This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository seaview.
commit 39908717ec73c2537ce630eca6ef1c747bd55c4d Author: Andreas Tille <[email protected]> Date: Sat Mar 19 23:54:02 2016 +0100 Imported Upstream version 4.6 --- csrc/raa_acnuc.c | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ csrc/raa_acnuc.h | 4 +++ macos_extras.mm | 16 +++++------ pdf_or_ps.h | 8 +++--- seaview.html | 4 +-- treedraw.cxx | 2 +- trees.cxx | 4 +-- win32_extras.cxx | 4 +-- 8 files changed, 104 insertions(+), 19 deletions(-) diff --git a/csrc/raa_acnuc.c b/csrc/raa_acnuc.c index 10e32d2..0ae115d 100644 --- a/csrc/raa_acnuc.c +++ b/csrc/raa_acnuc.c @@ -1795,6 +1795,87 @@ if(raa_current_db == NULL) return NULL; } +char *raa_readaut(raa_db_access *raa_current_db, int num, int *plref) +{ + Reponse *rep; + char *p, *reponse; + int code; + +if(raa_current_db == NULL) return NULL; + rep=initreponse(); + sock_printf(raa_current_db,"readaut&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(plref != NULL) { + p = val(rep, "plref"); + *plref = atoi_u(p); + free(p); + } + p = val(rep, "name"); + strcpy(raa_current_db->author, p); + free(p); + p = raa_current_db->author; + } + else p = NULL; + clear_reponse(rep); + return p; +} + + +char *raa_readbib(raa_db_access *raa_current_db, int num, int *plsub, int *plaut, int *pj, int *py) +{ + Reponse *rep; + char *p, *reponse; + int code; + + if (raa_current_db == NULL) return NULL; + rep=initreponse(); + sock_printf(raa_current_db,"readbib&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); + } + if (plaut != NULL) { + p = val(rep, "plaut"); + *plaut = atoi_u(p); + free(p); + } + if (pj != NULL) { + p = val(rep, "j"); + *pj = atoi_u(p); + free(p); + } + if (py != NULL) { + p = val(rep, "y"); + *py = atoi_u(p); + free(p); + } + p = val(rep, "name"); + strcpy(raa_current_db->biblio, p); + free(p); + p = raa_current_db->biblio; + } + 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; diff --git a/csrc/raa_acnuc.h b/csrc/raa_acnuc.h index 9022bfc..f9fa72b 100644 --- a/csrc/raa_acnuc.h +++ b/csrc/raa_acnuc.h @@ -152,6 +152,8 @@ typedef struct _raa_db_access { char mnemo[WIDTH_MAX]; char species[WIDTH_MAX]; char access[WIDTH_MAX]; + char author[WIDTH_MAX]; + char biblio[WIDTH_MAX]; char descript[WIDTH_MAX]; char date[12]; } raa_db_access; @@ -215,6 +217,8 @@ char *raa_readspec(raa_db_access *raa_current_db, int num, char **plibel, int * 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); +char *raa_readaut(raa_db_access *raa_current_db, int num, int *plsub); +char *raa_readbib(raa_db_access *raa_current_db, int num, int *plsub, int *plaut, int *pj, int *py); 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); diff --git a/macos_extras.mm b/macos_extras.mm index 5cd4552..d4f9736 100644 --- a/macos_extras.mm +++ b/macos_extras.mm @@ -438,7 +438,7 @@ void Fl_PICT_Graphics_Driver::draw(const char* str, int n, float fx, float fy) { #endif // USE_PICT -Fl_Copy_Surface::Fl_Copy_Surface(bool pict, int w, int h) : Fl_Surface_Device(NULL) +Copy_Surface::Copy_Surface(bool pict, int w, int h) : Fl_Surface_Device(NULL) { #ifdef USE_PICT use_pict = pict; @@ -466,7 +466,7 @@ Fl_Copy_Surface::Fl_Copy_Surface(bool pict, int w, int h) : Fl_Surface_Device(NU } } -Fl_Copy_Surface::~Fl_Copy_Surface() +Copy_Surface::~Copy_Surface() { if (use_pict) { #ifdef USE_PICT @@ -482,7 +482,7 @@ Fl_Copy_Surface::~Fl_Copy_Surface() delete driver(); } -size_t Fl_Copy_Surface::MyPutBytes (void* info, const void* buffer, size_t count) +size_t Copy_Surface::MyPutBytes (void* info, const void* buffer, size_t count) { CFDataAppendBytes ((CFMutableDataRef) info, (const UInt8 *)buffer, count); return count; @@ -490,7 +490,7 @@ size_t Fl_Copy_Surface::MyPutBytes (void* info, const void* buffer, size_t count #ifdef USE_PICT -QDPictRef Fl_Copy_Surface::MyPictToQDPict() +QDPictRef Copy_Surface::MyPictToQDPict() { CFIndex pictlen; CGDataProviderRef provider; @@ -509,7 +509,7 @@ QDPictRef Fl_Copy_Surface::MyPictToQDPict() } -void Fl_Copy_Surface::MyCopyPictToClipboard() +void Copy_Surface::MyCopyPictToClipboard() { CFDataRef data = NULL; PasteboardRef clipboard = NULL; @@ -550,7 +550,7 @@ void Fl_Copy_Surface::MyCopyPictToClipboard() } #endif // USE_PICT -void