[med-svn] r14162 - trunk/packages/phyml/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-15 00:56:08 + (Mon, 15 Jul 2013)
New Revision: 14162

Modified:
   trunk/packages/phyml/trunk/debian/changelog
   trunk/packages/phyml/trunk/debian/watch
Log:
Updated watch file to track stable versions only.


Modified: trunk/packages/phyml/trunk/debian/changelog
===
--- trunk/packages/phyml/trunk/debian/changelog 2013-07-14 16:00:51 UTC (rev 
14161)
+++ trunk/packages/phyml/trunk/debian/changelog 2013-07-15 00:56:08 UTC (rev 
14162)
@@ -1,3 +1,9 @@
+phyml (2:20110919-2) UNRELEASED; urgency=low
+
+  * Updated watch file to track stable versions only.
+
+ -- Charles Plessy   Mon, 15 Jul 2013 09:55:11 +0900
+
 phyml (2:20110919-1) unstable; urgency=low
 
   * New upstream version.

Modified: trunk/packages/phyml/trunk/debian/watch
===
--- trunk/packages/phyml/trunk/debian/watch 2013-07-14 16:00:51 UTC (rev 
14161)
+++ trunk/packages/phyml/trunk/debian/watch 2013-07-15 00:56:08 UTC (rev 
14162)
@@ -1,2 +1,4 @@
 version=3
-http://googlecode.debian.net/p/phyml/phyml[_-](20.+)\.tar\.gz
+opts=downloadurlmangle=s|^(http:)//code\.google\.com(//phyml\.googlecode\.com/)|$1$2|
 \
+http://code.google.com/p/phyml/downloads/list?can=3&q=PhyML+Sources \
+.*/phyml(?:-|\.|_|_v)(\d\S*)\.(?:tar\.xz|txz|tar\.bz2|tbz2|tar\.gz|tgz|zip|jar)


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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 660a5a94ad204d15d38e0e4488439d2b4f05b761
Author: Andrei Zavada 
Date:   Thu Jul 11 02:04:02 2013 +0300

even straighter CTypedSource (CTypedSource&& rv)

diff --git a/src/libsigfile/source.cc b/src/libsigfile/source.cc
index f5ffe73..cceb968 100644
--- a/src/libsigfile/source.cc
+++ b/src/libsigfile/source.cc
@@ -62,22 +62,8 @@ CTypedSource::
 CTypedSource (CTypedSource&& rv)
   : CHypnogram (move(rv))
 {
-   switch ( _type = rv._type ) {
-   case TType::ascii:
-   _obj = static_cast (rv._obj);
-   break;
-   case TType::edf:
-   _obj = static_cast (rv._obj);
-   break;
-
-   case TType::bin:
-   throw invalid_argument ("Source type 'bin' not yet supported");
-   case TType::unrecognised:
-   throw invalid_argument ("Unrecognised source type");
-   default:
-   throw invalid_argument ("Bad source type");
-   }
-
+   _type   = rv._type;
+   _obj= rv._obj;
rv._obj = nullptr;
 }
 

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 3603e7ef1289f9ec79a3eb415b6d141166e9498a
Author: Andrei Zavada 
Date:   Mon Jul 15 01:28:06 2013 +0300

not sure about headers in _SOURCES

diff --git a/src/common/Makefile.am b/src/common/Makefile.am
index fd78959..68a0609 100644
--- a/src/common/Makefile.am
+++ b/src/common/Makefile.am
@@ -13,7 +13,8 @@ liba_a_SOURCES := \
alg.hh \
fs.hh \
lang.hh \
-   subject_id.hh
+   subject_id.hh \
+   ../libsigfile/source-base.hh
 
 if DO_PCH
 BUILT_SOURCES := \

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit fa5e87e990d3717f9d2a3288f9ca1872d5931c43
Author: Andrei Zavada 
Date:   Sun Jul 14 00:37:32 2013 +0300

use enum class in place of bool for some args of cairo_draw_signal

diff --git a/src/aghermann/ui/libcommon.cc b/src/aghermann/ui/libcommon.cc
index 992c7a2..6ef69f0 100644
--- a/src/aghermann/ui/libcommon.cc
+++ b/src/aghermann/ui/libcommon.cc
@@ -194,8 +194,9 @@ cairo_draw_signal( cairo_t *cr, const valarray& V,
   const size_t hspan, const float hoff, const float voff, 
const float scale,
   const unsigned short decimate,
   const aghui::TDrawSignalDirection direction,
-  const bool continue_path)
+  const aghui::TDrawSignalPathOption continue_path_option)
 {
+   bool continue_path = continue_path_option == TDrawSignalPathOption::yes;
switch ( direction ) {
 
