Makefile

@@ -21,7 +21,7 @@
 CONFIG ?= fltk-config
 PDF_PS_FLAGS ?= -DNO_PDF
 
-EXTRALIBS = `$(CONFIG) --use-images --ldflags` -ldl -lpthread -lz
+EXTRALIBS = `$(CONFIG) --use-images --ldflags`
 
 CC = gcc
 CXX = g++

README

-           HOW TO COMPILE SEAVIEW ON UNIX/LINUX SYSTEMS
-
-The seaview program requires the FLTK library for its graphical user interface.
-Version 1.3.0 or later of FLTK is necessary.
-
-The FLTK library is available as packages for a number of Linux distributions.
-If this package is installed on your system, go to step II.
-If no such package is available for your system, or if version 1.3.0 is not available,
-or if you don't want to use such package, you can compile the FLTK library as follows.
-
-I COMPILING THE FLTK LIBRARY FROM SOURCE
-========================================
-
-The source code of the FLTK library is available at the "Download" item of http://www.fltk.org/.
-- Get the stable release source archive, currently fltk-1.3.3-source.tar.gz
-- Compile the FLTK library on your system:
-   cd fltk-1.3.3
-   ./configure
-   make
-It's not necessary to do "make install".
-
-II COMPILING THE SEAVIEW PROGRAM
-================================
-
-First unpack the seaview source archive (seaview.tar.gz).
-
-IIa Preparing the seaview makefile
-
-If the FLTK library is installed on your system (i.e., include files in /usr/include/FL,
-and libraries at /usr/lib/libfltk*), go to step IIb.
-Otherwise, edit Makefile from the seaview source directory which contains these 5 lines:
-#to use your own, uninstalled FLTK library,
-#uncomment the next 3 lines and adapt the 1st to your local file system 
-#FLTK = $(HOME)/fltk-1.3
-#IFLTK = -I$(FLTK)
-#CONFIG = $(FLTK)/fltk-config
-
-Transform these lines into:
-#to use your own, uninstalled FLTK library,
-#uncomment the next 3 lines and adapt the 1st to your local file system 
-FLTK = $(HOME)/fltk-1.3
-IFLTK = -I$(FLTK)
-CONFIG = $(FLTK)/fltk-config
-and also change the FLTK = $(HOME)/fltk-1.3 line so it gives the location in your system
-of the top of the FLTK source tree.
-
-IIb Compile/link the seaview program
-
-In the seaview source directory, run
-make
-
-III Install seaview external programs
-=====================================
-
-Seaview drives 4 external programs (clustalo, muscle, Gblocks, phyml). Linux executables
-of these are available from the linux items of http://pbil.univ-lyon1.fr/software/seaview.html
-They are also available as packages of most Linux distributions.
-
-These programs should be put in your PATH or in the same directory as the seaview
-executable for seaview to drive them.
-
-By default seaview searches for the phyml executable under the names PhyML-3.1_linux32
-or PhyML-3.1_linux64. If they are installed under other names on your system, seaview 
-will ask you for their name and location which are remembered for subsequent runs.
-

concatenate.cxx

@@ -170,12 +170,31 @@ void do_concatenate_callback( Fl_Widget *ob, void *data)
   set_seaview_modified(target, TRUE);
 }
 
+void store_concat_part_as_region(SEA_VIEW *target, char *name, int from, int to)
+{
+  list_segments ls = {from, to, NULL};
+  list_segments *pls = new list_segments; *pls = ls;
+  region *r = new region;
+  r->name = strdup(extract_filename(name));
+  r->list = pls;
+  list_regions *list = target->regions;
+  list_regions *list2 = new list_regions;
+  list2->element = r;
+  list2->next = NULL;
+  if (list) {
+    while (list->next) list = list->next;
+    list->next = list2;
+  } else target->regions = list2;
+}
 
 void concatenate_no_gui(int argc, char *argv[])
 {
   char *err_message;
   bool std_output = false;
   SEA_VIEW *target = cmdline_read_input_alignment(argc, argv);
+  bool record_partition = isarg(argc, argv, "-record_partition");
+
+  if (record_partition) store_concat_part_as_region(target, argv[argc-1], 1, target->seq_length);
   char *all_sources = argname(argc, argv, "-concatenate");
   known_format out_format = target->format_for_save;
   
@@ -184,7 +203,9 @@ void concatenate_no_gui(int argc, char *argv[])
   bool is_by_rank = isarg(argc, argv, "-by_rank");
   while (source_name) {
     SEA_VIEW *source = cmdline_read_input_alignment(1, &source_name);
+    int old_length = target->seq_length + 1;
     concatenate(target, source, !is_by_rank, !is_by_rank, true);
+    if (record_partition) store_concat_part_as_region(target, source_name, old_length, target->seq_length);
     source_name = strtok(NULL, ",");
     }
   

debian/changelog

+seaview (1:4.6.5-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Fri, 27 Apr 2018 17:20:34 +0200
+
 seaview (1:4.6.4-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -11,9 +11,9 @@ Build-Depends: debhelper (>= 11~),
                libxext-dev,
                libxinerama-dev,
                zlib1g-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/seaview.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/seaview.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/seaview
+Vcs-Git: https://salsa.debian.org/med-team/seaview.git
 Homepage: http://doua.prabi.fr/software/seaview
 
