[med-svn] [seaview] 01/08: New upstream version 4.6.1.2

[Andreas Tille]

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tille pushed a commit to branch debian/jessie-backports
in repository seaview.

commit be0a2e4dec11ea84cf893970b6f3ec4331827076
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 17 22:40:27 2016 +0100

    New upstream version 4.6.1.2
---
 macos_extras.mm |  2 +-
 pdf_or_ps.h     |  3 ++-
 svg.cxx         | 15 ++++++++++++++-
 trees.cxx       | 12 ++++++++++++
 4 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/macos_extras.mm b/macos_extras.mm
index fdcf8b7..db5be98 100644
--- a/macos_extras.mm
+++ b/macos_extras.mm
@@ -5,7 +5,7 @@
 #include <FL/x.H>
 #include <FL/Fl_Sys_Menu_Bar.H>
 #include <FL/Fl_Help_View.H>
-#if SEAVIEW_FLTK_VERSION >= 140
+#if 100*FL_MAJOR_VERSION + 10*FL_MINOR_VERSION + FL_PATCH_VERSION >= 140
 #include <src/drivers/Quartz/Fl_Quartz_Graphics_Driver.H>
 #endif
 #include <FL/filename.H>
diff --git a/pdf_or_ps.h b/pdf_or_ps.h
index 6dbd351..c4b3558 100644
--- a/pdf_or_ps.h
+++ b/pdf_or_ps.h
@@ -2,7 +2,7 @@
 #define PDF_OR_PS_H
 
 #include <FL/Fl_Paged_Device.H>
-#if SEAVIEW_FLTK_VERSION >= 140
+#if 100*FL_MAJOR_VERSION + 10*FL_MINOR_VERSION + FL_PATCH_VERSION >= 140
 #include <FL/Fl_Graphics_Driver.H>
 #endif
 
@@ -155,6 +155,7 @@ typedef Fl_PDF_File_Device Fl_PDF_or_PS_File_Device;
 
 #if defined(__APPLE__)
 #include <ApplicationServices/ApplicationServices.h>
+#undef check
 #if  (!__LP64__) && MAC_OS_X_VERSION_MAX_ALLOWED < 1070
 #define USE_PICT
 #endif
diff --git a/svg.cxx b/svg.cxx
index 62863b4..a8c198b 100644
--- a/svg.cxx
+++ b/svg.cxx
@@ -188,7 +188,11 @@ void svg_tree_save(FD_nj_plot *fd_nj_plot, Fl_SVG_File_Surface *svg)
   fl_color(FL_BLACK);
   fl_line_style(FL_CAP_SQUARE, 1);
   if(fd_nj_plot->fd_unrooted == NULL) {
+    extern double physy;
+    double old_physy = physy;
+    physy = svg->height();
     do_plot(fd_nj_plot, TRUE);
+    physy = old_physy;
     }
   else {
     FD_unrooted *fd_unrooted = (FD_unrooted *)fd_nj_plot->fd_unrooted;
@@ -227,7 +231,16 @@ void svg_tree_dialog_and_save(FD_nj_plot *fd_nj_plot)
   if (plotfilename == NULL) return;
   FILE *out;
   if (!(out = fopen(plotfilename, "w"))) return;
-  svg_tree_save(fd_nj_plot, new Fl_SVG_File_Surface(fd_nj_plot->panel->w(), fd_nj_plot->panel->h(), out));
+  int width, height;
+  if (fd_nj_plot->fd_unrooted) {
+    FD_unrooted *unrooted = (FD_unrooted*)fd_nj_plot->fd_unrooted;
+    width = unrooted->unrooted_plot->w() * unrooted->zoomvalue;
+    height = unrooted->unrooted_plot->h() * unrooted->zoomvalue;
+  } else {
+    width = fd_nj_plot->panel->w();
+    height = fd_nj_plot->panel->h() * fd_nj_plot->zoomvalue;
+  }
+  svg_tree_save(fd_nj_plot, new Fl_SVG_File_Surface(width, height, out));
 }
 
 
diff --git a/trees.cxx b/trees.cxx
index ef0dd57..974a27c 100644
--- a/trees.cxx
+++ b/trees.cxx
@@ -1161,6 +1161,10 @@ void run_phyml_callback(Fl_Widget *ob, void *data)
     sprintf(input, "%s.phy_phyml_stat.txt", base_fname);
     in = fopen(input, "r");
     }
+  if (in == NULL) {
+    sprintf(input, "%s.phy_phyml_stats", base_fname);
+    in = fopen(input, "r");
+    }
   logL = 0;
   if(in != NULL) {//search tree likelihood
 	  while(TRUE) {
@@ -1174,6 +1178,10 @@ void run_phyml_callback(Fl_Widget *ob, void *data)
 	  }
   sprintf(input, "%s.phy_phyml_tree.txt", base_fname);
   in = fopen(input, "r");
+  if (in == NULL) {
+    sprintf(input, "%s.phy_phyml_tree", base_fname);
+    in = fopen(input, "r");
+    }
   if( status != 0 || in == NULL ) {
 	  if(in != NULL) fclose(in);
 	  if (is_view_valid(view)) fl_message("%s: tree building cancelled", extract_filename(view->masename));
@@ -1196,6 +1204,10 @@ void run_phyml_callback(Fl_Widget *ob, void *data)
     if (replicates > 0 && b_keep_trees->value()) {
       sprintf(input, "%s.phy_phyml_boot_trees.txt", base_fname);
       in = fopen(input, "r");
+      if (!in) {
+      	sprintf(input, "%s.phy_phyml_boot_trees", base_fname);
+      	in = fopen(input, "r");
+      }
       if (in) {
         FILE *out = NULL;
         sprintf(input, "%s.phy_phyml_boot_trees_truename.txt", base_fname);

-- 
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