case TDrawSignalDirection::forward:
diff --git a/src/aghermann/ui/sf/d/patterns-draw.cc 
b/src/aghermann/ui/sf/d/patterns-draw.cc
index 2fa672a..8975eb1 100644
--- a/src/aghermann/ui/sf/d/patterns-draw.cc
+++ b/src/aghermann/ui/sf/d/patterns-draw.cc
@@ -108,7 +108,7 @@ draw_thing( cairo_t *cr)
  da_thing_wd, 0, zeroline, 
thing_display_scale);
aghui::cairo_draw_signal( cr, env_l, 0, env_l.size(),
  da_thing_wd, 0, zeroline, 
thing_display_scale,
- 1, 
aghui::TDrawSignalDirection::backward, true);
+ 1, 
aghui::TDrawSignalDirection::backward);
cairo_close_path( cr);
cairo_fill( cr);
cairo_stroke( cr);
@@ -178,8 +178,7 @@ draw_field( cairo_t *cr)
cr,
profile, 0, profile.size(),
da_field_wd, 0., da_field_ht/2,
-   field_display_scale,
-   1, TDrawSignalDirection::forward, true);
+   field_display_scale);
cairo_line_to( cr, da_field_wd, da_field_ht/2);
cairo_line_to( cr, 0, da_field_ht/2);
cairo_close_path( cr);
diff --git a/src/aghermann/ui/sf/montage.cc b/src/aghermann/ui/sf/montage.cc
index b45201f..22011a0 100644
--- a/src/aghermann/ui/sf/montage.cc
+++ b/src/aghermann/ui/sf/montage.cc
@@ -41,7 +41,7 @@ draw_signal( const valarray& signal,
  start - half_pad,
  end + half_pad,
  width, 0, vdisp, signal_display_scale,
- resample_signal ? max((unsigned short)1, 
(unsigned short)spp()) : 1);
+ resample_signal ? max(1u, (unsigned)spp()) : 
1);
 }
 
 
@@ -293,7 +293,9 @@ draw_page( cairo_t *cr,
aghui::cairo_draw_signal(
cr, env_l, 0, env_l.size(),
me-ma, ma, y0, 
signal_display_scale,
-   1, 
aghui::TDrawSignalDirection::backward, true);
+   1,
+   
aghui::TDrawSignalDirection::backward,
+   
aghui::TDrawSignalPathOption::yes);
cairo_close_path( cr);
cairo_fill( cr);
cairo_stroke( cr);
diff --git a/src/aghermann/ui/ui.hh b/src/aghermann/ui/ui.hh
index faeb2a9..9bcbc6c 100644
--- a/src/aghermann/ui/ui.hh
+++ b/src/aghermann/ui/ui.hh
@@ -121,7 +121,8 @@ void gtk_cell_layout_set_renderer( GtkComboBox*);
 
 
 
-enum TDrawSignalDirection { forward, backward };
+enum class TDrawSignalDirection { forward, backward };
+enum class TDrawSignalPathOption { yes, no };
 
 void
 cairo_draw_signal( cairo_t*,
@@ -130,7 +131,7 @@ cairo_draw_signal( cairo_t*,
   size_t da_wd, float hdisp, float vdisp, float display_scale,
   unsigned short decimate = 1,
   TDrawSignalDirection direction = 
TDrawSignalDirection::forward,
-  bool continue_path = false);
+  TDrawSignalPathOption continue_path = 
TDrawSignalPathOption::yes);
 void
 cairo_draw_envelope( cairo_t*,
 const valarray&,
@@ -144,7 +145,7 @@ cairo_draw_signal( cairo_t *cr,
   size_t width, double hdisp, double vdisp, float 
display_scale,
   unsigned short decimate = 1,
   TDrawSignalDirection direction = 
TDrawSignalDirection::forward,
-  bool continue_path = false)
+  TDrawSignalPathOption continue_path = 
TDrawSignalPathOption::ye

[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit daf52011238f1e95e20a35283705728ab19761a0
Author: Andrei Zavada 
Date:   Sat Jul 13 01:25:28 2013 +0300

fix a cute copypasto in SExpDesignUI::figure_binsize_item()

diff --git a/src/aghermann/ui/mw/mw.cc b/src/aghermann/ui/mw/mw.cc
index 5cede6e..7ee9dd0 100644
--- a/src/aghermann/ui/mw/mw.cc
+++ b/src/aghermann/ui/mw/mw.cc
@@ -404,7 +404,7 @@ aghui::SExpDesignUI::
 figure_binsize_item()
 {
size_t i = 0;
-   while ( FFTPageSizeValues[i] < ED->fft_params.pagesize )
+   while ( FFTBinSizeValues[i] < ED->fft_params.binsize )
++i;
return i;
 }

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 4a369e5ab809b9b5da935457ba913430e205a81e
Author: Andrei Zavada 
Date:   Mon Jul 15 01:21:03 2013 +0300

remove redundant safety check in CEDFFile::put_region_smpl()

diff --git a/src/libsigfile/edf-io.cc b/src/libsigfile/edf-io.cc
index b4170c1..4147752 100644
--- a/src/libsigfile/edf-io.cc
+++ b/src/libsigfile/edf-io.cc
@@ -73,8 +73,6 @@ put_region_smpl( const int h,
 {
if ( unlikely (_status & (CSource::TStatus::bad_header | 
TStatus::bad_version)) )
throw invalid_argument("CEDFFile::put_region_(): broken 
source");
-   if ( unlikely (_mmapping == NULL) )
-   throw invalid_argument("CEDFFile::put_region_(): no data");
if ( unlikely (offset >= samplerate(h) * recording_time()) )
throw range_error("CEDFFile::put_region_(): offset beyond end 
of file");
if ( unlikely (offset + src.size() > samplerate(h) * recording_time()) 
) {

