot_data.annotdiv, TRUE); return p; } int raa_iknum(raa_db_access *raa_current_db, char *name, raa_file cas) { char *reponse, *p; int val; if(raa_current_db == NULL) return 0; sock_printf(raa_current_db,"iknum&name=\"%s\"&type=%s\n", protect_quotes(name), (cas == raa_key ? "KW" : "SP") ); reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; p = strchr(reponse, '='); if(p == NULL) return 0; p++; sscanf(p, "%u", &val); return val; } int raa_isenum(raa_db_access *raa_current_db, char *name) { char *reponse, *p; int val; if(raa_current_db == NULL) return 0; sock_printf(raa_current_db,"isenum&name=\"%s\"\n", protect_quotes(name) ); reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; p = strchr(reponse, '='); if(p == NULL) return 0; p++; sscanf(p, "%u", &val); return val; } int raa_bcount(raa_db_access *raa_current_db, int lrank) { Reponse *rep; char *reponse, *code, *countstr; int count = 0; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db,"bcount&lrank=%d\n",lrank); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); code = val(rep,"code"); if(*code == '0') { countstr = val(rep,"count"); count = atoi(countstr); free(countstr); } free(code); clear_reponse(rep); return count; } void raa_bit1(raa_db_access *raa_current_db, int lrank, int num) { char *reponse; if(raa_current_db == NULL) return; sock_printf(raa_current_db,"bit1&lrank=%d&num=%d\n", lrank, num); reponse=read_sock(raa_current_db); } void raa_bit0(raa_db_access *raa_current_db, int lrank, int num) { char *reponse; if(raa_current_db == NULL) return; sock_printf(raa_current_db,"bit0&lrank=%d&num=%d\n", lrank, num); reponse=read_sock(raa_current_db); } int raa_btest(raa_db_access *raa_current_db, int lrank, int num) { char *reponse; if(raa_current_db == NULL) return 0; sock_printf(raa_current_db,"btest&lrank=%d&num=%d\n", lrank, num); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; return strcmp(reponse, "code=0&on") == 0; } void raa_copylist(raa_db_access *raa_current_db, int from, int to) { char *reponse; if(raa_current_db == NULL) return; sock_printf(raa_current_db,"copylist&lfrom=%d<o=%d\n", from, to); reponse=read_sock(raa_current_db); } void raa_zerolist(raa_db_access *raa_current_db, int rank) { char *reponse; if(raa_current_db == NULL) return; sock_printf(raa_current_db,"zerolist&lrank=%d\n", rank); reponse=read_sock(raa_current_db); } void raa_setliststate(raa_db_access *raa_current_db, int lrank, int locus, int type) { char *reponse, str_type[3]; if(raa_current_db == NULL) return; if(type == 'S') strcpy(str_type, "SQ"); else if(type == 'K') strcpy(str_type, "KW"); else strcpy(str_type, "SP"); sock_printf(raa_current_db,"setliststate&lrank=%d&locus=%c&type=%s\n", lrank, (locus ? 'T' : 'F'), str_type ); reponse=read_sock(raa_current_db); } char *raa_getliststate(raa_db_access *raa_current_db, int lrank, int *locus, int *type, int *count) /* list name is returned in static memory */ { Reponse *rep; char *reponse, *code, *countstr, *locusstr, *typestr, *retp = NULL; static char *namestr = NULL; if(raa_current_db == NULL) return NULL; rep=initreponse(); sock_printf(raa_current_db,"getliststate&lrank=%d\n",lrank); reponse=read_sock(raa_current_db); if(reponse == NULL) return NULL; parse(reponse, rep); code = val(rep,"code"); if(code != NULL && *code == '0') { typestr = val(rep,"type"); if(type != NULL) { if(strcmp(typestr, "SQ") == 0) *type = 'S'; else if(strcmp(typestr, "KW") == 0) *type = 'K'; else *type = 'E'; } if(namestr != NULL) free(namestr); /* allocation precedante */ namestr = val(rep, "name"); countstr = val(rep, "count"); if(count != NULL) *count = atoi(countstr); locusstr = val(rep, "locus"); if(locus != NULL) *locus = (*locusstr == 'T'); free(countstr); free(locusstr); free(typestr); retp = namestr; } if(code != NULL) free(code); clear_reponse(rep); return retp; } char *raa_residuecount(raa_db_access *raa_current_db, int lrank) { Reponse *rep; char *reponse, *code; static char total[30]; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db,"residuecount&lrank=%d\n",lrank); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); code = val(rep,"code"); strcpy(total, "0"); if(code != NULL && *code == '0') { free(code); code = val(rep,"count"); if(code != NULL) { strcpy(total, code); free(code); } } clear_reponse(rep); return total; } int raa_getemptylist(raa_db_access *raa_current_db, char *name) { Reponse *rep; char *reponse, *code, *rankstr; int rank = 0; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db, "getemptylist&name=\"%s\"\n", protect_quotes(name)); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); code = val(rep,"code"); if(code != NULL && (*code == '0' || *code == '3') ) { rankstr = val(rep, "lrank"); rank = atoi(rankstr); free(rankstr); } if(code != NULL) free(code); clear_reponse(rep); return rank; } int raa_setlistname(raa_db_access *raa_current_db, int lrank, char *name) { Reponse *rep; char *reponse, *code; int retval; if(raa_current_db == NULL) return -1; rep=initreponse(); sock_printf(raa_current_db, "setlistname&lrank=%d&name=\"%s\"\n", lrank, name); reponse=read_sock(raa_current_db); if(reponse == NULL) return -1; parse(reponse, rep); code = val(rep,"code"); if(*code == '0') retval = 0; else if(*code == '3') retval = 1; else retval = -1; free(code); clear_reponse(rep); return retval; } int raa_getlistrank(raa_db_access *raa_current_db, char *name) { Reponse *rep; char *reponse, *rankstr; int rank; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db, "getlistrank&name=\"%s\"\n", name); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); rankstr = val(rep,"lrank"); if(rankstr == NULL) return 0; rank = atoi(rankstr); free(rankstr); clear_reponse(rep); return rank; } int raa_releaselist(raa_db_access *raa_current_db, int lrank) { Reponse *rep; char *reponse, *rankstr; int rank; if(raa_current_db == NULL) return 1; rep=initreponse(); sock_printf(raa_current_db, "releaselist&lrank=%d\n", lrank); reponse=read_sock(raa_current_db); if(reponse == NULL) return 1; parse(reponse, rep); rankstr = val(rep,"code"); if(rankstr == NULL) return 1; rank = atoi(rankstr); free(rankstr); clear_reponse(rep); return rank; } int raa_countfilles(raa_db_access *raa_current_db, int lrank) { Reponse *rep; char *reponse, *rankstr; int rank; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db, "countsubseqs&lrank=%d\n", lrank); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); rankstr = val(rep,"count"); if(rankstr == NULL) return 0; rank = atoi(rankstr); free(rankstr); clear_reponse(rep); return rank; } int raa_alllistranks(raa_db_access *raa_current_db, int **pranks) { Reponse *rep; char *reponse, *rankstr, *p; int count, *ranks, i; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_fputs(raa_current_db, "alllistranks\n"); reponse=read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); rankstr = val(rep,"count"); p = strchr(reponse, '&'); if(rankstr == NULL || p == NULL) return 0; count = atoi(rankstr); ranks = (int *)malloc(count * sizeof(int)); if(ranks == NULL ) return 0; p++; for(i=0; i< count; i++) { sscanf(p, "%d", &ranks[i]); p = strchr(p, ','); if(p == NULL) break; p++; } *pranks = ranks; free(rankstr); clear_reponse(rep); return count; } int raa_fcode(raa_db_access *raa_current_db, raa_file cas, char *name) { char *reponse, *p, type[5]; int value; if(raa_current_db == NULL) return 0; if(cas == raa_aut) strcpy(type, "AUT"); else if(cas == raa_bib) strcpy(type, "BIB"); else if(cas == raa_acc) strcpy(type, "ACC"); else if(cas == raa_smj) strcpy(type, "SMJ"); else if(cas == raa_sub) strcpy(type, "SUB"); else return 0; sock_printf(raa_current_db,"fcode&name=\"%s\"&type=%s\n", protect_quotes(name), type ); reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; p = strchr(reponse, '='); if(p == NULL) return 0; p++; sscanf(p, "%u", &value); return value; } int raa_read_first_rec(raa_db_access *raa_current_db, raa_file cas) { int value; char type[5], *p, *reponse; if(raa_current_db == NULL) return 1; if(raa_current_db->first_recs[cas] != 0) return raa_current_db->first_recs[cas]; if(cas == raa_aut) strcpy(type, "AUT"); else if(cas == raa_bib) strcpy(type, "BIB"); else if(cas == raa_acc) strcpy(type, "ACC"); else if(cas == raa_smj) strcpy(type, "SMJ"); else if(cas == raa_sub) strcpy(type, "SUB"); else if(cas == raa_loc) strcpy(type, "LOC"); else if(cas == raa_key) strcpy(type, "KEY"); else if(cas == raa_spec) strcpy(type, "SPEC"); else if(cas == raa_shrt) strcpy(type, "SHRT"); else if(cas == raa_lng) strcpy(type, "LNG"); else if(cas == raa_ext) strcpy(type, "EXT"); else if(cas == raa_txt) strcpy(type, "TXT"); else return 0; sock_printf(raa_current_db,"readfirstrec&type=%s\n", type ); reponse = read_sock(raa_current_db); if(reponse == NULL) return 1; p = strstr(reponse, "count="); if(p == NULL) return 0; sscanf(p + 6, "%u", &value); raa_current_db->first_recs[cas] = value; return value; } char *raa_readsub_pannots(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus, int *pframe, int *pgencode, raa_long *paddr, int *pdiv) /* do both seq_to_annots and readsub and buffer result for one seq */ { Reponse *rep; char *p, *reponse; int code, l; if(raa_current_db == NULL) return NULL; if(num < 2 || num > raa_current_db->nseq) return NULL; if(num != raa_current_db->readsub_data.previous) { sock_printf(raa_current_db,"seq_to_annots&number=%d\nreadsub&num=%u\n", num, num); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; /* process reply to seq_to_annots */ rep=initreponse(); parse(reponse, rep); p = val(rep,"code"); code = atoi(p); free(p); if(code == 0) { p = val(rep,"offset"); raa_current_db->readsub_data.addr = scan_raa_long(p); free(p); p = val(rep,"div"); raa_current_db->readsub_data.div = atoi(p); free(p); } clear_reponse(rep); /* process reply to readsub */ reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; rep=initreponse(); parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return NULL; code = atoi(p); free(p); if(code != 0) { clear_reponse(rep); return NULL; } p = val(rep, "name"); l = strlen(p) + 1; if(l > raa_current_db->readsub_data.lname) { raa_current_db->readsub_data.lname = l; raa_current_db->readsub_data.name = (char *)realloc(raa_current_db->readsub_data.name, raa_current_db->readsub_data.lname); } strcpy(raa_current_db->readsub_data.name, p); free(p); p = val(rep, "length"); raa_current_db->readsub_data.length = atoi(p); free(p); p = val(rep, "type"); raa_current_db->readsub_data.type = atoi_u(p); free(p); p = val(rep, "is_sub"); raa_current_db->readsub_data.locus = atoi_u(p); free(p); p = val(rep, "toext"); raa_current_db->readsub_data.toext = atoi_u(p); if(raa_current_db->readsub_data.locus > 0) raa_current_db->readsub_data.toext = - raa_current_db->readsub_data.toext; free(p); p = val(rep, "plkey"); raa_current_db->readsub_data.lkey = atoi_u(p); free(p); p = val(rep, "frame"); raa_current_db->readsub_data.frame = atoi_u(p); free(p); p = val(rep, "genet"); raa_current_db->readsub_data.gencode = atoi_u(p); free(p); raa_current_db->readsub_data.previous = num; clear_reponse(rep); } if(plength != NULL) *plength = raa_current_db->readsub_data.length; if(ptype != NULL) *ptype = raa_current_db->readsub_data.type; if(plocus != NULL) *plocus = raa_current_db->readsub_data.locus; if(pext != NULL) *pext = raa_current_db->readsub_data.toext; if(plkey != NULL) *plkey = raa_current_db->readsub_data.lkey; if(pframe != NULL) *pframe = raa_current_db->readsub_data.frame; if(pgencode != NULL) *pgencode = raa_current_db->readsub_data.gencode; if(paddr != NULL) *paddr = raa_current_db->readsub_data.addr; if(pdiv != NULL) *pdiv = raa_current_db->readsub_data.div; return raa_current_db->readsub_data.name; } int raa_seq_to_annots(raa_db_access *raa_current_db, int numseq, raa_long *faddr, int *div) { char *p; p = raa_readsub_pannots(raa_current_db, numseq,NULL,NULL,NULL,NULL,NULL,NULL,NULL,faddr,div); return p == NULL; } char *raa_readsub(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus, int *pframe, int *pgencode) { return raa_readsub_pannots(raa_current_db, num,plength,ptype,pext,plkey,plocus,pframe,pgencode,NULL,NULL); } char *raa_readloc(raa_db_access *raa_current_db, int num, int *sub, int *pnuc, int *spec, int *host, int *plref, int *molec, int *placc, int *org) { Reponse *rep; char *p, *reponse; int code; static char date[50]; if(raa_current_db == NULL) return NULL; rep=initreponse(); sock_printf(raa_current_db,"readloc&num=%u\n", num); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return NULL; code = atoi(p); free(p); if(code == 0) { if(sub != NULL) { p = val(rep, "sub"); *sub = atoi_u(p); free(p); } if(pnuc != NULL) { p = val(rep, "pnuc"); *pnuc = atoi_u(p); free(p); } if(spec != NULL) { p = val(rep, "spec"); *spec = atoi_u(p); free(p); } if(host != NULL) { p = val(rep, "host"); *host = atoi_u(p); free(p); } if(plref != NULL) { p = val(rep, "plref"); *plref = atoi_u(p); free(p); } if(molec != NULL) { p = val(rep, "molec"); *molec = atoi_u(p); free(p); } if(placc != NULL) { p = val(rep, "placc"); *placc = atoi_u(p); free(p); } if(org != NULL) { p = val(rep, "org"); *org = atoi_u(p); free(p); } p = val(rep, "date"); strcpy(date, p); free(p); p = date; } else p = NULL; clear_reponse(rep); return p; } char *raa_readspec(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *pdesc, int *psyno, int *plhost) { Reponse *rep; char *p, *reponse; int code; if(raa_current_db == NULL) return NULL; if(num == raa_current_db->readspec_data.previous && raa_current_db->readspec_data.previous != 0) { if(plibel != NULL) { if(*(raa_current_db->readspec_data.libel) != 0) *plibel = raa_current_db->readspec_data.libel; else *plibel = NULL; } if(plsub != NULL) *plsub = raa_current_db->readspec_data.lsub; if(pdesc != NULL) *pdesc = raa_current_db->readspec_data.desc; if(psyno != NULL) *psyno = raa_current_db->readspec_data.syno; if(plhost != NULL) *plhost = raa_current_db->readspec_data.host; return raa_current_db->readspec_data.name; } rep=initreponse(); sock_printf(raa_current_db, "readspec&num=%u\n", num); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return NULL; code = atoi(p); free(p); if(code != 0) { clear_reponse(rep); return NULL; } raa_current_db->readspec_data.previous = num; p = val(rep, "plsub"); raa_current_db->readspec_data.lsub = atoi_u(p); free(p); p = val(rep, "desc"); raa_current_db->readspec_data.desc = atoi_u(p); free(p); p = val(rep, "syno"); raa_current_db->readspec_data.syno = atoi_u(p); free(p); p = val(rep, "host"); raa_current_db->readspec_data.host = atoi_u(p); free(p); p = val(rep, "libel"); if(p != NULL) { strcpy(raa_current_db->readspec_data.libel, p); free(p); } else *(raa_current_db->readspec_data.libel) = 0; p = val(rep, "name"); strcpy(raa_current_db->readspec_data.name, p ); free(p); clear_reponse(rep); return raa_readspec(raa_current_db, num, plibel, plsub, pdesc, psyno, plhost); } char *raa_readkey(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *pdesc, int *psyno) { Reponse *rep; char *p, *reponse; int code; if(raa_current_db == NULL) return NULL; if(num == raa_current_db->readkey_data.previous && raa_current_db->readkey_data.previous != 0) { if(plibel != NULL) { if(*(raa_current_db->readkey_data.libel) != 0) *plibel = raa_current_db->readkey_data.libel; else *plibel = NULL; } if(plsub != NULL) *plsub = raa_current_db->readkey_data.lsub; if(pdesc != NULL) *pdesc = raa_current_db->readkey_data.desc; if(psyno != NULL) *psyno = raa_current_db->readkey_data.syno; return raa_current_db->readkey_data.name; } rep=initreponse(); sock_printf(raa_current_db, "readkey&num=%u\n", num); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return NULL; code = atoi(p); free(p); if(code != 0) { clear_reponse(rep); return NULL; } raa_current_db->readkey_data.previous = num; p = val(rep, "plsub"); raa_current_db->readkey_data.lsub = atoi_u(p); free(p); p = val(rep, "desc"); raa_current_db->readkey_data.desc = atoi_u(p); free(p); p = val(rep, "syno"); raa_current_db->readkey_data.syno = atoi_u(p); free(p); p = val(rep, "libel"); if(p != NULL) { strcpy(raa_current_db->readkey_data.libel, p); free(p); } else *(raa_current_db->readkey_data.libel) = 0; p = val(rep, "name"); strcpy(raa_current_db->readkey_data.name, p); free(p); clear_reponse(rep); return raa_readkey(raa_current_db, num, plibel, plsub, pdesc, psyno); } static int load_smj(raa_db_access *raa_current_db, char ***names, unsigned **plongs, char ***libels) { Reponse *rep; char *reponse, *p; int nl, i, code, totsmj, recnum; if(raa_current_db == NULL) return 0; totsmj = raa_read_first_rec(raa_current_db, raa_smj); rep=initreponse(); sock_printf(raa_current_db,"readsmj&num=2&nl=%d\n", totsmj - 1); /* ==>readsmj&num=..&nl=.. code=0&nl=.. recnum=..&name=".."&plong=..{&libel=".."