[med-svn] [seaview] 01/03: Imported Upstream version 4.6
Andreas Tille
tille at debian.org
Sat Mar 19 22:55:55 UTC 2016
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 <tille at debian.org>
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);
--
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