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 32dcf340bd2fd1f3eee2fdd245d3745e67a6c181
Author: Andrei Zavada 
Date:   Sun Jul 14 00:39:06 2013 +0300

CSource::put_region_smpl() are not const, obviously

diff --git a/src/libsigfile/edf-io.cc b/src/libsigfile/edf-io.cc
index 3adc071..2e369b7 100644
--- a/src/libsigfile/edf-io.cc
+++ b/src/libsigfile/edf-io.cc
@@ -69,7 +69,7 @@ int
 CEDFFile::
 put_region_smpl( const int h,
 const valarray& src,
-const size_t offset) const
+const size_t offset)
 {
if ( unlikely (_status & (TStatus::bad_header | TStatus::bad_version)) )
throw invalid_argument("CEDFFile::put_region_(): broken 
source");
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index d28164d..a223b2e 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -204,13 +204,13 @@ class CEDFFile
 
   // put signal
int
-   put_region_smpl( int, const valarray&, size_t) const;
+   put_region_smpl( int, const valarray&, size_t);
int
-   put_region_sec( const int h, const valarray& src, const float 
offset) const
+   put_region_sec( const int h, const valarray& src, const float 
offset)
{ return put_region_smpl( h, src, (size_t)(offset * 
samplerate(h))); }
 
int
-   put_signal( const int h, const valarray& src) const
+   put_signal( const int h, const valarray& src)
{ return put_region_smpl( h, src, 0); }
 
   // signal data info
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index c35bc5a..b39c513 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -386,9 +386,9 @@ class CSource {
 
   // put samples
virtual int
-   put_region_smpl( int, const valarray&, size_t) const = 0;
+   put_region_smpl( int, const valarray&, size_t) = 0;
 
-   int put_region_sec( const int h, const valarray& src, const 
float offset) const
+   int put_region_sec( const int h, const valarray& src, const 
float offset)
{ return put_region_smpl( h, src, offset * samplerate(h)); }
 
int put_signal( const int h, const valarray& src)
diff --git a/src/libsigfile/tsv.cc b/src/libsigfile/tsv.cc
index f6139ed..8b1ffa6 100644
--- a/src/libsigfile/tsv.cc
+++ b/src/libsigfile/tsv.cc
@@ -219,9 +219,15 @@ _read_data()
 
 int
 CTSVFile::
-put_region_smpl( int, const valarray&, size_t) const
+put_region_smpl( int h, const valarray& V, size_t off)
 {
-   
+   if ( unlikely (h > (int)channels.size() - 1) )
+   throw out_of_range ("Bad channel index");
+   if ( unlikely (off + V.size() > channels[h].data.size()) )
+   throw out_of_range ("Bad offset");
+
+   channels[h].data[ slice (off, V.size(), 1) ] = V[ slice (0, V.size(), 
1) ];
+
return 0;
 }
 
diff --git a/src/libsigfile/tsv.hh b/src/libsigfile/tsv.hh
index eda499f..779f8f7 100644
--- a/src/libsigfile/tsv.hh
+++ b/src/libsigfile/tsv.hh
@@ -217,11 +217,11 @@ class CTSVFile
{ return get_region_filtered_smpl( h, 0, 
channels.front().data.size()); }
 
   // put signal
-   int put_region_smpl( int, const valarray&, size_t) const;
-   int put_region_sec( const int h, const valarray& src, const 
float offset) const
+   int put_region_smpl( int, const valarray&, size_t);
+   int put_region_sec( const int h, const valarray& src, const 
float offset)
{ return put_region_smpl( h, src, (size_t)(offset * 
_samplerate)); }
 
-   int put_signal( const int h, const valarray& src) const
+   int put_signal( const int h, const valarray& src)
{ return put_region_smpl( h, src, 0); }
 
   // signal data info

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 61c1ea3c8428674a79eee2db6b3edf18181017cd
Author: Andrei Zavada 
Date:   Mon Jul 15 01:25:02 2013 +0300

remove --samplerate option from agh-profile-gen

diff --git a/src/tools/agh-profile-gen.cc b/src/tools/agh-profile-gen.cc
index 2f7fb89..58e6144 100644
--- a/src/tools/agh-profile-gen.cc
+++ b/src/tools/agh-profile-gen.cc
@@ -49,7 +49,6 @@ enum TOptChar : char {
o_profile= 't',
o_page   = 'p',
o_step   = 'i',
-   o_samplearte = 's',
o_psd_params = 'P',
o_mc_params  = 'M',
o_swu_params = 'S',
@@ -61,7 +60,6 @@ static struct argp_option options[] = {
{"profile", o_profile,"pms",0, 
"profile(s) to generate (p=PSD, m=MC, s=SWU)"},
{"page",o_page,   "PAGESIZE",   
0, "page size (sec)"},
{"step",o_step,   "STEP",   
0, "step (sec)" },
-   {"samplerate",  o_samplearte, "SAMPLERATE", 0, 
"samplerate (1/sec)" },
{"psd-params",  o_psd_params, "BINSIZE",0, 
"PSD: binsize (sec, one of .1, .25, .5)" },
{"mc-params",   o_mc_params,  
"SCOPE:F0FC:BANDWIDTH:IIR_BACKPOLATE:GAIN:SMOOTH",
0, "MC 
parameters"  },
@@ -95,8 +93,6 @@ struct SArguments {
metrics::mc ::SPPack mc_pp;
metrics::swu::SPPack swu_pp;
 