} nl times */ reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return 0; code = atoi(p); free(p); if(code != 0) return 0; p = val(rep,"nl"); if(p == NULL) return 0; nl = atoi(p); free(p); clear_reponse(rep); if(nl == 0) return 0; *names = (char **)calloc(totsmj + 1 , sizeof(char *)); *plongs = (unsigned *)calloc(totsmj + 1 , sizeof(unsigned)); *libels = (char **)calloc(totsmj + 1 , sizeof(char *)); for(i = 0; i < nl; i++) { reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; rep=initreponse(); parse(reponse, rep); p = val(rep, "recnum"); recnum = atoi(p); free(p); p = val(rep, "plong"); (*plongs)[recnum] = atoi_u(p); free(p); p = val(rep, "name"); (*names)[recnum] = p; p = val(rep, "libel"); (*libels)[recnum] = p; clear_reponse(rep); } return totsmj; } char *raa_readsmj(raa_db_access *raa_current_db, int num, char **plibel, int *plong) { if(raa_current_db == NULL) return NULL; if(raa_current_db->readsmj_data.lastrec == 0) { raa_current_db->readsmj_data.lastrec = load_smj(raa_current_db, &raa_current_db->readsmj_data.names, &raa_current_db->readsmj_data.plongs, &raa_current_db->readsmj_data.libels); } if(num <= 1 || num > raa_current_db->readsmj_data.lastrec) return NULL; if(plong != NULL) *plong = raa_current_db->readsmj_data.plongs[num]; if(plibel != NULL) *plibel = raa_current_db->readsmj_data.libels[num]; return raa_current_db->readsmj_data.names[num]; } char *raa_readacc(raa_db_access *raa_current_db, int num, int *plsub) { Reponse *rep; char *p, *reponse; int code; static char name[100]; if(raa_current_db == NULL) return NULL; rep=initreponse(); sock_printf(raa_current_db,"readacc&num=%u\n", num); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return NULL; code = atoi(p); free(p); if(code == 0) { if(plsub != NULL) { p = val(rep, "plsub"); *plsub = atoi_u(p); free(p); } p = val(rep, "name"); strcpy(name, p); free(p); p = name; } else p = NULL; clear_reponse(rep); return p; } int raa_readext(raa_db_access *raa_current_db, int num, int *mere, int *deb, int *fin) { Reponse *rep; char *p, *reponse; int code, next; if(raa_current_db == NULL) return 0; rep=initreponse(); sock_printf(raa_current_db,"readext&num=%u\n", num); reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; parse(reponse, rep); p = val(rep,"code"); if(p == NULL) return 0; code = atoi(p); free(p); if(code == 0) { if(mere != NULL) { p = val(rep, "mere"); *mere = atoi_u(p); free(p); } if(deb != NULL) { p = val(rep, "debut"); *deb = atoi_u(p); free(p); } if(fin != NULL) { p = val(rep, "fin"); *fin = atoi_u(p); free(p); } p = val(rep, "next"); next = atoi_u(p); free(p); } else next = 0; clear_reponse(rep); return next; } int raa_readlng(raa_db_access *raa_current_db, int num) /* fills the rlng_buffer structure */ { char *p, *reponse; int count, i; if(raa_current_db == NULL) return 0; memset(raa_current_db->rlng_buffer, 0, (raa_current_db->SUBINLNG+1)*sizeof(int)); sock_printf(raa_current_db,"readlng&num=%u\n", num); /* retour code=0&n=xx&x1,x2,...{&next=xx} */ reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; if(strncmp(reponse, "code=0&n=", 9) != 0 || (count = atoi(reponse+9)) == 0) { return 0; } p = strchr(reponse+9, '&'); for(i=0; i < count && i < raa_current_db->SUBINLNG; i++) { raa_current_db->rlng_buffer->sub[i] = atoi_u(p+1); p = strchr(p+1, ','); if(p == NULL) break; } p = strstr(reponse, "next="); if(p!= NULL) raa_current_db->rlng_buffer->next = atoi_u(p+5); else raa_current_db->rlng_buffer->next=0; return raa_current_db->rlng_buffer->next; } static void load_shrt_buffer(raa_db_access *raa_current_db, unsigned point) { char *reponse, *p, *q; int n, i; unsigned val, next, previous; if(raa_current_db == NULL) return; sock_printf(raa_current_db, "readshrt&num=%u&max=%d\n", point, MAX_RDSHRT); /* reponse is: code=0&n=xx&val,next,.... n times ...\n */ reponse = read_sock(raa_current_db); if(reponse == NULL || strncmp(reponse, "code=0&n=", 9) != 0) { return; } n = atoi(reponse + 9); if (n == 0) return; p = strchr(reponse+9, '&'); if(p == NULL) return; q = p + 1; previous = point; for(i = 0; i < n; i++) { p = strtok(q, ","); q = NULL; sscanf(p, "%u", &val); p = strtok(NULL, ","); sscanf(p, "%u", &next); raa_current_db->readshrt_data.shrt_begin = (raa_current_db->readshrt_data.shrt_begin + 1) % S_BUF_SHRT; raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][0] = previous; raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][1] = val; raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][2] = next; previous = next; } if(raa_current_db->readshrt_data.shrt_begin > raa_current_db->readshrt_data.shrt_max - 1) { raa_current_db->readshrt_data.shrt_max = raa_current_db->readshrt_data.shrt_begin + 1; } return; } unsigned raa_readshrt(raa_db_access *raa_current_db, unsigned point, int *pval) { int i; if(raa_current_db == NULL) return 0; if(raa_current_db->readshrt_data.total == 0) raa_current_db->readshrt_data.total = (unsigned)raa_read_first_rec(raa_current_db, raa_shrt); if(point < 2 || point > raa_current_db->readshrt_data.total) return 0; for(i = 0; i < raa_current_db->readshrt_data.shrt_max; i++) { if(raa_current_db->readshrt_data.shrt_buffer[i][0] == point) { if(pval != NULL) *pval = raa_current_db->readshrt_data.shrt_buffer[i][1]; return raa_current_db->readshrt_data.shrt_buffer[i][2]; } } load_shrt_buffer(raa_current_db, point); return raa_readshrt(raa_current_db, point, pval); } char *raa_ghelp(raa_db_access *raa_current_db, char *fname, char *topic) /* returns all help topic in one string in private memory */ { char *reponse, *p, *fintext, *tmp; int nl, l, i; static char *text = NULL; static int ltext = 0; if(raa_current_db == NULL) return NULL; sock_printf(raa_current_db,"ghelp&file=%s&item=%s\n", fname, topic); reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; nl = 0; if(strncmp(reponse, "nl=", 3) == 0) nl = atoi(reponse+3); p = strchr(reponse, '&'); if(nl <= 0 || p == NULL) return NULL; fintext = text; p++; for(i = 0; i < nl; i++) { l = strlen(p) + 1; /* +1 pour ajouter \n */ if( (fintext - text) + l > ltext) { ltext += 1000; tmp = (char *)realloc(text, ltext + 1); if(tmp == NULL) { if(text != NULL) free(text); text = NULL; ltext = 0; return NULL; } fintext = tmp + (fintext - text); text = tmp; } memcpy(fintext, p, l -1); fintext += l; *(fintext - 1) = '\n'; if(i + 1 < nl) reponse = read_sock(raa_current_db); if(reponse == NULL) return NULL; p = reponse; } *fintext = 0; return text; } struct raa_matchkey { int *ranks; char **names; int count; int current; int no_more; }; static void raa_free_matchkeys(raa_db_access *raa_current_db) { int i; struct raa_matchkey *data = (struct raa_matchkey *)(raa_current_db->matchkey_data); if(data == NULL) return; if(data->count > 0) { for(i = 0; i < data->count; i++) free(data->names[i]); free(data->names); free(data->ranks); } free(data); raa_current_db->matchkey_data = NULL; } static void next_block_matchkeys(raa_db_access *raa_current_db, int num, char *pattern) { const int blocksize = 2001; char *reponse, *p; int count, i; struct raa_matchkey *data; if(raa_current_db == NULL) return; raa_free_matchkeys(raa_current_db); sock_printf(raa_current_db, "nextmatchkey&num=%d", num ); if(num == 2) sock_printf(raa_current_db, "&pattern=\"%s\"", protect_quotes(pattern) ); sock_printf(raa_current_db, "&count=%d\n", blocksize); reponse = read_sock(raa_current_db); if(reponse == NULL || strncmp(reponse, "code=0&count=", 13) != 0) return; sscanf(reponse + 13, "%d", &count); data = (struct raa_matchkey *)calloc(1, sizeof(struct raa_matchkey)); raa_current_db->matchkey_data = data; if(data == NULL || count == 0) return; data->ranks = (int *)malloc(count * sizeof(int)); data->names = (char **)malloc(count * sizeof(char *)); data->current = 0; data->no_more = (count < blocksize); data->count = count; if(data->ranks == NULL || data->names == NULL) data->count = 0; for(i = 0; i < data->count; i++) { reponse = read_sock(raa_current_db); sscanf(reponse + 4, "%d", &(data->ranks[i]) ); p = strchr(reponse, '&'); p = strchr(p, '=') + 1; data->names[i] = strdup(unprotect_quotes(p)); if(data->names[i] == NULL) { data->count = i; break; } } for(i = data->count; i < count; i++) { read_sock(raa_current_db); } return; } int raa_nextmatchkey(raa_db_access *raa_current_db, int num, char *pattern, char **matching) /* *matching returned in static memory */ { struct raa_matchkey *data; int no_more, count; if(raa_current_db == NULL) return 0; if(num == 2) { next_block_matchkeys(raa_current_db, 2, pattern); } data = (struct raa_matchkey *)(raa_current_db->matchkey_data); if(data == NULL) return 0; if(data->current < data->count) { if(matching != NULL) *matching = data->names[data->current]; return data->ranks[(data->current)++]; } count = data->count; if(count > 0) { no_more = data->no_more; } raa_free_matchkeys(raa_current_db); if(count == 0 || no_more) return 0; next_block_matchkeys(raa_current_db, num, NULL); return raa_nextmatchkey(raa_current_db, num, NULL, matching); } int atoi_u(const char *p) { unsigned value; sscanf(p, "%u", &value); return (int)value; } char *protect_quotes(char *name) /* remplacer tous les " par \" name : une chaine inchangee retourne un pointeur vers la chaine rendue privee pour cette fonction */ { char *p, *q; int l, count; static char *bis = NULL; static int lbis = 0; count = 0; p = name - 1; while( (p=strchr(p+1, '"')) != NULL) count++; if(count == 0) return name; l = strlen(name); if(l + count > lbis) { lbis = l + count; bis = (char *)realloc(bis, lbis + 1); } p = name; q = bis; while(TRUE) { if(*p == '"') *(q++) = '\\'; *q = *p; if(*p == 0) break; q++; p++; } return bis; } static char *prepare_remote_file(raa_db_access *raa_current_db, char *oldrequete, char *debut, char *type, int *plrank, char **badfname) { char *p, *q, *reponse, *fin; static char line[200]; int nl, l, code; FILE *in; Reponse *rep; *plrank = 0; *badfname = line; p = strchr(debut, '=') + 1; while(isspace(*p)) p++; if(*p == '"') { /* if filename is bracketed by " */ *(p++) = ' '; fin = strchr(p, '"'); if(fin == NULL) return NULL; *fin = ' '; } else { fin = p; do ++fin; while( *fin != 0 && *fin != ')' && !isspace(*fin) ); } l = fin - p; if(l >= sizeof(line)) l = sizeof(line) - 1; memcpy(line, p, l); line[l] = 0; if(fin - p >= sizeof(line)) return NULL; in = fopen(line, "r"); if(in == NULL) return NULL; nl = 0; while( fgets(line, sizeof(line), in) != NULL) nl++; rewind(in); sock_printf(raa_current_db, "crelistfromclientdata&type=%s&nl=%d\n", type, nl); if(nl > 0) { while( fgets(line, sizeof(line), in) != NULL) { l = strlen(line); if(line[l - 1] != '\n') strcpy(line + l, "\n"); sock_fputs(raa_current_db, line); } } fclose(in); reponse = read_sock(raa_current_db); if(reponse == NULL) { strcpy(line, "connection with server is down"); return NULL; } rep = initreponse(); parse(reponse, rep); q = val(rep,"code"); code = atoi(q); free(q); if(code != 0) { if(code == 3) strcpy(line, "too many lists, delete a few"); else sprintf(line, "code=%d", code); return NULL; } q = val(rep,"name"); l = strlen(q); reponse = (char *)malloc( (debut - oldrequete) + 1 + l + 1 + strlen(fin) + 1); p = reponse; memcpy(p, oldrequete, debut - oldrequete); p += debut - oldrequete; *(p++) = ' '; memcpy(p, q, l); p += l; *(p++) = ' '; free(q); strcpy(p, fin); free(oldrequete); q = val(rep,"lrank"); if(q != NULL) { *plrank = atoi(q); free(q); } clear_reponse(rep); return reponse; } static int *add_tmp_blist(int lrank, int *list) { static int total = 0, current, *prelist = NULL; /* need not be specific to each opened db */ if(list == NULL) { /* initialisation */ if(prelist != NULL) free(prelist); total = 10; current = 0; list = (int *)malloc(total*sizeof(int)); prelist = list; return list; } if(current >= total) { int *tmp; tmp = (int *)realloc(list, (total + 10)*sizeof(int)); if(tmp == NULL) return list; total += 10; list = tmp; } list[current++] = lrank; prelist = list; return list; } char *maj_strstr(char *in, char *target) { static char *buffer = NULL; static int lbuf = 0; int l; char *p; l = strlen(in); if(l > lbuf) { lbuf = l; buffer = (char *)realloc(buffer, lbuf + 1); } strcpy(buffer, in); majuscules(buffer); p = strstr(buffer, target); if(p != NULL) p = in + (p - buffer); return p; } static char *raa_requete_remote_file(raa_db_access *raa_current_db, char *oldrequete, int **plist, char **pbadfname) /* rend NULL ou une requete dont les F= FA= FS= FK= ont ete changes en list-name et qui a ete creee par malloc */ { char *oldori, *p; int lrank, *list; oldori = strdup(oldrequete); if(maj_strstr(oldori, "F=") == NULL && maj_strstr(oldori, "FA=") == NULL && maj_strstr(oldori, "FK=") == NULL && maj_strstr(oldori, "FS=") == NULL) { *plist = NULL; return oldori; } list = add_tmp_blist(0, NULL); /* initialisation a vide */ while(oldori != NULL && (p = maj_strstr(oldori, "F=")) != NULL) { oldori = prepare_remote_file(raa_current_db, oldori, p, "SQ", &lrank, pbadfname); if(lrank != 0) list = add_tmp_blist(lrank, list); } while(oldori != NULL && (p = maj_strstr(oldori, "FA=")) != NULL) { oldori = prepare_remote_file(raa_current_db, oldori, p, "AC", &lrank, pbadfname); if(lrank != 0) list = add_tmp_blist(lrank, list); } while(oldori != NULL && (p = maj_strstr(oldori, "FS=")) != NULL) { oldori = prepare_remote_file(raa_current_db, oldori, p, "SP", &lrank, pbadfname); if(lrank != 0) list = add_tmp_blist(lrank, list); } while(oldori != NULL && (p = maj_strstr(oldori, "FK=")) != NULL) { oldori = prepare_remote_file(raa_current_db, oldori, p, "KW", &lrank, pbadfname); if(lrank != 0) list = add_tmp_blist(lrank, list); } list = add_tmp_blist(0, list); /* marquage fin de liste par zero */ if(oldori == NULL && list != NULL) { while(*list != 0) raa_releaselist(raa_current_db, *(list++) ); list = NULL; } *plist = list; return oldori; } int raa_savelist(raa_db_access *raa_current_db, int lrank, FILE *out, int use_acc, char *prefix) { char *reponse; int err; if(raa_current_db == NULL) return 1; sock_printf(raa_current_db, "savelist&lrank=%d&type=%c\n", lrank, (use_acc ? 'A' : 'N') ); reponse = read_sock(raa_current_db); if(reponse == NULL) return 1; err = strcmp(reponse, "code=0"); if(err != 0) { return 1; } while(TRUE) { reponse = read_sock(raa_current_db); if(reponse == NULL) return 1; if(strcmp(reponse, "savelist END.") == 0) break; if(prefix != NULL) fputs(prefix, out); fprintf(out, "%s\n", reponse); } return 0; } int raa_modifylist(raa_db_access *raa_current_db, int lrank, char *type, char *operation, int *pnewlist, int (*check_interrupt)(void), int *p_processed ) { Reponse *rep; char *p, *reponse; int code; if(raa_current_db == NULL) return 3; sock_printf(raa_current_db, "modifylist&lrank=%d&type=%s&operation=\"%s\"\n", lrank, type, operation ); sock_flush(raa_current_db); /* tres important */ if(check_interrupt == NULL) { reponse = read_sock(raa_current_db); if(reponse == NULL) return 3; } else { while(TRUE) { reponse = read_sock_timeout(raa_current_db, 500 /* msec */); if(raa_current_db == NULL) return 3; if(reponse != NULL) break; if( check_interrupt() ) { sock_fputs(raa_current_db, "\033" /* esc */ ); sock_flush(raa_current_db); } } } rep = initreponse(); parse(reponse, rep); p = val(rep,"code"); code = atoi(p); free(p); if(code != 0) return code; p = val(rep,"lrank"); *pnewlist = atoi(p); free(p); p = val(rep,"processed"); if(p != NULL && p_processed != NULL) *p_processed = atoi(p); if(p != NULL) free(p); clear_reponse(rep); return 0; } int raa_knowndbs(raa_db_access *raa_current_db, char ***pnames, char ***pdescriptions) { int nl; char **names = NULL, **descriptions = NULL; char *reponse, *p, *q, *r; int l, i; if(raa_current_db == NULL) return 0; sock_printf(raa_current_db, "knowndbs\n" ); reponse = read_sock(raa_current_db); if(reponse == NULL || strncmp(reponse, "nl=", 3) != 0) { return 0; } nl = atoi(reponse + 3); if(nl == 0) return 0; names = (char **) malloc(nl * sizeof(char *)); descriptions = (char **) malloc(nl * sizeof(char *)); for(i = 0; i < nl; i++) { reponse = read_sock(raa_current_db); if(reponse == NULL) return 0; p = strchr(reponse, '|'); if(p != NULL) { *(p++) = 0; q = strchr(p, '|'); if(q != NULL) *(q++) = 0; } l = strlen(reponse); names[i] = (char *)malloc(l+1); strcpy(names[i], reponse); compact(names[i]); if(p != NULL && q != NULL) { while( (r=strchr(p, '\t')) != NULL) *r = ' '; majuscules(p); compact(p); l = strlen(q); descriptions[i] = (char *)malloc(l+20); descriptions[i][0] = 0; if(strcmp(p, "OFF") == 0) strcpy(descriptions[i], "(offline) "); strcat(descriptions[i], q); } else descriptions[i] = NULL; } *pnames = names; *pdescriptions = descriptions; return nl; } char *raa_short_descr(raa_db_access *raa_current_db, int seqnum, char *text, int maxlen, raa_long pinf, int div, char *name) /* to get a description of a sequence or of a subsequence seqnum the sequence number text the string to be loaded with description maxlen the max # of chars allowed in text (\0 is put but not counted in maxlen) return value a pointer to text */ { int l, deb; char *p; text[maxlen]=0; strcpy(text, name); l=strlen(text); if(strchr(name, '.') != NULL) { /* subsequence */ if( (p = raa_read_annots(raa_current_db, pinf, div)) == NULL) return text; p[20]=0; strcat(text,p+4); l=strlen(text); while(text[l-1]==' ') l--; text[l]=0; if( ( p = strchr(p + 21, '/') ) != NULL) { strncat(text, p, maxlen - l); l = strlen(text); if(l > 75) return text; } do { p = raa_next_annots(raa_current_db, NULL); if( strcmptrail(p,20,NULL,0) && strncmp(p,"FT ",10) ) return text; } while(p[21]!