Fl_Copy_Surface::init_PDF_context(int w, int h) +void Copy_Surface::init_PDF_context(int w, int h) { CGRect bounds = CGRectMake(0, 0, w, h ); pdfdata = CFDataCreateMutable(NULL, 0); @@ -567,7 +567,7 @@ void Fl_Copy_Surface::init_PDF_context(int w, int h) } //next 2 functions copy quartz data to clipboard both as pdf and as tiff bitmap -void Fl_Copy_Surface::prepare_copy_pdf_and_pict(int w, int h) +void Copy_Surface::prepare_copy_pdf_and_pict(int w, int h) { init_PDF_context(w, h); if (gc == NULL) return; @@ -577,7 +577,7 @@ void Fl_Copy_Surface::prepare_copy_pdf_and_pict(int w, int h) CGContextScaleCTM(gc, 1.0f, -1.0f); } -void Fl_Copy_Surface::complete_copy_pdf_and_pict() +void Copy_Surface::complete_copy_pdf_and_pict() { int w, h; CGContextEndPage (gc); diff --git a/pdf_or_ps.h b/pdf_or_ps.h index 6dbc0b3..9a4a30c 100644 --- a/pdf_or_ps.h +++ b/pdf_or_ps.h @@ -131,7 +131,7 @@ typedef Fl_PDF_File_Device Fl_PDF_or_PS_File_Device; #if (defined(__APPLE__) || defined(WIN32)) -class Fl_Copy_Surface : public Fl_Surface_Device { +class Copy_Surface : public Fl_Surface_Device { #ifdef __APPLE__ bool use_pict; CFMutableDataRef pdfdata; @@ -151,11 +151,11 @@ class Fl_Copy_Surface : public Fl_Surface_Device { #endif public: #ifdef __APPLE__ - Fl_Copy_Surface(bool use_pict, int w, int h); + Copy_Surface(bool use_pict, int w, int h); #else - Fl_Copy_Surface(int w, int h); + Copy_Surface(int w, int h); #endif - ~Fl_Copy_Surface(); + ~Copy_Surface(); }; #endif diff --git a/seaview.html b/seaview.html index 2fb86a7..a9748aa 100644 --- a/seaview.html +++ b/seaview.html @@ -44,11 +44,11 @@ Molecular Biology and Evolution 27(2):221-224. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.</a> Comput. Appl. Biosci., 12:543-548. <p> -Version 4.5.4 +Version 4.6 <p>Binaries and full source code available from <a href=http://doua.prabi.fr/software/seaview>http://doua.prabi.fr/software/seaview</a> -<p>© 1996-2015 Manolo Gouy +<p>© 1996-2016 Manolo Gouy <br>Laboratoire de Biométrie et Biologie Evolutive <br>CNRS / Université de Lyon <p>Licensed under the GNU <a href=http://www.gnu.org/licenses/gpl.txt>General Public Licence</a>. diff --git a/treedraw.cxx b/treedraw.cxx index 8c0072d..2a2b88c 100644 --- a/treedraw.cxx +++ b/treedraw.cxx @@ -438,7 +438,7 @@ static void copy(Fl_Widget *wgt, void *data) else g = fd_nj_plot->panel; Fl_Surface_Device *current = Fl_Surface_Device::surface(); - Fl_Copy_Surface *copy_surf = new Fl_Copy_Surface( + Copy_Surface *copy_surf = new Copy_Surface( #ifdef __APPLE__ fd_nj_plot->fd_unrooted == NULL, #endif diff --git a/trees.cxx b/trees.cxx index 63e7f5b..74ebada 100644 --- a/trees.cxx +++ b/trees.cxx @@ -504,7 +504,7 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int free_after_view_to_allseq(phyml_seqs); return NULL; } - phyml_mat->method = !use_bionj; //1:NJ 0:BioNJ + phyml_mat->method = use_bionj; //0:NJ 1:BioNJ phyml_mat->tree = Make_Tree_From_Scratch(phyml_seqs->n_otu, phyml_seqs); Bionj(phyml_mat); sprintf(tree_label, "%s %d sites %s", use_bionj ? "BioNJ" : "NJ", @@ -525,7 +525,7 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int if (!tree_build_interrupted) total = 0; break; } - phyml_mat->method = ! use_bionj; //1:NJ 0:BioNJ + phyml_mat->method = use_bionj; // 0:NJ 1:BioNJ phyml_mat->tree = Make_Tree_From_Scratch(phyml_seqs->n_otu, phyml_seqs); Bionj(phyml_mat); char *one_replicate_tree = Write_Tree(phyml_mat->tree); diff --git a/win32_extras.cxx b/win32_extras.cxx index 3a1beb7..1212f72 100644 --- a/win32_extras.cxx +++ b/win32_extras.cxx @@ -15,7 +15,7 @@ char **getutf8args(int *pargc); int mysystem(const char *cmd); -Fl_Copy_Surface::Fl_Copy_Surface(int w, int h) : Fl_Surface_Device(new Fl_GDI_Graphics_Driver()) +Copy_Surface::Copy_Surface(int w, int h) : Fl_Surface_Device(new Fl_GDI_Graphics_Driver()) { HDC oldflgc = fl_gc; //int factor = 32; // empirically set @@ -40,7 +40,7 @@ Fl_Copy_Surface::Fl_Copy_Surface(int w, int h) : Fl_Surface_Device(new Fl_GDI_Gr } } -Fl_Copy_Surface::~Fl_Copy_Surface() +Copy_Surface::~Copy_Surface() { if(oldflgc == fl_gc) oldflgc = NULL; HENHMETAFILE hmf = CloseEnhMetaFile (fl_gc); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seaview.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