-   size_t  samplerate;
-
SArguments()
  : h (-1),
pagesize (NAN),
@@ -128,10 +124,6 @@ parse_opt( int key, char *arg, struct argp_state *state)
Q.step = atof( arg);
break;
 
-   case TOptChar::o_samplearte:
-   Q.samplerate = atof( arg);
-   break;
-
case TOptChar::o_channel:
Q.h = atoi( arg);
break;

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 13769576d9715c5985d186783f577b7beaf96292
Author: Andrei Zavada 
Date:   Mon Jul 15 01:26:46 2013 +0300

this is not going to be 1.0 yet

diff --git a/configure.ac b/configure.ac
index e2cce79..571b67d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,6 +1,6 @@
 AC_COPYRIGHT([Copyright (c) 2008-13 Andrei Zavada ])
 
-AC_INIT([Aghermann], [1.0_rc], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [0.9.1], [johnhom...@gmail.com])
 AC_CONFIG_SRCDIR([src/aghermann/main.cc])
 AC_CONFIG_MACRO_DIR([m4])
 AC_PREREQ(2.61)
diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade
index 95da68c..5e30fe4 100644
--- a/data/mw-dialogs.glade
+++ b/data/mw-dialogs.glade
@@ -328,7 +328,7 @@
 0
 5
 15
-Aghermann 1.0_rc 

+Aghermann 0.9.1 

 johnhommer.com/academic/code/aghermann;
 True
   

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit da05a9c9b36279b5d82a3e0121bbf1199e6b323b
Author: Andrei Zavada 
Date:   Mon Jul 15 01:24:16 2013 +0300

CTSVFile now functional

diff --git a/src/libsigfile/tsv.cc b/src/libsigfile/tsv.cc
index 2c11920..c37ba07 100644
--- a/src/libsigfile/tsv.cc
+++ b/src/libsigfile/tsv.cc
@@ -72,7 +72,8 @@ CTSVFile (const string& fname_, const int flags_)
}
// channels now available
 
-   _read_data();
+   if ( _read_data() )
+   throw invalid_argument (explain_status(_status)); // _status 
set in _parse_header()
 
if ( not (flags_ & CSource::no_ancillary_files) )
load_ancillary_files();
@@ -88,12 +89,13 @@ CTSVFile (const string& fname_, const TSubtype subtype_, 
const int flags_,
  const double recording_time_)
   : CSource (fname_, flags_),
_subtype (subtype_),
-   _samplerate (samplerate_)
+   _samplerate (samplerate_),
+   _line0 (nullptr)
 {
_f = fopen( fname_.c_str(), "r");
if ( !_f ) {
fprintf( stderr, "CTSVFile::CTSVFile(\"%s\"): Failed to open 
file for writing\n", fname_.c_str());
-   throw invalid_argument (explain_status(_status |= 
TStatus::sysfail));
+   throw invalid_argument (explain_status(_status |= 
CSource::TStatus::sysfail));
}
 
   // fill out some essential header fields
@@ -138,6 +140,11 @@ CTSVFile (CTSVFile&& rv)
 
_f = rv._f;
rv._f = nullptr;
+
+   _line0_mallocked_bytes = rv._line0_mallocked_bytes;
+   _line0 = rv._line0;
+   rv._line0 = nullptr;
+
 }
 
 
@@ -146,6 +153,8 @@ CTSVFile::
 {
if ( not (flags() & sigfile::CSource::no_ancillary_files) )
save_ancillary_files();
+   if ( _line0 )
+   free( (void*)_line0);
 }
 
 
@@ -156,29 +165,54 @@ int
 CTSVFile::
 _parse_header()
 {
-   size_t  n_channels;
-
   // 1. read metadata
-
regex_t RE;
-   assert (0 == regcomp( &RE, "^#\\W*(\\w+)\\W*(:|=)\\", REG_EXTENDED));
-   regmatch_t M[1+2];
-
-   size_t n = 4096;
-   char *line = (char*)malloc( n);
-   while ( getline( &line, &n, _f) > 0 ) {
-   if ( regexec( &RE, line, 1+2, M, 0) == 0 ) {
-   metadata[string (line, M[1].rm_so, M[1].rm_eo)] =
-   string (line, M[2].rm_so, M[2].rm_eo);
-   printf( "matched metadata [%s] = %s\n", string (line, 
M[1].rm_so, M[1].rm_eo).c_str(), string (line, M[2].rm_so, M[2].rm_eo).c_str());
-   } else
-   if ( line[0] != '#' )
-   break; // end of header
+   assert (0 == regcomp( &RE, 
"^#\\W*([a-zA-Z_][a-zA-Z_0-9]*)\\W*(:|=)\\W*(.+)\\W*\n", REG_EXTENDED));
+   regmatch_t M[1+1+2];
+
+   _line0_mallocked_bytes = 4096;
+   _line0 = (char*)malloc( _line0_mallocked_bytes);
+
+   while ( getline( &_line0, &_line0_mallocked_bytes, _f) != -1 ) {
+   if ( _line0[0] == '\n' )
+   continue;
+   if ( regexec( &RE, _line0, 1+1+2, M, 0) == 0 ) {
+   string  K = agh::str::trim( string (_line0, M[1].rm_so, 
(M[1].rm_eo - M[1].rm_so))),
+   V = agh::str::trim( string (_line0, M[3].rm_so, 
(M[3].rm_eo - M[3].rm_so)));
+   metadata[K] = V;
+   } else if ( _line0[0] != '#' )
+   break; // end of header
}
-   free( (void*)line);
 