='/'); do { strncat(text,p+20,maxlen-l); l=strlen(text); if(l>75) return text; p = raa_next_annots(raa_current_db, NULL); } while ( !strcmptrail(p,20,NULL,0) || !strncmp(p,"FT ",10) ); } else { /* parent sequence */ if( (p = raa_read_annots(raa_current_db, pinf, div)) == NULL) return text; p = raa_next_annots(raa_current_db, NULL); if(raa_current_db->nbrf) { deb=17; } else { deb=13; if(raa_current_db->embl || raa_current_db->swissprot) { while (strncmp(p,"DE",2)) { p = raa_next_annots(raa_current_db, NULL); } deb=6; } } do { strncat(text,p+deb-2,maxlen-l); l=strlen(text); if(l>=77) return text; p = raa_next_annots(raa_current_db, NULL); } while( !strncmp(p," ",2) || !strncmp(p,"DE",2) ); } return text; } struct chain_void *raa_get_list_open_dbs(void) { return raa_list_open_dbs; } #define END_COORDINATE_TEST(line) strncmp(line, "extractseqs END.", 16) static int *next_1_coordinate_set(raa_db_access *raa_current_db) { char *p, *line, *q; int start, last, seqnum, elt, i, count; int *table = NULL; line = read_sock(raa_current_db); if(END_COORDINATE_TEST(line) == 0) return NULL; count = 0; p = line; while(TRUE) { p = strchr(p+1, '|'); if( p == NULL) break; count++; } table = (int *)malloc( (3 * count + 1) * sizeof(int)); if(table == NULL) { do line = read_sock(raa_current_db); while(END_COORDINATE_TEST(line) != 0) ; return NULL; } table[0] = count; elt = 1; for(i = 0; i < count; i++) { p = strchr(line, '|'); if(p == NULL) break; q = strchr(line, '='); if(q == NULL || q > p) break; sscanf(q+1, "%d", &seqnum); q = strchr(q+1, '='); if(q == NULL || q > p) break; sscanf(q+1, "%d", &start); q = strchr(q+1, '='); if(q == NULL || q > p) break; sscanf(q+1, "%d", &last); table[elt++] = seqnum; table[elt++] = start; table[elt++] = last; line = p + 1; } return table; } struct coord_series_struct { int count; int **table; int next; } ; void *raa_prep_coordinates(raa_db_access *raa_current_db, int lrank, int seqnum, char *operation, /* "simple","fragment","feature","region" */ char *feature_name, char *bounds, char *min_bounds) /* only one of lrank and seqnum is != 0 to work on a sequence list or on an individual sequence feature_name: used for operations feature and region, NULL otherwise bounds: used for operations fragment and region, NULL otherwise syntax by examples "45,155" "-100,100" "-10,e+100" "E-10,e+100" min_bounds: NULL for operations other than fragment and region can be NULL for fragment and region and means min_bounds same as bounds if not NULL, same syntax as bounds pcount: upon return, set to number of coordinate series return value: NULL if error, or pointer to opaque data */ { char message[200]; char *line; int *v, maxi, **table, rank; struct coord_series_struct *retval; sprintf(message, "extractseqs&%s=%d&format=coordinates&operation=%s", seqnum == 0 ? "lrank" : "seqnum", seqnum == 0 ? lrank : seqnum, operation); sock_fputs(raa_current_db, message); if(strcmp(operation, "feature") == 0 || strcmp(operation, "region") == 0) { sprintf(message, "&feature=%s", feature_name); sock_fputs(raa_current_db, message); } if(strcmp(operation, "fragment") == 0 || strcmp(operation, "region") == 0) { sprintf(message, "&bounds=%s", bounds); sock_fputs(raa_current_db, message); } if(min_bounds != NULL) { sprintf(message, "&minbounds=%s", min_bounds); sock_fputs(raa_current_db, message); } sock_fputs(raa_current_db, "\n"); sock_flush(raa_current_db); line = read_sock(raa_current_db); if(strcmp(line, "code=0") != 0) { return NULL; } maxi = 100; rank = 0; table = (int **)malloc(maxi*sizeof(int *)); if(table == NULL) { do line = read_sock(raa_current_db); while(END_COORDINATE_TEST(line) != 0) ; return NULL; } while( (v = next_1_coordinate_set(raa_current_db)) != NULL) { if(rank >= maxi) { int **vv; vv = (int **)realloc(table, 2*maxi*sizeof(int *)); if(vv == NULL) { do line = read_sock(raa_current_db); while(END_COORDINATE_TEST(line) != 0) ; break; } maxi = 2*maxi; table = vv; } table[rank++] = v; } table = realloc(table, rank*sizeof(int *)); retval = (struct coord_series_struct *)malloc(sizeof(struct coord_series_struct)); if(retval == NULL) return NULL; retval->count = rank; retval->table = table; retval->next = 0; return retval; } int *raa_1_coordinate_set(void *v) /* to be called repetitively as table = raa_1_coordinate_set(v); until returns NULL with the opaque pointer returned by the raa_prep_coordinates call returns int array table in private memory containing 1 + 3*table[0] elements count = table[0] ; j = 0; for(i=0; i < count; i++) { table[j+1] is the acnuc number of the sequence table[j+2] is the start position in this sequence table[j+3] is the end position in this sequence j += 3; } start position > end position <==> fragment is on the complementary strand of the acnuc seq returns NULL when all coordinate series have been processed */ { int *retval, i; struct coord_series_struct *s = (struct coord_series_struct *)v; if(s->next >= s->count) { for(i=0; i < s->count; i++) free(s->table[i]); free(s->table); free(s); return NULL; } retval = s->table[(s->next)++]; return retval; } char *raa_translate_cds(raa_db_access *raa_current_db, int seqnum) /* traduction d'un cds avec codon initiateur traite et * internes ==> X rendue dans memoire allouee ici qu'il ne faut pas modifier retour NULL si pb lecture de la seq */ { static char *buffer = NULL; static int lbuffer = 0; int debut_codon, longueur, pos, code, phase; char codon[4], *p; raa_readsub(raa_current_db, seqnum,&longueur,NULL,NULL,NULL,NULL,&phase,&code); debut_codon = phase + 1; longueur = (longueur - debut_codon + 1)/3; if(longueur > lbuffer) { if(buffer != NULL) free(buffer); buffer = (char *)malloc(longueur + 1); lbuffer = longueur; } if(buffer == NULL) {lbuffer = 0; return NULL; } buffer[0] = raa_translate_init_codon(raa_current_db, seqnum); debut_codon += 3; for(pos = 1; pos < longueur; pos++) { if( raa_gfrag(raa_current_db, seqnum, debut_codon, 3, codon) == 0) return NULL; buffer[pos] = codaa(codon,code); debut_codon += 3; } buffer[longueur] = 0; while( (p = strchr(buffer, '*') ) != NULL && p - buffer < longueur - 1 ) *p = 'X'; return buffer; } char raa_translate_init_codon(raa_db_access *raa_current_db, int numseq) { char codon[4]; int point, special_init = TRUE, val, gc, phase; static int num_5_partial = 0; if(num_5_partial == 0) num_5_partial = raa_iknum(raa_current_db, "5'-PARTIAL", raa_key); raa_readsub(raa_current_db, numseq, NULL, NULL,NULL, &point, NULL, &phase, &gc); if(phase != 0) special_init = FALSE; else { /* la seq est-elle 5'-PARTIAL ? */ while(point != 0) { point = raa_readshrt(raa_current_db, point, &val); if(val == num_5_partial) { special_init = FALSE; break; } } } raa_gfrag(raa_current_db, numseq, phase + 1, 3, codon); if(special_init) /* traduction speciale du codon initiateur */ return init_codon_to_aa(codon, gc); else return codaa(codon, gc); } static void ajout_synonyme(raa_node *secondaire, raa_node *principal) { raa_node *next; if(principal->syno == NULL) { principal->syno = secondaire; secondaire->syno = principal; } else { next = principal->syno; principal->syno = secondaire; secondaire->syno = next; } } static void redresse_branches(raa_node *pere) /* Recursively reverse the order of descendants because it has been reversed */ { struct raa_pair *point, *next1, *next2, *last; point = pere->list_desc; if (!point) return; next1 = point->next; if (next1) point->next = NULL; while (TRUE) { last = point; redresse_branches(point->value); if (!next1) break; next2 = next1->next; next1->next = point; point = next1; next1 = next2; } pere->list_desc = last; } static void ajout_branche(raa_node *pere, raa_node *fils) /* adds a pere->fils branch. The last added branch is the first child of pere. */ { struct raa_pair *point, *nouveau; nouveau = (struct raa_pair *)calloc(1,sizeof(struct raa_pair)); nouveau->value = fils; if( (point = pere->list_desc) == NULL) { pere->list_desc = nouveau; } else { nouveau->next = pere->list_desc; pere->list_desc = nouveau; } } static void raa_decode_desc_arbre(char *reponse, raa_node **tab_noeud) /* reponse contient rank&pere&count&"...name..."&"...libel..." synonyme est identifie par pere < 0 et -pere = son principal */ { int num, pere, count, l; char *p, *q, *name, *libel; num = atoi(reponse); p = strchr(reponse, '&'); pere = atoi(p + 1); p = strchr(p+1, '&'); count = atoi(p + 1); /* ne pas brancher un noeud deja branche ailleurs auparavant */ if(tab_noeud[num] != NULL ) return; tab_noeud[num] = (raa_node *)calloc(1, sizeof(raa_node)); tab_noeud[num]->rank = num; if(pere < 0) { /* un synonyme */ ajout_synonyme(tab_noeud[num], tab_noeud[-pere]); } else { tab_noeud[num]->count = count; tab_noeud[num]->parent = tab_noeud[pere]; if(num != 2) ajout_branche(tab_noeud[pere], tab_noeud[num]); } p = strchr(p+1, '&') + 1; q = p; do { q++; if(*q == 0) break; } while(*q != '"' || *(q-1) == '\\'); l = q-p+1; name = (char *)malloc(l+1); strncpy(name, p, l); name[l] = 0; unprotect_quotes(name); tab_noeud[num]->name = name; q++; if(*q == '&') { p = q+1; q = p; do { q++; if(*q == 0) break; } while(*q != '"' || *(q-1) == '\\'); l = q-p+1; libel = (char *)malloc(l+1); strncpy(libel, p, l); libel[l] = 0; unprotect_quotes(libel); tab_noeud[num]->libel = libel; p = (char *)malloc(l+1); strcpy(p, libel); majuscules(p); tab_noeud[num]->libel_upcase = p; if(strncmp(p, "ID:", 3) == 0 || (p = strstr(p, "|ID:")) != NULL) { p += 2; if(*p != ':') p++; sscanf(p + 1, "%d", &(tab_noeud[num]->tid) ); } } } static void raa_calc_taxo_count(raa_node *racine) { struct raa_pair *paire; int count = 0; paire = racine->list_desc; while(paire != NULL) { raa_calc_taxo_count(paire->value); count += paire->value->count; paire = paire->next; } racine->count += count; } int raa_loadtaxonomy(raa_db_access *raa_current_db, char *rootname, int (*progress_function)(int, void *), void *progress_arg, int (*need_interrupt_f)(void *), void *interrupt_arg) /* charge la taxo complete dans raa_current_db->sp_tree et rend 0 ssi OK */ { int totspec, i, maxtid; raa_node **tab_noeud; struct raa_pair *pair, *pair2; char *reponse; int count, pourcent, prev_pourcent = 0; void *opaque; int interrupted; if(raa_current_db == NULL) return 1; if(raa_current_db->sp_tree != NULL) return 0; interrupted = FALSE; sock_fputs(raa_current_db, "zlibloadtaxonomy\n"); sock_flush(raa_current_db); /* reply: code=0&total=xx rank&pere&count&"...name..."&"...libel..." loadtaxonomy END. */ opaque = prepare_sock_gz_r( raa_current_db->raa_sockfdr ); reponse = z_read_sock(opaque); if(reponse == NULL || strncmp(reponse, "code=0&total=", 13) != 0) { return 1; } totspec = atoi(reponse + 13); tab_noeud = (raa_node **)calloc(totspec + 1, sizeof(raa_node *)); count = 0; while(TRUE) { reponse = z_read_sock(opaque); if(strcmp(reponse, "loadtaxonomy END.") == 0) { if(interrupted && (tab_noeud != NULL) ) { for(i = 2; i <= totspec; i++) { if(tab_noeud[i] == NULL) continue; if(tab_noeud[i]->name != NULL) free(tab_noeud[i]->name); if(tab_noeud[i]->libel != NULL) free(tab_noeud[i]->libel); if(tab_noeud[i]->libel_upcase != NULL) free(tab_noeud[i]->libel_upcase); pair = tab_noeud[i]->list_desc; while(pair != NULL) { pair2 = pair->next; free(pair); pair = pair2; } free(tab_noeud[i]); } free(tab_noeud); tab_noeud = NULL; /* just to consume ESC that may have arrived after loadtaxonomy END. */ sock_fputs(raa_current_db, "null_command\n"); read_sock(raa_current_db); } break; } if(tab_noeud != NULL) raa_decode_desc_arbre(reponse, tab_noeud); pourcent = ((++count) * 100) / totspec; if(pourcent > prev_pourcent) { prev_pourcent = pourcent; if( progress_function != NULL && progress_function(pourcent, progress_arg) ) { if( need_interrupt_f != NULL && (! interrupted) && need_interrupt_f(interrupt_arg) ) { sock_fputs(raa_current_db, "\033" /* esc */); sock_flush(raa_current_db); interrupted = TRUE; } } } } close_sock_gz_r(opaque); if(tab_noeud != NULL) { redresse_branches(tab_noeud[2]); raa_calc_taxo_count(tab_noeud[2]); free(tab_noeud[2]->name); tab_noeud[2]->name = strdup(rootname); maxtid = 0; for(i = 2; i <= totspec; i++) if(tab_noeud[i] != NULL && tab_noeud[i]->tid > maxtid) maxtid = tab_noeud[i]->tid; raa_current_db->tid_to_rank = (int *)calloc(maxtid + 1, sizeof(int)); if(raa_current_db->tid_to_rank != NULL) { raa_current_db->max_tid = maxtid; for(i = 2; i <= totspec; i++) { if(tab_noeud[i] != NULL && tab_noeud[i]->tid != 0) raa_current_db->tid_to_rank[tab_noeud[i]->tid] = tab_noeud[i]->rank; } } raa_current_db->sp_tree = tab_noeud; } return (tab_noeud == NULL ? 1 : 0); } char *raa_get_taxon_info(raa_db_access *raa_current_db, char *name, int rank, int tid, int *p_rank, int *p_tid, int *p_parent, struct raa_pair **p_desc_list) /* from a taxon identified by its name or, if name is NULL, by its rank or, if rank is 0, by its taxon ID (tid) computes : - if p_rank != NULL, the taxon rank in *p_rank - if p_tid != NULL, the taxon ID in *p_tid - if p_parent != NULL, the taxon's parent rank in *p_parent (2 indicates that taxon is at top level) - if p_desc_list != NULL, the start of the linked chain of taxon's descending taxa in *p_desc_list returns the taxon name, or NULL if any error */ { int totspec; if(raa_current_db == NULL) return NULL; if(raa_current_db->sp_tree == NULL) raa_loadtaxonomy(raa_current_db, "root", NULL, NULL, NULL, NULL); if(raa_current_db->sp_tree == NULL) return NULL; totspec = raa_read_first_rec(raa_current_db, raa_spec); if(name != NULL) { name = strdup(name); if(name == NULL) return NULL; trim_key(name); majuscules(name); for(rank = 3; rank <= totspec; rank++) { if(raa_current_db->sp_tree[rank] != NULL && strcmp(name, raa_current_db->sp_tree[rank]->name) == 0) break; } free(name); } if(name == NULL && rank == 0 && tid >= 1 && tid <= raa_current_db->max_tid) rank = raa_current_db->tid_to_rank[tid]; if(rank > totspec || rank < 2 || raa_current_db->sp_tree[rank] == NULL) return NULL; if(rank != 2) { while(raa_current_db->sp_tree[rank]->parent == NULL) { rank = raa_current_db->sp_tree[rank]->syno->rank; } } if(p_rank != NULL) *p_rank = rank; if(p_tid != NULL) *p_tid = raa_current_db->sp_tree[rank]->tid; if(p_parent != NULL) *p_parent = ( raa_current_db->sp_tree[rank]->parent != NULL ? raa_current_db->sp_tree[rank]->parent->rank : 0); if(p_desc_list != NULL) *p_desc_list = raa_current_db->sp_tree[rank]->list_desc; return raa_current_db->sp_tree[rank]->name; } char *raa_getattributes_both(raa_db_access *raa_current_db, const char *id, int rank, int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq) /* for a sequence identified by name or acc. no. (id != NULL) or by rank returns rank, name, accession, length, frame, acnuc genetic code ID, one-line description, species, and full sequence. return value: NULL if not found or name (in private memory) pacc, pdesc, pspecies and pseq point to private memory upon return prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq can be NULL is no such information is needed */ { Reponse *rep; char *p, *reponse; int err; static char mnemo[WIDTH_MAX], species[WIDTH_MAX], access[WIDTH_MAX], descript[WIDTH_MAX]; if(raa_current_db == NULL) return NULL; if(id != NULL) sock_printf(raa_current_db, "getattributes&id=%s&seq=%c\n", id, pseq == NULL ? 'F' : 'T'); else sock_printf(raa_current_db, "getattributes&rank=%d&seq=%c\n", rank, pseq == NULL ? 'F' : 'T'); reponse = read_sock(raa_current_db); if(reponse == NULL) { return NULL; } rep=initreponse(); parse(reponse,rep); p=val(rep,"code"); err = atoi(p); free(p); if(err == 0) { if(prank != NULL) { p=val(rep,"rank"); *prank = atoi(p); free(p); } if(plength != NULL) { p=val(rep,"length"); *plength = atoi(p); free(p); } if(pframe != NULL) { p=val(rep,"fr"); if(p != NULL) { *pframe = atoi(p); free(p); } else *pframe = 0; } if(pgc != NULL) { p=val(rep,"gc"); if(p != NULL) { *pgc = atoi(p); free(p); } else *pgc = 0; } p = val(rep, "name"); strcpy(mnemo, p); free(p); if(pacc != NULL) { p = val(rep, "acc"); strcpy(access, p); free(p); *pacc = access; } if(pspecies != NULL) { p = val(rep, "spec"); strcpy(species, p); free(p); *pspecies = species; p = species; while(*(++p) != 0) *p = tolower(*p); } if(pdesc != NULL) { p = val(rep, "descr"); strcpy(descript, p); free(p); *pdesc = descript; } if(pseq != NULL) { *pseq = read_sock(raa_current_db); if(*pseq != NULL) { *pseq += 4; /* seq=xxxx */ } } err = 0; } clear_reponse(rep); return (err ? NULL : mnemo); } char *raa_getattributes(raa_db_access *raa_current_db, const char *id, int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq) { return raa_getattributes_both(raa_current_db, id, 0, prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq); } char *raa_seqrank_attributes(raa_db_access *raa_current_db, int rank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq) { return raa_getattributes_both(raa_current_db, NULL, rank, NULL, plength, pframe, pgc, pacc, pdesc, pspecies, pseq); } bpp-raa-2.2.0/src/Bpp/Raa/md5.c000664 001750 001750 00000021673 12372454333 017404 0ustar00jdutheiljdutheil000000 000000 /* * $Id: md5.c,v 1.1.1.1 2009-06-24 14:37:29 jdutheil Exp $ * * This code implements the MD5 message-digest algorithm. * The algorithm is due to Ron Rivest. This code was * written by Colin Plumb in 1993, no copyright is claimed. * This code is in the public domain; do with it what you wish. * * Equivalent code is available from RSA Data Security, Inc. * This code has been tested against that, and is equivalent, * except that you don't need to include two pages of legalese * with every copy. * * To compute the message digest of a chunk of bytes, declare an * MD5Context structure, pass it to MD5_Init, call MD5_Update as * needed on buffers full of bytes, and then call MD5_Final, which * will fill a supplied 16-byte array with the digest. * * Modified 12 June 2003 Jeremy Katz to handle * endianness better * */ // taken from DEBIAN package isomd5sum #include #include #ifdef WIN32 #define IS_BIG_ENDIAN 0 #else #include #if !