 Package: seaview

seaview.appdata.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Copyright 2015 Manolo Gouy <manolo.gouy_at_univ-lyon1.fr> -->
-<component type="desktop">
- <id>seaview.desktop</id>
- <metadata_license>CC0-1.0</metadata_license>
- <project_license>GPL-3.0</project_license>
- <name>SeaView</name>
- <summary>GUI for multiple sequence alignment and molecular phylogeny</summary>
- <description>
-<p>SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.</p>
-<ul>
-	<li>SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP,
-	MASE, Newick) of DNA and protein sequences and of phylogenetic trees.</li>
-	<li>SeaView drives programs muscle or Clustal-Omega for multiple sequence alignment, 
-	and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.</li>
-	<li>Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.</li>
-	<li>SeaView computes phylogenetic trees by:</li>
-	<li>- parsimony, using PHYLIP's dnapars/protpars algorithm,</li>
-	<li>- distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,</li>
-	<li>- maximum likelihood, driving program PhyML 3.1.</li>
-	<li>SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.</li>
-	<li>SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.</li>
-</ul>
- </description>
- <screenshots>
-  <screenshot type="default">
-   <image>http://doua.prabi.fr/binaries/seaview4.png</image>
-   <caption>The main alignment window used in the color-by-codon mode</caption>
-  </screenshot>
-  <screenshot>
-   <image>http://doua.prabi.fr/binaries/seaview-tree.png</image>
-   <caption>The tree window with some zoom-in applied</caption>
-  </screenshot>
-  <screenshot>
-   <image>  http://doua.prabi.fr/software/seaview_data/PhyML-dialog.png</image>
-   <caption>Dialog window to perform Maximum-Likelihood tree-building</caption>
-  </screenshot>
- </screenshots>
- <url type="homepage">http://doua.prabi.fr/software/seaview</url>
- <updatecontact>manolo.gouy_at_univ-lyon1.fr</updatecontact>
- 
- <developer_name>Manolo Gouy</developer_name>
-
-  <keywords>
-  <keyword>molecular phylogeny</keyword>
-  <keyword>phylogenetic tree</keyword>
-  <keyword>sequence alignment</keyword>
-  <keyword>parsimony</keyword>
-  <keyword>neighbor-joining/keyword>
-  <keyword>maximum likelihood</keyword>
-  </keywords>
-
-</component>

seaview.cxx

@@ -310,6 +310,7 @@ int main(int argc, char *argv[])
 	    "           Use '-' as last argument to read alignment from standard input\n"
 	    "-concatenate align1,...    name(s) of alignment files to add at the end of the input alignment\n"
 	    "-by_rank      identify sequences by their rank in alignments (rather than by their name)\n"
+      "-record_partition record the locations of the concatenated pieces in the final concatenate\n"
 	    "-output_format fmt    format of the concatenated alignment (mase, phylip, clustal, msf, fasta, or nexus)\n"
 	    "-o fname      use fname as name of the concatenated alignment (default is built from input filename)\n"
 	    "-o -          write the concatenated alignment to standard output\n"
@@ -1052,7 +1053,10 @@ else if(view->draw_names == -2) { /* ecrire tous les noms mais rien qu'eux */
 	}
 else	{ /* ecrire un seul nom */
 	debut = fin = view->draw_names - 1;
-	if(debut < view->first_seq - 1) return;
+  if (debut < view->first_seq - 1) {
+    fl_pop_clip();
+    return;
+  }
 	y += view->line_height * (view->draw_names - view->first_seq);
 	if( !view->sel_seqs[view->draw_names - 1] ) {
 		fl_color(ob->color());
@@ -4047,7 +4051,7 @@ else if(view->mod_comment_line) {
 	}
 else	{
 	if(view->tot_seqs == 0) {
-#define DRAG_MESS "alignment file drag zone"
+#define DRAG_MESS "alignment/tree file drop zone"
 		fl_color(FL_WHITE);
 		fl_font(FL_TIMES_BOLD_ITALIC, 28 );
 		fl_draw(DRAG_MESS, (int)(this->x()+this->w()/2-fl_width(DRAG_MESS)/2 + 0.5), this->y()+this->h()/2);

seaview.html

@@ -44,7 +44,7 @@ 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 4.6.4
+Version 4.6.5
 
 <p>Binaries and full source code available from <a href=http://doua.prabi.fr/software/seaview>http://doua.prabi.fr/software/seaview</a>
 
@@ -844,6 +844,10 @@ or <tt>nexus</tt>). The format of the input file is the default.</td></tr>
 <tr><td><tt>-by_rank</tt></td><td>identify sequences by their rank in alignments, <i>i.e.</i>, the 1st seq. of <i>align1</i> will be added
 at the end of the 1st seq of the input file, the 2nd with the 2nd, and so on. 
 Without this option, sequences with the same name in alignment files are concatenated.</td></tr>
+
+<tr><td><tt>-record_partition</tt></td><td>  record as 'site sets' the locations of the concatenated pieces in the final concatenate</td></tr>
+
+
 <tr><td><tt>-output_format</tt> <i>fmt</i></td><td>format of the concatenated alignment file 
 (<tt>mase, phylip, clustal, msf, fasta</tt>, or <tt>nexus</tt>). Default is the format of the input alignment.</td></tr>
 <tr><td><tt>-o</tt> <i>fname</i></td><td>     use <i>fname</i> as name of the concatenated alignment