   // 2. pick essential bits
-   
+   if ( metadata.find( "recording_id") == metadata.end() ) {
+   fprintf( stderr, "No session/episode in header\n");
+   _status |= (nosession | noepisode);
+   return -1;
+   }
+   _recording_id = metadata["recording_id"];
+
+   if ( metadata.find( "patient_id") == metadata.end() ) {
+   fprintf( stderr, "No patient_id in header\n");
+   _status |= (nosession | noepisode);
+   return -1;
+   }
+   _patient_id = metadata["patient_id"];
+
+   if ( metadata.find( "samplerate") == metadata.end() ||
+(_samplerate = stoi( metadata["samplerate"])) > 2048 ) {
+   fprintf( stderr, "Samplerate missing or too high in header\n");
+   _status |= bad_header;
+   return -1;
+   }
+
+   if ( metadata.find( "channels") == metadata.end() ) {
+   fprintf( stderr, "No channels in header\n");
+   _status |= bad_header;
+   return -1;
+   }
+   for ( const auto& h : agh::str::tokens( metadata["channels"], " ,;\t") )
+   channels.emplace_back( h);
 
   // 3. deal with episode and session
int parsed_with_issues;
@@ -187,7 +221,7 @@ _parse_header()
if ( parsed_with_issues )
_status |= (nosession | noepisode);
 
-   // are channels unique?
+  // 4. are c

[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit b05f5e32a291426b672722102963972b4b564d80
Author: Andrei Zavada 
Date:   Thu Jul 11 02:04:23 2013 +0300

remove debugging traces

diff --git a/src/libsigfile/source-base.cc b/src/libsigfile/source-base.cc
index b4740cb..46c58c7 100644
--- a/src/libsigfile/source-base.cc
+++ b/src/libsigfile/source-base.cc
@@ -130,7 +130,6 @@ load_ancillary_files()
 {
int retval = 0;
 
-   FAFA;
for ( int h = 0; h < (int)n_channels(); ++h ) {
auto& H = channel_by_id(h);
 
@@ -152,7 +151,6 @@ load_ancillary_files()
}
}
 
-   FAFA;
step2:
  // 2. annotations
{
@@ -184,7 +182,6 @@ load_ancillary_files()
step3:
;
}
-   FAFA;
 
   // 3. filters
{
@@ -203,7 +200,6 @@ load_ancillary_files()
}
}
 
-   FAFA;
return retval;
 }
 

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 004d57ff90777c6630da1656b2277d34c530f7cc
Author: Andrei Zavada 
Date:   Mon Jul 15 01:14:39 2013 +0300

properly rename metrics::pages() to steps(), correctly compute steps()

diff --git a/src/aghermann/ui/sf/channel.cc b/src/aghermann/ui/sf/channel.cc
index e15cd0d..154c580 100644
--- a/src/aghermann/ui/sf/channel.cc
+++ b/src/aghermann/ui/sf/channel.cc
@@ -227,7 +227,7 @@ get_psd_in_bands()
 {
crecording.psd_profile.compute();
if ( resample_power ) {
-   auto xi = vector (crecording.psd_profile.pages());
+   auto xi = vector (crecording.psd_profile.steps());
for ( size_t i = 0; i < xi.size(); ++i )
xi[i] = i;
for ( size_t b = 0; b <= psd.uppermost_band; ++b ) {
diff --git a/src/libmetrics/mc.cc b/src/libmetrics/mc.cc
index edf2031..82b3fed 100644
--- a/src/libmetrics/mc.cc
+++ b/src/libmetrics/mc.cc
@@ -75,7 +75,7 @@ int
 metrics::mc::CProfile::
 go_compute()
 {
-   _data.resize( pages() * _bins);
+   _data.resize( steps() * _bins);
auto S = _using_F().get_signal_filtered( _using_sig_no);
for ( size_t b = 0; b < bins(); ++b ) {
auto su_ss = metrics::mc::do_sssu_reduction(
@@ -87,7 +87,7 @@ go_compute()
Pp.bandwidth);
auto suss = su_ss.first - su_ss.second;  // make it positive
 
-   for ( size_t p = 0; p < pages(); ++p )
+   for ( size_t p = 0; p < steps(); ++p )
nmth_bin(p, b) =
agh::alg::value_within( suss[p], (TFloat)0., 
(TFloat)INFINITY);
}
@@ -124,12 +124,12 @@ export_tsv( const string& fname) const
 _using_F().subject().name.c_str(), _using_F().session(), 
_using_F().episode(),
 (int)strlen(asctime_)-1, asctime_,
 _using_F().channel_by_id(_using_sig_no).name(),
-pages(), Pp.pagesize, Pp.step, Pp.freq_from, Pp.freq_from + 
Pp.bandwidth * bins(), Pp.bandwidth);
+steps(), Pp.pagesize, Pp.step, Pp.freq_from, Pp.freq_from + 
Pp.bandwidth * bins(), Pp.bandwidth);
 
for ( bin = 0; bin < _bins; ++bin, bum += Pp.bandwidth )
fprintf( f, "%g%c", bum, bin+1 == _bins ? '\n' : '\t');
 