(defined(_BIG_ENDIAN) || defined(BIG_ENDIAN)) #define IS_BIG_ENDIAN 0 #else #define IS_BIG_ENDIAN 1 #endif #endif typedef unsigned int uint32; struct MD5Context { uint32 buf[4]; uint32 bits[2]; unsigned char in[64]; int doByteReverse; }; static void MD5_Transform(uint32 *buf, uint32 const *in); static void byteReverse(unsigned char *buf, unsigned longs); #ifndef ASM_MD5 /* * Note: this code is harmless on little-endian machines. */ static void byteReverse(unsigned char *buf, unsigned longs) { uint32 t; do { t = (uint32) ((unsigned) buf[3] << 8 | buf[2]) << 16 | ((unsigned) buf[1] << 8 | buf[0]); *(uint32 *) buf = t; buf += 4; } while (--longs); } #endif /* * Start MD5 accumulation. Set bit count to 0 and buffer to mysterious * initialization constants. */ static void MD5_Init(struct MD5Context *ctx) { ctx->buf[0] = 0x67452301U; ctx->buf[1] = 0xefcdab89U; ctx->buf[2] = 0x98badcfeU; ctx->buf[3] = 0x10325476U; ctx->bits[0] = 0; ctx->bits[1] = 0; if (IS_BIG_ENDIAN) ctx->doByteReverse = 1; else ctx->doByteReverse = 0; } /* * Update context to reflect the concatenation of another buffer full * of bytes. */ static void MD5_Update(struct MD5Context *ctx, unsigned const char *buf, unsigned len) { uint32 t; /* Update bitcount */ t = ctx->bits[0]; if ((ctx->bits[0] = t + ((uint32) len << 3)) < t) ctx->bits[1]++; /* Carry from low to high */ ctx->bits[1] += len >> 29; t = (t >> 3) & 0x3f; /* Bytes already in shsInfo->data */ /* Handle any leading odd-sized chunks */ if (t) { unsigned char *p = (unsigned char *) ctx->in + t; t = 64 - t; if (len < t) { memcpy(p, buf, len); return; } memcpy(p, buf, t); if (ctx->doByteReverse) byteReverse(ctx->in, 16); MD5_Transform(ctx->buf, (uint32 *) ctx->in); buf += t; len -= t; } /* Process data in 64-byte chunks */ while (len >= 64) { memcpy(ctx->in, buf, 64); if (ctx->doByteReverse) byteReverse(ctx->in, 16); MD5_Transform(ctx->buf, (uint32 *) ctx->in); buf += 64; len -= 64; } /* Handle any remaining bytes of data. */ memcpy(ctx->in, buf, len); } /* * Final wrapup - pad to 64-byte boundary with the bit pattern * 1 0* (64-bit count of bits processed, MSB-first) */ static void MD5_Final(unsigned char digest[16], struct MD5Context *ctx) { unsigned count; unsigned char *p; /* Compute number of bytes mod 64 */ count = (ctx->bits[0] >> 3) & 0x3F; /* Set the first char of padding to 0x80. This is safe since there is always at least one byte free */ p = ctx->in + count; *p++ = 0x80; /* Bytes of padding needed to make 64 bytes */ count = 64 - 1 - count; /* Pad out to 56 mod 64 */ if (count < 8) { /* Two lots of padding: Pad the first block to 64 bytes */ memset(p, 0, count); if (ctx->doByteReverse) byteReverse(ctx->in, 16); MD5_Transform(ctx->buf, (uint32 *) ctx->in); /* Now fill the next block with 56 bytes */ memset(ctx->in, 0, 56); } else { /* Pad block to 56 bytes */ memset(p, 0, count - 8); } if (ctx->doByteReverse) byteReverse(ctx->in, 14); /* Append length in bits and transform */ ((uint32 *) ctx->in)[14] = ctx->bits[0]; ((uint32 *) ctx->in)[15] = ctx->bits[1]; MD5_Transform(ctx->buf, (uint32 *) ctx->in); if (ctx->doByteReverse) byteReverse((unsigned char *) ctx->buf, 4); memcpy(digest, ctx->buf, 16); memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ } #ifndef ASM_MD5 /* The four core functions - F1 is optimized somewhat */ /* #define F1(x, y, z) (x & y | ~x & z) */ #define F1(x, y, z) (z ^ (x & (y ^ z))) #define F2(x, y, z) F1(z, x, y) #define F3(x, y, z) (x ^ y ^ z) #define F4(x, y, z) (y ^ (x | ~z)) /* This is the central step in the MD5 algorithm. */ #define MD5STEP(f, w, x, y, z, data, s) \ ( w += f(x, y, z) + data, w = w<>(32-s), w += x ) /* * The core of the MD5 algorithm, this alters an existing MD5 hash to * reflect the addition of 16 longwords of new data. MD5_Update blocks * the data and converts bytes into longwords for this routine. */ static void MD5_Transform(uint32 buf[4], uint32 const in[16]) { register uint32 a, b, c, d; a = buf[0]; b = buf[1]; c = buf[2]; d = buf[3]; MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478U, 7); MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756U, 12); MD5STEP(F1, c, d, a, b, in[2] + 0x242070dbU, 17); MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceeeU, 22); MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0fafU, 7); MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62aU, 12); MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613U, 17); MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501U, 22); MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8U, 7); MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7afU, 12); MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1U, 17); MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7beU, 22); MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122U, 7); MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193U, 12); MD5STEP(F1, c, d, a, b, in[14] + 0xa679438eU, 17); MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821U, 22); MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562U, 5); MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340U, 9); MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51U, 14); MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aaU, 20); MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105dU, 5); MD5STEP(F2, d, a, b, c, in[10] + 0x02441453U, 9); MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681U, 14); MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8U, 20); MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6U, 5); MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6U, 9); MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87U, 14); MD5STEP(F2, b, c, d, a, in[8] + 0x455a14edU, 20); MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905U, 5); MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8U, 9); MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9U, 14); MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8aU, 20); MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942U, 4); MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681U, 11); MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122U, 16); MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380cU, 23); MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44U, 4); MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9U, 11); MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60U, 16); MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70U, 23); MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6U, 4); MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127faU, 11); MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085U, 16); MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05U, 23); MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039U, 4); MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5U, 11); MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8U, 16); MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665U, 23); MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244U, 6); MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97U, 10); MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7U, 15); MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039U, 21); MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3U, 6); MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92U, 10); MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47dU, 15); MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1U, 21); MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4fU, 6); MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0U, 10); MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314U, 15); MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1U, 21); MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82U, 6); MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235U, 10); MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bbU, 15); MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391U, 21); buf[0] += a; buf[1] += b; buf[2] += c; buf[3] += d; } #endif /* function for very simple interface */ void raa_MD5String (char *in_string, char out_digest[33]) /* in_string: string to be MD5-digested out_digest: resulting digest as 32 hexadecimal digits plus final NULL */ { struct MD5Context context; unsigned int len = strlen (in_string); char *p; int i; unsigned char digest[16]; MD5_Init (&context); MD5_Update (&context, (unsigned const char *)in_string, len); MD5_Final (digest, &context); p = out_digest; for (i = 0; i < 16; i++) { sprintf (p, "%02x", digest[i]); p += 2; } memset(&context, 0, sizeof(struct MD5Context)); } bpp-raa-2.2.0/INSTALL.txt000664 001750 001750 00000000700 12372454333 016373 0ustar00jdutheiljdutheil000000 000000 This software needs cmake >= 2.6 to build. After installing cmake, run it with the following command: cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] . If available, you can also use ccmake instead of cmake for a more user-friendly interface. Then compile and install the software with make install You may also consider installing and using the software checkinstall for easier system administration. bpp-raa-2.2.0/COPYING.txt000664 001750 001750 00000051134 12372454333 016404 0ustar00jdutheiljdutheil000000 000000 CeCILL FREE SOFTWARE LICENSE AGREEMENT Notice This Agreement is a Free Software license agreement that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting: * firstly, compliance with the principles governing the distribution of Free Software: access to source code, broad rights granted to users, * secondly, the election of a governing law, French law, with which it is conformant, both as regards the law of torts and intellectual property law, and the protection that it offers to both authors and holders of the economic rights over software. The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[logiciel] L[ibre]) license are: Commissariat ŕ l'Energie Atomique - CEA, a public scientific, technical and industrial establishment, having its principal place of business at 31-33 rue de la Fédération, 75752 Paris cedex 15, France. Centre National de la Recherche Scientifique - CNRS, a public scientific and technological establishment, having its principal place of business at 3 rue Michel-Ange 75794 Paris cedex 16, France. Institut National de Recherche en Informatique et en Automatique - INRIA, a public scientific and technological establishment, having its principal place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le Chesnay cedex, France. Preamble The purpose of this Free Software license agreement is to grant users the right to modify and redistribute the software governed by this license within the framework of an open source distribution model. The exercising of these rights is conditional upon certain obligations for users so as to preserve this status for all subsequent redistributions. In consideration of access to the source code and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its Free Software status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the Software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom. This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions. Article 1 - DEFINITIONS For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning: Agreement: means this license agreement, and its possible subsequent versions and annexes. Software: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. Initial Software: means the Software in its Source Code and possibly its Object Code form and, where applicable, its documentation, "as is" when it is first distributed under the terms and conditions of the Agreement. Modified Software: means the Software modified by at least one Contribution. Source Code: means all the Software's instructions and program lines to which access is required so as to modify the Software. Object Code: means the binary files originating from the compilation of the Source Code. Holder: means the holder(s) of the economic rights over the Initial Software. Licensee: means the Software user(s) having accepted the Agreement. Contributor: means a Licensee having made at least one Contribution. Licensor: means the Holder, or any other individual or legal entity, who distributes the Software under the Agreement. Contribution: means any or all modifications, corrections, translations, adaptations and/or new functions integrated into the Software by any or all Contributors, as well as any or all Internal Modules. Module: means a set of sources files including their documentation that enables supplementary functions or services in addition to those offered by the Software. External Module: means any or all Modules, not derived from the Software, so that this Module and the Software run in separate address spaces, with one calling the other when they are run. Internal Module: means any or all Module, connected to the Software so that they both execute in the same address space. GNU GPL: means the GNU General Public License version 2 or any subsequent version, as published by the Free Software Foundation Inc. Parties: mean both the Licensee and the Licensor. These expressions may be used both in singular and plural form. Article 2 - PURPOSE The purpose of the Agreement is the grant by the Licensor to the Licensee of a non-exclusive, transferable and worldwide license for the Software as set forth in Article 5 hereinafter for the whole term of the protection granted by the rights over said Software. Article 3 - ACCEPTANCE 3.1 The Licensee shall be deemed as having accepted the terms and conditions of this Agreement upon the occurrence of the first of the following events: * (i) loading the Software by any or all means, notably, by downloading from a remote server, or by loading from a physical medium; * (ii) the first time the Licensee exercises any of the rights granted hereunder. 3.2 One copy of the Agreement, containing a notice relating to the characteristics of the Software, to the limited warranty, and to the fact that its use is restricted to experienced users has been provided to the Licensee prior to its acceptance as set forth in Article 3.1 hereinabove, and the Licensee hereby acknowledges that it has read and understood it. Article 4 - EFFECTIVE DATE AND TERM 4.1 EFFECTIVE DATE The Agreement shall become effective on the date when it is accepted by the Licensee as set forth in Article 3.1. 4.2 TERM The Agreement shall remain in force for the entire legal term of protection of the economic rights over the Software. Article 5 - SCOPE OF RIGHTS GRANTED The Licensor hereby grants to the Licensee, who accepts, the following rights over the Software for any or all use, and for the term of the Agreement, on the basis of the terms and conditions set forth hereinafter. Besides, if the Licensor owns or comes to own one or more patents protecting all or part of the functions of the Software or of its components, the Licensor undertakes not to enforce the rights granted by these patents against successive Licensees using, exploiting or modifying the Software. If these patents are transferred, the Licensor undertakes to have the transferees subscribe to the obligations set forth in this paragraph. 5.1 RIGHT OF USE The Licensee is authorized to use the Software, without any limitation as to its fields of application, with it being hereinafter specified that this comprises: 1. permanent or temporary reproduction of all or part of the Software by any or all means and in any or all form. 2. loading, displaying, running, or storing the Software on any or all medium. 3. entitlement to observe, study or test its operation so as to determine the ideas and principles behind any or all constituent elements of said Software. This shall apply when the Licensee carries out any or all loading, displaying, running, transmission or storage operation as regards the Software, that it is entitled to carry out hereunder. 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS The right to make Contributions includes the right to translate, adapt, arrange, or make any or all modifications to the Software, and the right to reproduce the resulting Software. The Licensee is authorized to make any or all Contributions to the Software provided that it includes an explicit notice that it is the author of said Contribution and indicates the date of the creation thereof. 5.3 RIGHT OF DISTRIBUTION In particular, the right of distribution includes the right to publish, transmit and communicate the Software to the general public on any or all medium, and by any or all means, and the right to market, either in consideration of a fee, or free of charge, one or more copies of the Software by any means. The Licensee is further authorized to distribute copies of the modified or unmodified Software to third parties according to the terms and conditions set forth hereinafter. 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION The Licensee is authorized to distribute true copies of the Software in Source Code or Object Code form, provided that said distribution complies with all the provisions of the Agreement and is accompanied by: 1. a copy of the Agreement, 2. a notice relating to the limitation of both the Licensor's warranty and liability as set forth in Articles 8 and 9, and that, in the event that only the Object Code of the Software is redistributed, the Licensee allows future Licensees unhindered access to the full Source Code of the Software by indicating how to access it, it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data. 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE When the Licensee makes a Contribution to the Software, the terms and conditions for the distribution of the Modified Software become subject to all the provisions of this Agreement. The Licensee is authorized to distribute the Modified Software, in Source Code or Object Code form, provided that said distribution complies with all the provisions of the Agreement and is accompanied by: 1. a copy of the Agreement, 2. a notice relating to the limitation of both the Licensor's warranty and liability as set forth in Articles 8 and 9, and that, in the event that only the Object Code of the Modified Software is redistributed, the Licensee allows future Licensees unhindered access to the full Source Code of the Modified Software by indicating how to access it, it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data. 5.3.3 DISTRIBUTION OF EXTERNAL MODULES When the Licensee has developed an External Module, the terms and conditions of this Agreement do not apply to said External Module, that may be distributed under a separate license agreement. 5.3.4 COMPATIBILITY WITH THE GNU GPL The Licensee can include a code that is subject to the provisions of one of the versions of the GNU GPL in the Modified or unmodified Software, and distribute that entire code under the terms of the same version of the GNU GPL. The Licensee can include the Modified or unmodified Software in a code that is subject to the provisions of one of the versions of the GNU GPL, and distribute that entire code under the terms of the same version of the GNU GPL. Article 6 - INTELLECTUAL PROPERTY 6.1 OVER THE INITIAL SOFTWARE The Holder owns the economic rights over the Initial Software. Any or all use of the Initial Software is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to modify the terms and conditions for the distribution of said Initial Software. The Holder undertakes that the Initial Software will remain ruled at least by the current license, for the duration set forth in article 4.2. 6.2 OVER THE CONTRIBUTIONS A Licensee who develops a Contribution is the owner of the intellectual property rights over this Contribution as defined by applicable law. 6.3 OVER THE EXTERNAL MODULES A Licensee who develops an External Module is the owner of the intellectual property rights over this External Module as defined by applicable law and is free to choose the type of agreement that shall govern its distribution. 