-   for ( p = 0; p < pages(); ++p ) {
+   for ( p = 0; p < steps(); ++p ) {
fprintf( f, "%zu", p);
for ( bin = 0; bin < _bins; ++bin )
fprintf( f, "\t%g", nmth_bin( p, bin));
@@ -158,9 +158,9 @@ export_tsv( size_t bin,
 _using_F().subject().name.c_str(), _using_F().session(), 
_using_F().episode(),
 (int)strlen(asctime_)-1, asctime_,
 _using_F().channel_by_id(_using_sig_no).name(),
-pages(), Pp.pagesize, Pp.step, Pp.freq_from, Pp.freq_from + 
(bin+1) * Pp.bandwidth);
+steps(), Pp.pagesize, Pp.step, Pp.freq_from, Pp.freq_from + 
(bin+1) * Pp.bandwidth);
 
-   for ( size_t p = 0; p < pages(); ++p )
+   for ( size_t p = 0; p < steps(); ++p )
fprintf( f, "%zu\t%g\n", p, nmth_bin(p, bin));
 
fclose( f);
diff --git a/src/libmetrics/page-metrics-base.cc 
b/src/libmetrics/page-metrics-base.cc
index cd2ac81..6de2003 100644
--- a/src/libmetrics/page-metrics-base.cc
+++ b/src/libmetrics/page-metrics-base.cc
@@ -50,9 +50,9 @@ samplerate() const
 
 size_t
 metrics::CProfile::
-pages() const
+steps() const
 {
-   return _using_F().recording_time() / Pp.step;
+   return (_using_F().recording_time() - Pp.pagesize) / Pp.step;
 }
 
 
@@ -187,7 +187,7 @@ mirror_back( const string& fname)
try {
if ( (fd = open( fname.c_str(), O_RDONLY)) == -1 )
throw -1;
-   _data.resize( pages() * _bins);
+   _data.resize( steps() * _bins);
if ( read( fd, &_data[0], _data.size() * sizeof(TFloat))
 != (ssize_t)(_data.size() * sizeof(TFloat)) )
throw -2;
@@ -231,7 +231,7 @@ export_tsv( const string& fname) const
for ( bin = 0; bin < _bins; ++bin )
fprintf( f, "%zu%c", bin, bin+1 == _bins ? '\n' : '\t');
 
-   for ( p = 0; p < pages(); ++p ) {
+   for ( p = 0; p < steps(); ++p ) {
fprintf( f, "%zu", p);
for ( bin = 0; bin < _bins; ++bin )
fprintf( f, "\t%g", nmth_bin( p, bin));
diff --git a/src/libmetrics/page-metrics-base.hh 
b/src/libmetrics/page-metrics-base.hh
index 0fffa3d..219ce0a 100644
--- a/src/libmetrics/page-metrics-base.hh
+++ b/src/libmetrics/page-metrics-base.hh
@@ -107,7 +107,7 @@ class CProfile {
return _bins;
}
 
-   size_t pages() const;
+   size_t steps() const; // overlapping pages
size_t samplerate() const;
 
   // accessors
@@ -136,7 +136,7 @@ class CProfile {
 

[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 8fdfabfb4a8ed8c893e186c0ad29c651fa1d876f
Author: Andrei Zavada 
Date:   Mon Jul 15 01:11:09 2013 +0300

sink some common code in libsigfile

diff --git a/src/common/subject_id.cc b/src/common/subject_id.cc
index 93518d3..cacede8 100644
--- a/src/common/subject_id.cc
+++ b/src/common/subject_id.cc
@@ -14,6 +14,7 @@
 #include 
 #include 
 #include "string.hh"
+#include "libsigfile/source-base.hh" // for CEDFFile::TStatus flags
 #include "subject_id.hh"
 
 #if HAVE_CONFIG_H && !defined(VERSION)
@@ -181,6 +182,31 @@ update_from( const SSubjectId& j)
 }
 
 
+int
+SSubjectId::
+parse_recording_id_edf_style( const string& s)
+{
+   using namespace agh::str;
+   int_least32_t status = 0;
+   auto subfields = tokens( s, " ");
+   if ( subfields.size() < 4 ) {
+   id = subfields.front();
+   status |= sigfile::CSource::nonconforming_patient_id;
+   } else {
+   if ( subfields.size() > 4 )
+   status |= sigfile::CSource::extra_patientid_subfields;
+   auto i = subfields.begin();
+   id = *i++;
+   gender = agh::SSubjectId::char_to_gender((*i++)[0]);
+   dob = agh::SSubjectId::str_to_dob(*i++);
+   name = join( tokens(*i++, "_"), " ");
+   if ( not valid() )
+   status |= sigfile::CSource::invalid_subject_details;
+   }
+   return status;
+}
+
+
 // Local Variables:
 // Mode: c++
 // indent-tabs-mode: 8
diff --git a/src/common/subject_id.hh b/src/common/subject_id.hh
index ff1442a..b9ee48e 100644
--- a/src/common/subject_id.hh
+++ b/src/common/subject_id.hh
@@ -82,7 +82,7 @@ struct SSubjectId {
}
int update_from( const SSubjectId&);
 
-   string make_recording_id() const
+   string make_recording_id_edf_style() const
{
return agh::str::sasprintf(
"%s %c %s %s",
@@ -90,6 +90,9 @@ struct SSubjectId {
name.c_str());
}
 
+   // flag bits as in CEDFFile::TStatus
+   int parse_recording_id_edf_style( const string&);
+
static char gender_sign( TGender);
static TGender char_to_gender( char);
static time_t str_to_dob( const string&);
diff --git a/src/libsigfile/edf-io.cc b/src/libsigfile/edf-io.cc
index 2e369b7..b4170c1 100644
--- a/src/libsigfile/edf-io.cc
+++ b/src/libsigfile/edf-io.cc
@@ -20,7 +20,7 @@ CEDFFile::
 get_region_original_smpl( const int h,
  const size_t sa, const size_t sz) const
 {
-   if ( unlikely (_status & (TStatus::bad_header | TStatus::bad_version)) )
+   if ( unlikely (_status & (CSource::TStatus::bad_header | 
TStatus::bad_version)) )
throw invalid_argument ("CEDFFile::get_region_original(): 
broken source");
if ( unlikely (_mmapping == NULL) )
throw invalid_argument ("CEDFFile::get_region_original(): no 
data");
@@ -71,7 +71,7 @@ put_region_smpl( const int h,
 const valarray& src,
 const size_t offset)
 {
-   if ( unlikely (_status & (TStatus::bad_header | TStatus::bad_version)) )
+   if ( unlikely (_status & (CSource::TStatus::bad_header | 
TStatus::bad_version)) )
throw invalid_argument("CEDFFile::put_region_(): broken 
source");
if ( unlikely (_mmapping == NULL) )
throw invalid_argument("CEDFFile::put_region_(): no data");
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 827c7ab..5428814 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -124,12 +124,12 @@ CEDFFile (const string& fname_, const int flags_)
struct stat stat0;
int stst = stat( fname_.c_str(), &stat0);
if ( stst == -1 )
-   throw invalid_argument (explain_status(_status |= 
TStatus::sysfail));
+   throw invalid_argument (explain_status(_status |= 
CSource::TStatus::sysfail));
_fsize = stat0.st_size;
}
_fd = open( fname_.c_str(), O_RDWR);
if ( _fd == -1 )
-   throw invalid_argument (explain_status(_status |= 
TStatus::sysfail));
+   throw invalid_argument (explain_status(_status |= sysfail));
 
   // mmap
_mmapping =
@@ -195,7 +195,7 @@ CEDFFile (const string& fname_, const TSubtype subtype_, 
const int flags_,
 {
_fd = open( fname_.c_str(), O_RDWR | O_CREAT | O_TRUNC, S_IRUSR | 
S_IWUSR | S_IRGRP);
if ( _fd == -1 )
-   throw invalid_argument (explain_status(_status |= 
TStatus::sysfail));
+   throw invalid_argument (explain_status(_status |= 
CSource::TStatus::sysfail));
 
header_length = 256 + (channels_.size() * 256);
size_t total_samplerate = 0;
@@ -205,7 +205,7 @@ CEDFFile (const string& fname_, const TSubtype sub

[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 5c4c5dff91f1163c4aa30d2a160dcb483f85bf2b
Author: Andrei Zavada 
Date:   Mon Jul 15 01:16:51 2013 +0300

CSource::get_signal_* sz arg means 'last sample', so size()-1

diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index 04f0358..cbf1d9c 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -195,12 +195,12 @@ class CEDFFile
valarray
get_signal_original( const int h) const // there is a 
CSource::get_signal_original already, but this one is a little better
{ return get_region_original_smpl(
-   h, 0, n_data_records * 
operator[](h).samples_per_record); }
+   h, 0, n_data_records * 
operator[](h).samples_per_record - 1); }
 
valarray
get_signal_filtered( const int h) const
{ return get_region_filtered_smpl(
-   h, 0, n_data_records * 
operator[](h).samples_per_record); }
+   h, 0, n_data_records * 
operator[](h).samples_per_record - 1); }
 
   // put signal
int
diff --git a/src/libsigfile/tsv.hh b/src/libsigfile/tsv.hh
index 528639a..a80edb6 100644
--- a/src/libsigfile/tsv.hh
+++ b/src/libsigfile/tsv.hh
@@ -210,11 +210,11 @@ class CTSVFile
 
valarray
get_signal_original( const int h) const // there is a 
CSource::get_signal_original already, but this one is a little better
-   { return get_region_original_smpl( h, 0, 
channels.front().data.size()); }
+   { return get_region_original_smpl( h, 0, 
channels.front().data.size()-1); }
 
valarray
get_signal_filtered( const int h) const
-   { return get_region_filtered_smpl( h, 0, 
channels.front().data.size()); }
+   { return get_region_filtered_smpl( h, 0, 
channels.front().data.size()-1); }
 