6.4 JOINT PROVISIONS The Licensee expressly undertakes: 1. not to remove, or modify, in any manner, the intellectual property notices attached to the Software; 2. to reproduce said notices, in an identical manner, in the copies of the Software modified or not. The Licensee undertakes not to directly or indirectly infringe the intellectual property rights of the Holder and/or Contributors on the Software and to take, where applicable, vis-ŕ-vis its staff, any and all measures required to ensure respect of said intellectual property rights of the Holder and/or Contributors. Article 7 - RELATED SERVICES 7.1 Under no circumstances shall the Agreement oblige the Licensor to provide technical assistance or maintenance services for the Software. However, the Licensor is entitled to offer this type of services. The terms and conditions of such technical assistance, and/or such maintenance, shall be set forth in a separate instrument. Only the Licensor offering said maintenance and/or technical assistance services shall incur liability therefor. 7.2 Similarly, any Licensor is entitled to offer to its licensees, under its sole responsibility, a warranty, that shall only be binding upon itself, for the redistribution of the Software and/or the Modified Software, under terms and conditions that it is free to decide. Said warranty, and the financial terms and conditions of its application, shall be subject of a separate instrument executed between the Licensor and the Licensee. Article 8 - LIABILITY 8.1 Subject to the provisions of Article 8.2, the Licensee shall be entitled to claim compensation for any direct loss it may have suffered from the Software as a result of a fault on the part of the relevant Licensor, subject to providing evidence thereof. 8.2 The Licensor's liability is limited to the commitments made under this Agreement and shall not be incurred as a result of in particular: (i) loss due the Licensee's total or partial failure to fulfill its obligations, (ii) direct or consequential loss that is suffered by the Licensee due to the use or performance of the Software, and (iii) more generally, any consequential loss. In particular the Parties expressly agree that any or all pecuniary or business loss (i.e. loss of data, loss of profits, operating loss, loss of customers or orders, opportunity cost, any disturbance to business activities) or any or all legal proceedings instituted against the Licensee by a third party, shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor. Article 9 - WARRANTY 9.1 The Licensee acknowledges that the scientific and technical state-of-the-art when the Software was distributed did not enable all possible uses to be tested and verified, nor for the presence of possible defects to be detected. In this respect, the Licensee's attention has been drawn to the risks associated with loading, using, modifying and/or developing and reproducing the Software which are reserved for experienced users. The Licensee shall be responsible for verifying, by any or all means, the product's suitability for its requirements, its good working order, and for ensuring that it shall not cause damage to either persons or properties. 9.2 The Licensor hereby represents, in good faith, that it is entitled to grant all the rights over the Software (including in particular the rights set forth in Article 5). 9.3 The Licensee acknowledges that the Software is supplied "as is" by the Licensor without any other express or tacit warranty, other than that provided for in Article 9.2 and, in particular, without any warranty as to its commercial value, its secured, safe, innovative or relevant nature. Specifically, the Licensor does not warrant that the Software is free from any error, that it will operate without interruption, that it will be compatible with the Licensee's own equipment and software configuration, nor that it will meet the Licensee's requirements. 9.4 The Licensor does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent, software or any other property right. Therefore, the Licensor disclaims any and all liability towards the Licensee arising out of any or all proceedings for infringement that may be instituted in respect of the use, modification and redistribution of the Software. Nevertheless, should such proceedings be instituted against the Licensee, the Licensor shall provide it with technical and legal assistance for its defense. Such technical and legal assistance shall be decided on a case-by-case basis between the relevant Licensor and the Licensee pursuant to a memorandum of understanding. The Licensor disclaims any and all liability as regards the Licensee's use of the name of the Software. No warranty is given as regards the existence of prior rights over the name of the Software or as regards the existence of a trademark. Article 10 - TERMINATION 10.1 In the event of a breach by the Licensee of its obligations hereunder, the Licensor may automatically terminate this Agreement thirty (30) days after notice has been sent to the Licensee and has remained ineffective. 10.2 A Licensee whose Agreement is terminated shall no longer be authorized to use, modify or distribute the Software. However, any licenses that it may have granted prior to termination of the Agreement shall remain valid subject to their having been granted in compliance with the terms and conditions hereof. Article 11 - MISCELLANEOUS 11.1 EXCUSABLE EVENTS Neither Party shall be liable for any or all delay, or failure to perform the Agreement, that may be attributable to an event of force majeure, an act of God or an outside cause, such as defective functioning or interruptions of the electricity or telecommunications networks, network paralysis following a virus attack, intervention by government authorities, natural disasters, water damage, earthquakes, fire, explosions, strikes and labor unrest, war, etc. 11.2 Any Failure by either Party, on one or more occasions, to invoke one or more of the provisions hereof, shall under no circumstances be interpreted as being a waiver by the interested Party of its right to invoke said provision(s) subsequently. 11.3 The Agreement cancels and replaces any or all previous agreements, whether written or oral, between the Parties and having the same purpose, and constitutes the entirety of the agreement between said Parties concerning said purpose. No supplement or modification to the terms and conditions hereof shall be effective as between the Parties unless it is made in writing and signed by their duly authorized representatives. 11.4 In the event that one or more of the provisions hereof were to conflict with a current or future applicable act or legislative text, said act or legislative text shall prevail, and the Parties shall make the necessary amendments so as to comply with said act or legislative text. All other provisions shall remain effective. Similarly, invalidity of a provision of the Agreement, for any reason whatsoever, shall not cause the Agreement as a whole to be invalid. 11.5 LANGUAGE The Agreement is drafted in both French and English and both versions are deemed authentic. Article 12 - NEW VERSIONS OF THE AGREEMENT 12.1 Any person is authorized to duplicate and distribute copies of this Agreement. 12.2 So as to ensure coherence, the wording of this Agreement is protected and may only be modified by the authors of the License, who reserve the right to periodically publish updates or new versions of the Agreement, each with a separate number. These subsequent versions may address new issues encountered by Free Software. 12.3 Any Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version, subject to the provisions of Article 5.3.4. Article 13 - GOVERNING LAW AND JURISDICTION 13.1 The Agreement is governed by French law. The Parties agree to endeavor to seek an amicable solution to any disagreements or disputes that may arise during the performance of the Agreement. 13.2 Failing an amicable solution within two (2) months as from their occurrence, and unless emergency proceedings are necessary, the disagreements or disputes shall be referred to the Paris Courts having jurisdiction, by the more diligent Party. Version 2.0 dated 2005-05-21. bpp-raa-2.2.0/Doxyfile000664 001750 001750 00000240220 12407766441 016242 0ustar00jdutheiljdutheil000000 000000 # Doxyfile 1.8.3.1-20130209 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project # # All text after a hash (#) is considered a comment and will be ignored # The format is: # TAG = value [value, ...] # For lists items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- # This tag specifies the encoding used for all characters in the config file # that follow. The default is UTF-8 which is also the encoding used for all # text before the first occurrence of this tag. Doxygen uses libiconv (or the # iconv built into libc) for the transcoding. See # http://www.gnu.org/software/libiconv for the list of possible encodings. DOXYFILE_ENCODING = UTF-8 # The PROJECT_NAME tag is a single word (or sequence of words) that should # identify the project. Note that if you do not use Doxywizard you need # to put quotes around the project name if it contains spaces. PROJECT_NAME = bpp-raa # The PROJECT_NUMBER tag can be used to enter a project or revision number. # This could be handy for archiving the generated documentation or # if some version control system is used. PROJECT_NUMBER = 2.2.0 # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer # a quick idea about the purpose of the project. Keep the description short. PROJECT_BRIEF = # With the PROJECT_LOGO tag one can specify an logo or icon that is # included in the documentation. The maximum height of the logo should not # exceed 55 pixels and the maximum width should not exceed 200 pixels. # Doxygen will copy the logo to the output directory. PROJECT_LOGO = # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. # If a relative path is entered, it will be relative to the location # where doxygen was started. If left blank the current directory will be used. OUTPUT_DIRECTORY = # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create # 4096 sub-directories (in 2 levels) under the output directory of each output # format and will distribute the generated files over these directories. # Enabling this option can be useful when feeding doxygen a huge amount of # source files, where putting all generated files in the same directory would # otherwise cause performance problems for the file system. CREATE_SUBDIRS = NO # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. # The default language is English, other supported languages are: # Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, # Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, # Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English # messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian, Persian, # Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, # Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. OUTPUT_LANGUAGE = English # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will # include brief member descriptions after the members that are listed in # the file and class documentation (similar to JavaDoc). # Set to NO to disable this. BRIEF_MEMBER_DESC = YES # If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend # the brief description of a member or function before the detailed description. # Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the # brief descriptions will be completely suppressed. REPEAT_BRIEF = YES # This tag implements a quasi-intelligent brief description abbreviator # that is used to form the text in various listings. Each string # in this list, if found as the leading text of the brief description, will be # stripped from the text and the result after processing the whole list, is # used as the annotated text. Otherwise, the brief description is used as-is. # If left blank, the following values are used ("$name" is automatically # replaced with the name of the entity): "The $name class" "The $name widget" # "The $name file" "is" "provides" "specifies" "contains" # "represents" "a" "an" "the" ABBREVIATE_BRIEF = # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then # Doxygen will generate a detailed section even if there is only a brief # description. ALWAYS_DETAILED_SEC = NO # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all # inherited members of a class in the documentation of that class as if those # members were ordinary class members. Constructors, destructors and assignment # operators of the base classes will not be shown. INLINE_INHERITED_MEMB = YES # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full # path before files name in the file list and in the header files. If set # to NO the shortest path that makes the file name unique will be used. FULL_PATH_NAMES = YES # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag # can be used to strip a user-defined part of the path. Stripping is # only done if one of the specified strings matches the left-hand part of # the path. The tag can be used to show relative paths in the file list. # If left blank the directory from which doxygen is run is used as the # path to strip. Note that you specify absolute paths here, but also # relative paths, which will be relative from the directory where doxygen is # started. STRIP_FROM_PATH = ./src/ # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of # the path mentioned in the documentation of a class, which tells # the reader which header file to include in order to use a class. # If left blank only the name of the header file containing the class # definition is used. Otherwise one should specify the include paths that # are normally passed to the compiler using the -I flag. STRIP_FROM_INC_PATH = ./src/ # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter # (but less readable) file names. This can be useful if your file system # doesn't support long names like on DOS, Mac, or CD-ROM. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like regular Qt-style comments # (thus requiring an explicit @brief command for a brief description.) JAVADOC_AUTOBRIEF = NO # If the QT_AUTOBRIEF tag is set to YES then Doxygen will # interpret the first line (until the first dot) of a Qt-style # comment as the brief description. If set to NO, the comments # will behave just like regular Qt-style comments (thus requiring # an explicit \brief command for a brief description.) QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen # treat a multi-line C++ special comment block (i.e. a block of //! or /// # comments) as a brief description. This used to be the default behaviour. # The new default is to treat a multi-line C++ comment block as a detailed # description. Set this tag to YES if you prefer the old behaviour instead. MULTILINE_CPP_IS_BRIEF = NO # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented # member inherits the documentation from any documented member that it # re-implements. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce # a new page for each member. If set to NO, the documentation of a member will # be part of the file/class/namespace that contains it. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. # Doxygen uses this value to replace tabs by spaces in code fragments. TAB_SIZE = 2 # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user-defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # This tag can be used to specify a number of word-keyword mappings (TCL only). # A mapping has the form "name=value". For example adding # "class=itcl::class" will allow you to use the command class in the # itcl::class meaning. TCL_SUBST = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C # sources only. Doxygen will then generate output that is more tailored for C. # For instance, some of the names that are used will be different. The list # of all members will be omitted, etc. OPTIMIZE_OUTPUT_FOR_C = NO # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java # sources only. Doxygen will then generate output that is more tailored for # Java. For instance, namespaces will be presented as packages, qualified # scopes will look different, etc. OPTIMIZE_OUTPUT_JAVA = NO # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources only. Doxygen will then generate output that is more tailored for # Fortran. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for # VHDL. OPTIMIZE_OUTPUT_VHDL = NO # Doxygen selects the parser to use depending on the extension of the files it # parses. With this tag you can assign which parser to use for a given # extension. Doxygen has a built-in mapping, but you can override or extend it # using this tag. The format is ext=language, where ext is a file extension, # and language is one of the parsers supported by doxygen: IDL, Java, # Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, # C++. For instance to make doxygen treat .inc files as Fortran files (default # is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note # that for custom extensions you also need to set FILE_PATTERNS otherwise the # files are not read by doxygen. EXTENSION_MAPPING = # If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all # comments according to the Markdown format, which allows for more readable # documentation. See http://daringfireball.net/projects/markdown/ for details. # The output of markdown processing is further processed by doxygen, so you # can mix doxygen, HTML, and XML commands with Markdown formatting. # Disable only in case of backward compatibilities issues. MARKDOWN_SUPPORT = YES # When enabled doxygen tries to link words that correspond to documented classes, # or namespaces to their corresponding documentation. Such a link can be # prevented in individual cases by by putting a % sign in front of the word or # globally by setting AUTOLINK_SUPPORT to NO. AUTOLINK_SUPPORT = YES # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want # to include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. # func(std::string) {}). This also makes the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. BUILTIN_STL_SUPPORT = YES # If you use Microsoft's C++/CLI language, you should set this option to YES to # enable parsing support. CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. # Doxygen will parse them like normal C++ but will assume all classes use public # instead of private inheritance when no explicit protection keyword is present. SIP_SUPPORT = NO # For Microsoft's IDL there are propget and propput attributes to indicate # getter and setter methods for a property. Setting this option to YES (the # default) will make doxygen replace the get and set methods by a property in # the documentation. This will only work if the methods are indeed getting or # setting a simple type. If this is not the case, or you want to show the # methods anyway, you should set this option to NO. IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES, then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES (the default) to allow class member groups of # the same type (for instance a group of public functions) to be put as a # subgroup of that type (e.g. under the Public Functions section). Set it to # NO to prevent subgrouping. Alternatively, this can be done per class using # the \nosubgrouping command. SUBGROUPING = YES # When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and # unions are shown inside the group in which they are included (e.g. using # @ingroup) instead of on a separate page (for HTML and Man pages) or # section (for LaTeX and RTF). INLINE_GROUPED_CLASSES = NO # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and # unions with only public data fields or simple typedef fields will be shown # inline in the documentation of the scope in which they are defined (i.e. file, # namespace, or group documentation), provided this scope is documented. If set # to NO (the default), structs, classes, and unions are shown on a separate # page (for HTML and Man pages) or section (for LaTeX and RTF). INLINE_SIMPLE_STRUCTS = NO # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum # is documented as struct, union, or enum with the name of the typedef. So # typedef struct TypeS {} TypeT, will appear in the documentation as a struct # with name TypeT. When disabled the typedef will appear as a member of a file, # namespace, or class. And the struct will be named TypeS. This can typically # be useful for C code in case the coding convention dictates that all compound # types are typedef'ed and only the typedef is referenced, never the tag name. TYPEDEF_HIDES_STRUCT = NO # The SYMBOL_CACHE_SIZE determines the size of the internal cache use to # determine which symbols to keep in memory and which to flush to disk. # When the cache is full, less often used symbols will be written to disk. # For small to medium size projects (<1000 input files) the default value is # probably good enough. For larger projects a too small cache size can cause # doxygen to be busy swapping symbols to and from disk most of the time # causing a significant performance penalty. # If the system has enough physical memory increasing the cache will improve the # performance by keeping more symbols in memory. Note that the value works on # a logarithmic scale so increasing the size by one will roughly double the # memory usage. The cache size is given by this formula: # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. SYMBOL_CACHE_SIZE = 0 # Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be # set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given # their name and scope. Since this can be an expensive process and often the # same symbol appear multiple times in the code, doxygen keeps a cache of # pre-resolved symbols. If the cache is too small doxygen will become slower. # If the cache is too large, memory is wasted. The cache size is given by this # formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. LOOKUP_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = YES # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = NO # If the EXTRACT_PACKAGE tag is set to YES all members with package or internal # scope will be included in the documentation. EXTRACT_PACKAGE = NO # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. EXTRACT_STATIC = YES # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. # If set to NO only classes defined in header files are included. EXTRACT_LOCAL_CLASSES = NO # This flag is only useful for Objective-C code. When set to YES local # methods, which are defined in the implementation section but not in # the interface are included in the documentation. # If set to NO (the default) only methods in the interface are included. EXTRACT_LOCAL_METHODS = NO # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called # 'anonymous_namespace{file}', where file will be replaced with the base # name of the file that contains the anonymous namespace. By default # anonymous namespaces are hidden. EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all # undocumented members of documented classes, files or namespaces. # If set to NO (the default) these members will be included in the # various overviews, but no documentation section is generated. # This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_MEMBERS = NO # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. # If set to NO (the default) these classes will be included in the various # overviews. This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all # friend (class|struct|union) declarations. # If set to NO (the default) these declarations will be included in the # documentation. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any # documentation blocks found inside the body of a function. # If set to NO (the default) these blocks will be appended to the # function's detailed documentation block. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation # that is typed after a \internal command is included. If the tag is set # to NO (the default) then the documentation will be excluded. # Set it to YES to include the internal documentation. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate # file names in lower-case letters. If set to YES upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. CASE_SENSE_NAMES = YES # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put a list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen # will list include files with double quotes in the documentation # rather than with sharp brackets. FORCE_LOCAL_INCLUDES = NO # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] # is inserted in the documentation for inline members. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen # will sort the (detailed) documentation of file and class members # alphabetically by member name. If set to NO the members will appear in # declaration order. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically # by member name. If set to NO (the default) the members will appear in # declaration order. SORT_BRIEF_DOCS = NO # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen # will sort the (brief and detailed) documentation of class members so that # constructors and destructors are listed first. If set to NO (the default) # the constructors will appear in the respective orders defined by # SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. # This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO # and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. SORT_MEMBERS_CTORS_1ST = NO # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the # hierarchy of group names into alphabetical order. If set to NO (the default) # the group names will appear in their defined order. SORT_GROUP_NAMES = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be # sorted by fully-qualified names, including namespaces. If set to # NO (the default), the class list will be sorted only by class name, # not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the # alphabetical list. SORT_BY_SCOPE_NAME = NO # If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to # do proper type resolution of all parameters of a function it will reject a # match between the prototype and the implementation of a member function even # if there is only one candidate or it is obvious which candidate to choose # by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen # will still accept a match between prototype and implementation in such cases. STRICT_PROTO_MATCHING = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo # commands in the documentation. GENERATE_TODOLIST = NO # The GENERATE_TESTLIST tag can be used to enable (YES) or # disable (NO) the test list. This list is created by putting \test # commands in the documentation. GENERATE_TESTLIST = NO # The GENERATE_BUGLIST tag can be used to enable (YES) or # disable (NO) the bug list. This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = NO # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or # disable (NO) the deprecated list. This list is created by putting # \deprecated commands in the documentation. GENERATE_DEPRECATEDLIST= NO # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if section-label ... \endif # and \cond section-label ... \endcond blocks. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or macro consists of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. Use a value of 0 to hide initializers completely. # The appearance of the initializer of individual variables and macros in the # documentation can be controlled using \showinitializer or \hideinitializer # command in the documentation regardless of this setting. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated # at the bottom of the documentation of classes and structs. If set to YES the # list will mention the files that were used to generate the documentation. SHOW_USED_FILES = YES # Set the SHOW_FILES tag to NO to disable the generation of the Files page. # This will remove the Files entry from the Quick Index and from the # Folder Tree View (if specified). The default is YES. SHOW_FILES = YES # Set the SHOW_NAMESPACES tag to NO to disable the generation of the # Namespaces page. This will remove the Namespaces entry from the Quick Index # and from the Folder Tree View (if specified). The default is YES. SHOW_NAMESPACES = YES # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from # the version control system). Doxygen will invoke the program by executing (via # popen()) the command , where is the value of # the FILE_VERSION_FILTER tag, and is the name of an input file # provided by doxygen. Whatever the program writes to standard output # is used as the file version. See the manual for examples. FILE_VERSION_FILTER = # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed # by doxygen. The layout file controls the global structure of the generated # output files in an output format independent way. To create the layout file # that represents doxygen's defaults, run doxygen with the -l option. # You can optionally specify a file name after the option, if omitted # DoxygenLayout.xml will be used as the name of the layout file. LAYOUT_FILE = # The CITE_BIB_FILES tag can be used to specify one or more bib files # containing the references data. This must be a list of .bib files. The # .bib extension is automatically appended if omitted. Using this command # requires the bibtex tool to be installed. See also # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this # feature you need bibtex and perl available in the search path. Do not use # file names with spaces, bibtex cannot handle them. CITE_BIB_FILES = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated # by doxygen. Possible values are YES and NO. If left blank NO is used. QUIET = NO # The WARNINGS tag can be used to turn on/off the warning messages that are # generated by doxygen. Possible values are YES and NO. If left blank # NO is used. WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = YES # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some # parameters in a documented function, or documenting parameters that # don't exist or using markup commands wrongly. WARN_IF_DOC_ERROR = YES # The WARN_NO_PARAMDOC option can be enabled to get warnings for # functions that are documented, but have no documentation for their parameters # or return value. If set to NO (the default) doxygen will only warn about # wrong or incomplete parameter documentation, but not about the absence of # documentation. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. Optionally the format may contain # $version, which will be replaced by the version of the file (if it could # be obtained via FILE_VERSION_FILTER) WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = src # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is # also the default input encoding. Doxygen uses libiconv (or the iconv built # into libc) for the transcoding. See http://www.gnu.org/software/libiconv for # the list of possible encodings. INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py # *.f90 *.f *.for *.vhd *.vhdl FILE_PATTERNS = Raa*.h \ *.cpp \ RAA.h # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = YES # The EXCLUDE tag can be used to specify files and/or directories that should be # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. # Note that relative paths are relative to the directory from which doxygen is # run. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded # from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the # wildcard * is used, a substring. Examples: ANamespace, AClass, # AClass::ANamespace, ANamespace::*Test EXCLUDE_SYMBOLS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. If FILTER_PATTERNS is specified, this tag will be # ignored. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. Doxygen will compare the file name with each pattern and apply the # filter if there is a match. The filters are a list of the form: # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further # info on how filters are used. If FILTER_PATTERNS is empty or if # non of the patterns match the file name, INPUT_FILTER is applied. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse (i.e. when SOURCE_BROWSER is set to YES). FILTER_SOURCE_FILES = NO # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file # pattern. A pattern will override the setting for FILTER_PATTERN (if any) # and it is also possible to disable source filtering for a specific pattern # using *.ext= (so without naming a filter). This option only has effect when # FILTER_SOURCE_FILES is enabled. FILTER_SOURCE_PATTERNS = # If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that # is part of the input, its contents will be placed on the main page (index.html). # This can be useful if you have a project on for instance GitHub and want reuse # the introduction page also for the doxygen output. USE_MDFILE_AS_MAINPAGE = #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. # Note: To get rid of all source code in the generated output, make sure also # VERBATIM_HEADERS is set to NO. SOURCE_BROWSER = YES # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct # doxygen to hide any special comment blocks from generated source code # fragments. Normal C, C++ and Fortran comments will always remain visible. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = YES # If the REFERENCES_RELATION tag is set to YES # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = YES # If the REFERENCES_LINK_SOURCE tag is set to YES (the default) # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will # link to the source code. Otherwise they will link to the documentation. REFERENCES_LINK_SOURCE = YES # If the USE_HTAGS tag is set to YES then the references to source code # will point to the HTML generated by the htags(1) tool instead of doxygen # built-in source browser. The htags tool is part of GNU's global source # tagging system (see http://www.gnu.org/software/global/global.html). You # will need version 4.8.6 or higher. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = NO # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. Note that when using a custom header you are responsible # for the proper inclusion of any scripts and style sheets that doxygen # needs, which is dependent on the configuration options used. # It is advised to generate a default header using "doxygen -w html # header.html footer.html stylesheet.css YourConfigFile" and then modify # that header. Note that the header is subject to change so you typically # have to redo this when upgrading to a newer version of doxygen or when # changing the value of configuration settings such as GENERATE_TREEVIEW! HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If left blank doxygen will # generate a default style sheet. Note that it is recommended to use # HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this # tag will in the future become obsolete. HTML_STYLESHEET = # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional # user-defined cascading style sheet that is included after the standard # style sheets created by doxygen. Using this option one can overrule # certain style aspects. This is preferred over using HTML_STYLESHEET # since it does not replace the standard style sheet and is therefor more # robust against future updates. Doxygen will copy the style sheet file to # the output directory. HTML_EXTRA_STYLESHEET = # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or # other source files which should be copied to the HTML output directory. Note # that these files will be copied to the base HTML output directory. Use the # $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these # files. In the HTML_STYLESHEET file, use the file name only. Also note that # the files will be copied as-is; there are no commands or markers available. HTML_EXTRA_FILES = # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. # Doxygen will adjust the colors in the style sheet and background images # according to this color. Hue is specified as an angle on a colorwheel, # see http://en.wikipedia.org/wiki/Hue for more information. # For instance the value 0 represents red, 60 is yellow, 120 is green, # 180 is cyan, 240 is blue, 300 purple, and 360 is red again. # The allowed range is 0 to 359. HTML_COLORSTYLE_HUE = 220 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of # the colors in the HTML output. For a value of 0 the output will use # grayscales only. A value of 255 will produce the most vivid colors. HTML_COLORSTYLE_SAT = 100 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to # the luminance component of the colors in the HTML output. Values below # 100 gradually make the output lighter, whereas values above 100 make # the output darker. The value divided by 100 is the actual gamma applied, # so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, # and 100 does not change the gamma. HTML_COLORSTYLE_GAMMA = 80 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML # page will contain the date and time when the page was generated. Setting # this to NO can help when comparing the output of multiple runs. HTML_TIMESTAMP = YES # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. HTML_DYNAMIC_SECTIONS = YES # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of # entries shown in the various tree structured indices initially; the user # can expand and collapse entries dynamically later on. Doxygen will expand # the tree to such a level that at most the specified number of entries are # visible (unless a fully collapsed tree already exceeds this amount). # So setting the number of entries 1 will produce a full collapsed tree by # default. 0 is a special value representing an infinite number of entries # and will result in a full expanded tree by default. HTML_INDEX_NUM_ENTRIES = 100 # If the GENERATE_DOCSET tag is set to YES, additional index files # will be generated that can be used as input for Apple's Xcode 3 # integrated development environment, introduced with OSX 10.5 (Leopard). # To create a documentation set, doxygen will generate a Makefile in the # HTML output directory. Running make will produce the docset in that # directory and running "make install" will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find # it at startup. # See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html # for more information. GENERATE_DOCSET = YES # When GENERATE_DOCSET tag is set to YES, this tag determines the name of the # feed. A documentation feed provides an umbrella under which multiple # documentation sets from a single provider (such as a company or product suite) # can be grouped. DOCSET_FEEDNAME = "Bio++ RAA" # When GENERATE_DOCSET tag is set to YES, this tag specifies a string that # should uniquely identify the documentation set bundle. This should be a # reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen # will append .docset to the name. DOCSET_BUNDLE_ID = bpp.RAA # When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely # identify the documentation publisher. This should be a reverse domain-name # style string, e.g. com.mycompany.MyDocSet.documentation. DOCSET_PUBLISHER_ID = org.doxygen.Publisher # The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. DOCSET_PUBLISHER_NAME = Publisher # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compiled HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can # be used to specify the file name of the resulting .chm file. You # can add a path in front of the file if the result should not be # written to the html output directory. CHM_FILE = # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can # be used to specify the location (absolute path including file name) of # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run # the HTML help compiler on the generated index.hhp. HHC_LOCATION = # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING # is used to encode HtmlHelp index (hhk), content (hhc) and project file # content. CHM_INDEX_ENCODING = # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the HTML help documentation and to the tree view. TOC_EXPAND = NO # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated # that can be used as input for Qt's qhelpgenerator to generate a # Qt Compressed Help (.qch) of the generated HTML documentation. GENERATE_QHP = NO # If the QHG_LOCATION tag is specified, the QCH_FILE tag can # be used to specify the file name of the resulting .qch file. # The path specified is relative to the HTML output folder. QCH_FILE = # The QHP_NAMESPACE tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#namespace QHP_NAMESPACE = org.doxygen.Project # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#virtual-folders QHP_VIRTUAL_FOLDER = doc # If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to # add. For more information please see # http://doc.trolltech.com/qthelpproject.html#custom-filters QHP_CUST_FILTER_NAME = # The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the # custom filter to add. For more information please see # # Qt Help Project / Custom Filters. QHP_CUST_FILTER_ATTRS = # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this # project's # filter section matches. # # Qt Help Project / Filter Attributes. QHP_SECT_FILTER_ATTRS = # If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can # be used to specify the location of Qt's qhelpgenerator. # If non-empty doxygen will try to run qhelpgenerator on the generated # .qhp file. QHG_LOCATION = # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files # will be generated, which together with the HTML files, form an Eclipse help # plugin. To install this plugin and make it available under the help contents # menu in Eclipse, the contents of the directory containing the HTML and XML # files needs to be copied into the plugins directory of eclipse. The name of # the directory within the plugins directory should be the same as # the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before # the help appears. GENERATE_ECLIPSEHELP = NO # A unique identifier for the eclipse help plugin. When installing the plugin # the directory name containing the HTML and XML files should also have # this name. ECLIPSE_DOC_ID = org.doxygen.Project # The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) # at top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. Since the tabs have the same information as the # navigation tree you can set this option to NO if you already set # GENERATE_TREEVIEW to YES. DISABLE_INDEX = NO # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. # If the tag value is set to YES, a side panel will be generated # containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). # Windows users are probably better off using the HTML help feature. # Since the tree basically has the same information as the tab index you # could consider to set DISABLE_INDEX to NO when enabling this option. GENERATE_TREEVIEW = YES # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values # (range [0,1..20]) that doxygen will group on one line in the generated HTML # documentation. Note that a value of 0 will completely suppress the enum # values from appearing in the overview section. ENUM_VALUES_PER_LINE = 4 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 # When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open # links to external symbols imported via tag files in a separate window. EXT_LINKS_IN_WINDOW = NO # Use this tag to change the font size of Latex formulas included # as images in the HTML documentation. The default is 10. Note that # when you change the font size after a successful doxygen run you need # to manually remove any form_*.png images from the HTML output directory # to force them to be regenerated. FORMULA_FONTSIZE = 10 # Use the FORMULA_TRANPARENT tag to determine whether or not the images # generated for formulas are transparent PNGs. Transparent PNGs are # not supported properly for IE 6.0, but are supported on all modern browsers. # Note that when changing this option you need to delete any form_*.png files # in the HTML output before the changes have effect. FORMULA_TRANSPARENT = YES # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax # (see http://www.mathjax.org) which uses client side Javascript for the # rendering instead of using prerendered bitmaps. Use this if you do not # have LaTeX installed or if you want to formulas look prettier in the HTML # output. When enabled you may also need to install MathJax separately and # configure the path to it using the MATHJAX_RELPATH option. USE_MATHJAX = NO # When MathJax is enabled you can set the default output format to be used for # thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and # SVG. The default value is HTML-CSS, which is slower, but has the best # compatibility. MATHJAX_FORMAT = HTML-CSS # When MathJax is enabled you need to specify the location relative to the # HTML output directory using the MATHJAX_RELPATH option. The destination # directory should contain the MathJax.js script. For instance, if the mathjax # directory is located at the same level as the HTML output directory, then # MATHJAX_RELPATH should be ../mathjax. The default value points to # the MathJax Content Delivery Network so you can quickly see the result without # installing MathJax. However, it is strongly recommended to install a local # copy of MathJax from http://www.mathjax.org before deployment. MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest # The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension # names that should be enabled during MathJax rendering. MATHJAX_EXTENSIONS = # When the SEARCHENGINE tag is enabled doxygen will generate a search box # for the HTML output. The underlying search engine uses javascript # and DHTML and should work on any modern browser. Note that when using # HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets # (GENERATE_DOCSET) there is already a search function so this one should # typically be disabled. For large projects the javascript based search engine # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. SEARCHENGINE = YES # When the SERVER_BASED_SEARCH tag is enabled the search engine will be # implemented using a web server instead of a web client using Javascript. # There are two flavours of web server based search depending on the # EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for # searching and an index file used by the script. When EXTERNAL_SEARCH is # enabled the indexing and searching needs to be provided by external tools. # See the manual for details. SERVER_BASED_SEARCH = NO # When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP # script for searching. Instead the search results are written to an XML file # which needs to be processed by an external indexer. Doxygen will invoke an # external search engine pointed to by the SEARCHENGINE_URL option to obtain # the search results. Doxygen ships with an example indexer (doxyindexer) and # search engine (doxysearch.cgi) which are based on the open source search engine # library Xapian. See the manual for configuration details. EXTERNAL_SEARCH = NO # The SEARCHENGINE_URL should point to a search engine hosted by a web server # which will returned the search results when EXTERNAL_SEARCH is enabled. # Doxygen ships with an example search engine (doxysearch) which is based on # the open source search engine library Xapian. See the manual for configuration # details. SEARCHENGINE_URL = # When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed # search data is written to a file for indexing by an external tool. With the # SEARCHDATA_FILE tag the name of this file can be specified. SEARCHDATA_FILE = searchdata.xml # When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the # EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is # useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple # projects and redirect the results back to the right project. EXTERNAL_SEARCH_ID = # The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen # projects other than the one defined by this configuration file, but that are # all added to the same external search index. Each project needs to have a # unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id # of to a relative location where the documentation can be found. # The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ... EXTRA_SEARCH_MAPPINGS = #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. If left blank `latex' will be used as the default command name. # Note that when enabling USE_PDFLATEX this option is only used for # generating bitmaps for formulas in the HTML output, but not in the # Makefile that is written to the output directory. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4wide # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = amsmath # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for # the generated latex document. The footer should contain everything after # the last chapter. If it is left blank doxygen will generate a # standard footer. Notice: only use this tag if you know what you are doing! LATEX_FOOTER = # The LATEX_EXTRA_FILES tag can be used to specify one or more extra images # or other source files which should be copied to the LaTeX output directory. # Note that the files will be copied as-is; there are no commands or markers # available. LATEX_EXTRA_FILES = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = NO # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = NO # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO # If LATEX_HIDE_INDICES is set to YES then doxygen will not # include the index chapters (such as File Index, Compound Index, etc.) # in the output. LATEX_HIDE_INDICES = NO # If LATEX_SOURCE_CODE is set to YES then doxygen will include # source code with syntax highlighting in the LaTeX output. # Note that which sources are shown also depends on other settings # such as SOURCE_BROWSER. LATEX_SOURCE_CODE = NO # The LATEX_BIB_STYLE tag can be used to specify the style to use for the # bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See # http://en.wikipedia.org/wiki/BibTeX for more info. LATEX_BIB_STYLE = plain #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimized for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = rtf # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load style sheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assignments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = man # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = .3 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. GENERATE_XML = NO # The XML_OUTPUT tag is used to specify where the XML pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `xml' will be used as the default path. XML_OUTPUT = xml # The XML_SCHEMA tag can be used to specify an XML schema, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_SCHEMA = # The XML_DTD tag can be used to specify an XML DTD, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_DTD = # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that # enabling this will significantly increase the size of the XML output. XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options related to the DOCBOOK output #--------------------------------------------------------------------------- # If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files # that can be used to generate PDF. GENERATE_DOCBOOK = NO # The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be put in # front of it. If left blank docbook will be used as the default path. DOCBOOK_OUTPUT = docbook #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- # If the GENERATE_PERLMOD tag is set to YES Doxygen will # generate a Perl module file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_PERLMOD = NO # If the PERLMOD_LATEX tag is set to YES Doxygen will generate # the necessary Makefile rules, Perl scripts and LaTeX code to be able # to generate PDF and DVI output from the Perl module output. PERLMOD_LATEX = NO # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be # nicely formatted so it can be parsed by a human reader. This is useful # if you want to understand what is going on. On the other hand, if this # tag is set to NO the size of the Perl module output will be much smaller # and Perl will parse it just the same. PERLMOD_PRETTY = YES # The names of the make variables in the generated doxyrules.make file # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. # This is useful so different doxyrules.make files included by the same # Makefile don't overwrite each other's variables. PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # pointed to by INCLUDE_PATH will be searched when a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. To prevent a macro definition from being # undefined via #undef or recursively expanded use the := operator # instead of the = operator. PREDEFINED = # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition that # overrules the definition found in the source code. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all references to function-like macros # that are alone on a line, have an all uppercase name, and do not end with a # semicolon, because these will confuse the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- # The TAGFILES option can be used to specify one or more tagfiles. For each # tag file the location of the external documentation should be added. The # format of a tag file without this location is as follows: # TAGFILES = file1 file2 ... # Adding location for the tag files is done as follows: # TAGFILES = file1=loc1 "file2 = loc2" ... # where "loc1" and "loc2" can be relative or absolute paths # or URLs. Note that each tag file must have a unique name (where the name does # NOT include the path). If a tag file is not located in the directory in which # doxygen is run, you must also specify the path to the tagfile here. TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html \ ../bpp-seq/BppSeq.tag=../../bpp-seq/html # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = BppRaa.tag # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # If the EXTERNAL_PAGES tag is set to YES all external pages will be listed # in the related pages index. If set to NO, only the current project's # pages will be listed. EXTERNAL_PAGES = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base # or super classes. Setting the tag to NO turns the diagrams off. Note that # this option also works with HAVE_DOT disabled, but it is recommended to # install and use dot, since it yields more powerful graphs. CLASS_DIAGRAMS = NO # You can define message sequence charts within doxygen comments using the \msc # command. Doxygen will then run the mscgen tool (see # http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the # documentation. The MSCGEN_PATH tag allows you to specify the directory where # the mscgen tool resides. If left empty the tool is assumed to be found in the # default search path. MSCGEN_PATH = # If set to YES, the inheritance and collaboration graphs will hide # inheritance and usage relations if the target is undocumented # or is not a class. HIDE_UNDOC_RELATIONS = YES # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is # available from the path. This tool is part of Graphviz, a graph visualization # toolkit from AT&T and Lucent Bell Labs. The other options in this section # have no effect if this option is set to NO (the default) HAVE_DOT = YES # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is # allowed to run in parallel. When set to 0 (the default) doxygen will # base this on the number of processors available in the system. You can set it # explicitly to a value larger than 0 to get control over the balance # between CPU load and processing speed. DOT_NUM_THREADS = 0 # By default doxygen will use the Helvetica font for all dot files that # doxygen generates. When you want a differently looking font you can specify # the font name using DOT_FONTNAME. You need to make sure dot is able to find # the font, which can be done by putting it in a standard location or by setting # the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the # directory containing the font. DOT_FONTNAME = FreeSans # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. # The default size is 10pt. DOT_FONTSIZE = 10 # By default doxygen will tell dot to use the Helvetica font. # If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to # set the path where dot can find it. DOT_FONTPATH = # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = YES # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen # will generate a graph for groups, showing the direct groups dependencies GROUP_GRAPHS = YES # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. UML_LOOK = NO # If the UML_LOOK tag is enabled, the fields and methods are shown inside # the class node. If there are many fields or methods and many nodes the # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS # threshold limits the number of items for each type to make the size more # managable. Set this to 0 for no limit. Note that the threshold may be # exceeded by 50% before the limit is enforced. UML_LIMIT_NUM_FIELDS = 10 # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. TEMPLATE_RELATIONS = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented # file showing the direct and indirect include dependencies of the file with # other documented files. INCLUDE_GRAPH = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and # HAVE_DOT tags are set to YES then doxygen will generate a graph for each # documented header file showing the documented files that directly or # indirectly include this file. INCLUDED_BY_GRAPH = YES # If the CALL_GRAPH and HAVE_DOT options are set to YES then # doxygen will generate a call dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable call graphs # for selected functions only using the \callgraph command. CALL_GRAPH = NO # If the CALLER_GRAPH and HAVE_DOT tags are set to YES then # doxygen will generate a caller dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable caller # graphs for selected functions only using the \callergraph command. CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will generate a graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories # in a graphical way. The dependency relations are determined by the #include # relations between the files in the directories. DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. Possible values are svg, png, jpg, or gif. # If left blank png will be used. If you choose svg you need to set # HTML_FILE_EXTENSION to xhtml in order to make the SVG files # visible in IE 9+ (other browsers do not have this requirement). DOT_IMAGE_FORMAT = png # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to # enable generation of interactive SVG images that allow zooming and panning. # Note that this requires a modern browser other than Internet Explorer. # Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you # need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files # visible. Older versions of IE do not have SVG support. INTERACTIVE_SVG = NO # The tag DOT_PATH can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found in the path. DOT_PATH = # The DOTFILE_DIRS tag can be used to specify one or more directories that # contain dot files that are included in the documentation (see the # \dotfile command). DOTFILE_DIRS = # The MSCFILE_DIRS tag can be used to specify one or more directories that # contain msc files that are included in the documentation (see the # \mscfile command). MSCFILE_DIRS = # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of # nodes that will be shown in the graph. If the number of nodes in a graph # becomes larger than this value, doxygen will truncate the graph, which is # visualized by representing a node as a red box. Note that doxygen if the # number of direct children of the root node in a graph is already larger than # DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note # that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. DOT_GRAPH_MAX_NODES = 50 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the # graphs generated by dot. A depth value of 3 means that only nodes reachable # from the root by following a path via at most 3 edges will be shown. Nodes # that lay further from the root node will be omitted. Note that setting this # option to 1 or 2 may greatly reduce the computation time needed for large # code bases. Also note that the size of a graph can be further restricted by # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is disabled by default, because dot on Windows does not # seem to support this out of the box. Warning: Depending on the platform used, # enabling this option may lead to badly anti-aliased labels on the edges of # a graph (i.e. they become hard to read). DOT_TRANSPARENT = NO # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) # support this, this feature is disabled by default. DOT_MULTI_TARGETS = YES # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermediate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES bpp-raa-2.2.0/debian/rules000775 001750 001750 00000005307 12407767006 017041 0ustar00jdutheiljdutheil000000 000000 #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # 24/01/10 Modification for use with CMake by Julien Dutheil. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # These are used for cross-compiling and for saving the configure script # from having to guess our platform (since we know it already) DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) CFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif # shared library versions version=`ls src/lib*.so.* | \ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'` major=`ls src/lib*.so.* | \ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'` configure: cmake -DCMAKE_INSTALL_PREFIX=/usr . config.status: configure dh_testdir build: build-arch build-indep build-arch: build-stamp build-indep: build-stamp build-stamp: config.status dh_testdir # Add here commands to compile the package. $(MAKE) touch $@ clean: dh_testdir dh_testroot # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean; [ ! -f Makefile ] || rm Makefile; [ ! -f src/Makefile ] || rm src/Makefile; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f src/*.cmake #rm -f test/*.cmake rm -rf CMakeFiles rm -rf src/CMakeFiles #rm -rf test/CMakeFiles rm -rf _CPack_Packages #rm -rf Testing #rm -f DartConfiguration.tcl dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # Add here commands to install the package into debian/tmp $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples dh_install # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_installinit # dh_installcron # dh_installinfo dh_installman dh_link dh_strip dh_compress dh_fixperms # dh_perl # dh_python dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install bpp-raa-2.2.0/debian/libbpp-raa-dev.install000664 001750 001750 00000000116 12372454333 022124 0ustar00jdutheiljdutheil000000 000000 debian/tmp/usr/include/* debian/tmp/usr/lib/lib*.a debian/tmp/usr/lib/lib*.so bpp-raa-2.2.0/debian/compat000664 001750 001750 00000000002 12372454333 017147 0ustar00jdutheiljdutheil000000 000000 5 bpp-raa-2.2.0/debian/copyright000664 001750 001750 00000005642 12407766641 017722 0ustar00jdutheiljdutheil000000 000000 This package was debianized by Julien Dutheil on Thu, 22 Sep 2014 14:00:00 +0100. It was downloaded from Upstream Author: Julien Dutheil Copyright: Copyright (C) 2014 Bio++ Development Team License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. The Debian packaging is (C) 2014, Julien Dutheil and is licensed under the GPL, see above. The provided software is distributed under the CeCILL license: This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. The complete text of the license may be found here: http://www.cecill.info/licences/Licence_CeCILL_V2-en.html bpp-raa-2.2.0/debian/source/format000664 001750 001750 00000000014 12372454333 020457 0ustar00jdutheiljdutheil000000 000000 3.0 (quilt) bpp-raa-2.2.0/debian/changelog000664 001750 001750 00000002334 12407766604 017633 0ustar00jdutheiljdutheil000000 000000 libbpp-raa (2.2.0-1) unstable; urgency=low * Recompilation because of dependencies. -- Julien Dutheil Mon, 22 Sep 2014 14:00:00 +0100 libbpp-raa (2.1.0-1) unstable; urgency=low * Recompilation because of dependencies. -- Julien Dutheil Thu, 07 Mar 2013 11:46:00 +0100 libbpp-raa (2.0.3-1) unstable; urgency=low * Recompilation because of dependencies. -- Julien Dutheil Thu, 09 Feb 2012 16:45:00 +0100 libbpp-raa (2.0.2-1) unstable; urgency=low * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373). * Packages are now non-native. -- Julien Dutheil Thu, 09 Jun 2011 11:00:00 +0100 libbpp-raa (2.0.1) unstable; urgency=low * Fixed copyright and rules issue in package. -- Julien Dutheil Mon, 28 Feb 2011 09:00:00 +0100 libbpp-raa (2.0.0) unstable; urgency=low * Compatibility with Bio++ 2.0.0. -- Julien Dutheil Mon, 07 Feb 2011 09:00:00 +0100 libbpp-raa (1.0.0) unstable; urgency=low * Initial Release. -- Julien Dutheil Thu, 25 Mar 2010 15:30:13 +0100 bpp-raa-2.2.0/debian/postinst000775 001750 001750 00000002062 12407767006 017565 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in configure) # Actualize .all files createGeneric /usr/include/Bpp ;; abort-upgrade|abort-remove|abort-deconfigure) echo "$1" ;; *) echo "postinst called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-raa-2.2.0/debian/postrm000775 001750 001750 00000002171 12407767006 017227 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in remove) # Automatically added by dh_makeshlibs ldconfig # Actualize .all files createGeneric /usr/include/Bpp ;; purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear) echo $1 ;; *) echo "postrm called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-raa-2.2.0/debian/control000664 001750 001750 00000002007 12407767034 017357 0ustar00jdutheiljdutheil000000 000000 Source: libbpp-raa Section: libs Priority: optional Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), zlib1g-dev (>= 1.2.3), libbpp-seq-dev (>= 2.2.0), zlib1g (>= 1.2.3) Standards-Version: 3.9.4 Package: libbpp-raa-dev Section: libdevel Architecture: any Depends: libbpp-raa1 (= ${binary:Version}), ${misc:Depends}, zlib1g-dev (>= 1.2.3), libbpp-seq-dev (>= 2.2.0) Description: Bio++ Remote Acnuc Access library development files. This library contains utilitary and classes to query public databases (GenBank, EMBL, SwissProt, etc) using acnuc. It is part of the Bio++ project. Package: libbpp-raa1 Section: libs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, zlib1g (>= 1.2.3), libbpp-seq9 (>= 2.2.0) Description: Bio++ Remote Acnuc Access library. This library contains utilitary and classes to query public databases (GenBank, EMBL, SwissProt, etc) using acnuc. It is part of the Bio++ project. bpp-raa-2.2.0/debian/libbpp-raa1.install000664 001750 001750 00000000035 12372454333 021431 0ustar00jdutheiljdutheil000000 000000 debian/tmp/usr/lib/lib*.so.* bpp-raa-2.2.0/debian/prerm000775 001750 001750 00000001217 12407767006 017030 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } case "$1" in remove|upgrade|deconfigure) # Actualize .all files removeGeneric /usr/include/Bpp ;; failed-upgrade) echo "$1" ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-raa-2.2.0/CMakeLists.txt000664 001750 001750 00000013552 12407766427 017306 0ustar00jdutheiljdutheil000000 000000 # CMake script for Bio++ Remote Acnuc Access # Author: Sylvain Gaillard and Julien Dutheil # Created: 11/09/2009 # Global parameters cmake_minimum_required(VERSION 2.6) project(bpp-raa C CXX) if(NOT DEFINED CMAKE_BUILD_TYPE) set(CMAKE_BUILD_TYPE "Release") endif(NOT DEFINED CMAKE_BUILD_TYPE) set(CMAKE_CXX_FLAGS "-Wall") IF(NOT NO_DEP_CHECK) SET(NO_DEP_CHECK FALSE CACHE BOOL "Disable dependencies check for building distribution only." FORCE) ENDIF(NOT NO_DEP_CHECK) IF(NO_DEP_CHECK) MESSAGE("-- Dependencies checking disabled. Only distribution can be built.") ELSE(NO_DEP_CHECK) # Libtool-like version number # CURRENT:REVISION:AGE => file.so.(C-A).A.R # current: The most recent interface number that this library implements. # revision: The implementation number of the current interface. # age: The difference between the newest and oldest interfaces that this # library implements. # In other words, the library implements all the interface numbers in the # range from number current - age to current. set(BPPRAA_VERSION_CURRENT "2") set(BPPRAA_VERSION_REVISION "1") set(BPPRAA_VERSION_AGE "1") # Effective version number computation math(EXPR BPPRAA_VERSION_MAJOR "${BPPRAA_VERSION_CURRENT} - ${BPPRAA_VERSION_AGE}") set(BPPRAA_VERSION_MINOR ${BPPRAA_VERSION_AGE}) set(BPPRAA_VERSION_PATCH ${BPPRAA_VERSION_REVISION}) set(BPPRAA_VERSION "${BPPRAA_VERSION_MAJOR}.${BPPRAA_VERSION_MINOR}.${BPPRAA_VERSION_PATCH}") # Set the CMAKE_PREFIX_PATH for the find_library fonction when using non # standard install location IF(CMAKE_INSTALL_PREFIX) SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH}) ENDIF(CMAKE_INSTALL_PREFIX) #here is a useful function: MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find) #start: FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find}) SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll) FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX}) IF(${lib_name}_LIBRARY) MESSAGE("-- Library ${lib_name} found here:") MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}") MESSAGE(" libraries: ${${lib_name}_LIBRARY}") ELSE(${lib_name}_LIBRARY) MESSAGE(FATAL_ERROR "${lib_name} required but not found.") ENDIF(${lib_name}_LIBRARY) #add the dependency: INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR}) SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY}) ENDMACRO(IMPROVED_FIND_LIBRARY) #Find the Bio++ libraries: IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h) #Not explicitely needed: #IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h) # Find the zlib installation find_package(ZLIB REQUIRED) include_directories(${ZLIB_INCLUDE_DIR}) set(LIBS ${LIBS} ${ZLIB_LIBRARIES}) # Subdirectories add_subdirectory(src) # Doxygen find_package(Doxygen) if (DOXYGEN_FOUND) ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}) ADD_CUSTOM_TARGET (apidoc-stable cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}) endif (DOXYGEN_FOUND) ENDIF(NO_DEP_CHECK) # Packager set(CPACK_PACKAGE_NAME "libbpp-raa") set(CPACK_PACKAGE_VENDOR "Bio++ Development Team") set(CPACK_PACKAGE_VERSION "2.2.0") set(CPACK_PACKAGE_VERSION_MAJOR "2") set(CPACK_PACKAGE_VERSION_MINOR "2") set(CPACK_PACKAGE_VERSION_PATCH "0") set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library") set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt") set(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt") set(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt") set(CPACK_SOURCE_GENERATOR "TGZ") SET(CPACK_SOURCE_IGNORE_FILES "CMakeFiles" "Makefile" "_CPack_Packages" "CMakeCache.txt" ".*\\\\.cmake" ".*\\\\.git" ".*\\\\.gz" ".*\\\\.deb" ".*\\\\.rpm" ".*\\\\.dmg" ".*\\\\.sh" ".*\\\\..*\\\\.swp" "src/\\\\..*" "src/libbpp*" "debian/tmp" "debian/libbpp.*/" "debian/libbpp.*\\\\.so.*" "debian/libbpp.*\\\\.a" "debian/libbpp.*\\\\.substvars" "debian/libbpp.*\\\\.debhelper" "debian/debhelper\\\\.log" "html" "Raa.tag" "Testing" "build-stamp" "install_manifest.txt" "DartConfiguration.tcl" ${CPACK_SOURCE_IGNORE_FILES} ) IF (MACOS) SET(CPACK_GENERATOR "Bundle") ENDIF() SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig") INCLUDE(CPack) #This adds the 'dist' target ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source) # 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources: IF("${CMAKE_GENERATOR}" MATCHES "Make") ADD_CUSTOM_TARGET(make_clean COMMAND ${CMAKE_MAKE_PROGRAM} clean WORKING_DIRECTORY ${CMAKE_CURRENT_DIR} ) ADD_DEPENDENCIES(dist make_clean) ENDIF() IF(NOT NO_DEP_CHECK) IF (UNIX) #This creates deb packages: ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(origdist dist) ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(deb origdist) #This creates rpm packages: ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(rpm dist) ENDIF() ENDIF(NOT NO_DEP_CHECK) bpp-raa-2.2.0/ChangeLog000664 001750 001750 00000000277 12372454333 016307 0ustar00jdutheiljdutheil000000 000000 07/03/13 -*- version 2.1.0 -*- 09/02/12 -*- version 2.0.3 -*- 09/06/11 -*- version 2.0.2 -*- 28/02/11 -*- version 2.0.1 -*- 07/02/11 -*- version 2.0.0 -*- ??/??/?? -*- version 1.0.0 -*- bpp-raa-2.2.0/AUTHORS.txt000664 001750 001750 00000000055 12372454333 016415 0ustar00jdutheiljdutheil000000 000000 Manolo Gouy