   // put signal
int put_region_smpl( int, const valarray&, size_t);

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 57ef2b2bd30d889c7b632bb0d5584b846d3100eb
Author: Andrei Zavada 
Date:   Tue Jul 9 09:30:14 2013 +0300

WIP

diff --git a/src/libsigfile/edf-io.cc b/src/libsigfile/edf-io.cc
index d88f239..3adc071 100644
--- a/src/libsigfile/edf-io.cc
+++ b/src/libsigfile/edf-io.cc
@@ -116,40 +116,6 @@ put_region_smpl( const int h,
 
 
 
-
-int
-CEDFFile::
-export_original( const int h,
-const string& fname) const
-{
-   valarray signal = get_signal_original( h);
-   FILE *fd = fopen( fname.c_str(), "w");
-   if ( fd ) {
-   for ( size_t i = 0; i < signal.size(); ++i )
-   fprintf( fd, "%g\n", signal[i]);
-   fclose( fd);
-   return 0;
-   } else
-   return -1;
-}
-
-
-int
-CEDFFile::
-export_filtered( const int h,
-const string& fname) const
-{
-   valarray signal = get_signal_filtered( h);
-   FILE *fd = fopen( fname.c_str(), "w");
-   if ( fd ) {
-   for ( size_t i = 0; i < signal.size(); ++i )
-   fprintf( fd, "%g\n", signal[i]);
-   fclose( fd);
-   return 0;
-   } else
-   return -1;
-}
-
 // Local Variables:
 // Mode: c++
 // indent-tabs-mode: 8
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index 589bd72..d28164d 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -245,14 +245,6 @@ class CEDFFile
resize_records( size_t new_records);
// unused, undefined
 
-  // export
-   int export_original( int h, const string& fname) const;
-   int export_filtered( int h, const string& fname) const;
-
-   int export_original_( int h, const string& fname) const;
-   int export_filtered_( int h, const string& fname) const;
-
-
   // reporting & misc
string details( int which) const;
 
diff --git a/src/libsigfile/source-base.cc b/src/libsigfile/source-base.cc
index b826290..b4740cb 100644
--- a/src/libsigfile/source-base.cc
+++ b/src/libsigfile/source-base.cc
@@ -130,6 +130,7 @@ load_ancillary_files()
 {
int retval = 0;
 
+   FAFA;
for ( int h = 0; h < (int)n_channels(); ++h ) {
auto& H = channel_by_id(h);
 
@@ -151,6 +152,7 @@ load_ancillary_files()
}
}
 
+   FAFA;
step2:
  // 2. annotations
{
@@ -182,6 +184,7 @@ load_ancillary_files()
step3:
;
}
+   FAFA;
 
   // 3. filters
{
@@ -200,6 +203,7 @@ load_ancillary_files()
}
}
 
+   FAFA;
return retval;
 }
 
@@ -429,6 +433,40 @@ get_region_filtered_smpl( const int h,
 
 
 
+int
+CSource::
+export_original( const int h,
+const string& fname) const
+{
+   valarray signal = get_signal_original( h);
+   FILE *fd = fopen( fname.c_str(), "w");
+   if ( fd ) {
+   for ( size_t i = 0; i < signal.size(); ++i )
+   fprintf( fd, "%g\n", signal[i]);
+   fclose( fd);
+   return 0;
+   } else
+   return -1;
+}
+
+
+int
+CSource::
+export_filtered( const int h,
+const string& fname) const
+{
+   valarray signal = get_signal_filtered( h);
+   FILE *fd = fopen( fname.c_str(), "w");
+   if ( fd ) {
+   for ( size_t i = 0; i < signal.size(); ++i )
+   fprintf( fd, "%g\n", signal[i]);
+   fclose( fd);
+   return 0;
+   } else
+   return -1;
+}
+
+
 // Local Variables:
 // Mode: c++
 // indent-tabs-mode: 8
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index 1141059..98df897 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -216,6 +216,11 @@ struct SFilterPack {
 
 class CSource {
friend class CTypedSource;
+public:
+   enum TFlags {
+   no_ancillary_files = 1<<1,
+   no_field_consistency_check = 1<<2,
+   };
 protected:
string  _filename;
 
@@ -223,10 +228,6 @@ class CSource {
void clear_status()
{ _status = 0; }
 
-   enum TFlags {
-   no_ancillary_files = 1<<1,
-   no_field_consistency_check = 1<<2,
-   };
int _flags;
 
agh::SSubjectId
@@ -401,9 +402,9 @@ class CSource {
 
   // export
virtual int
-   export_original( int, const string& fname) const = 0;
+   export_original( int, const string& fname) const;
virtual int
-   export_filtered( int, const string& fname) const = 0;
+   export_filtered( int, const string& fname) const;
 
   // filenames
string make_fname_artifacts( const SChannel& channel) const
diff --git a/src/libsigfile/tsv.cc b/src/libsigfile/tsv.cc
index 0f125e4..f6139ed 100644
--- a/src/libsigfile/t

[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 5bf60d0e92a757431cf1cef260a8cf56531ae75e
Author: Andrei Zavada 
Date:   Wed Jul 10 01:22:28 2013 +0300

think straight in CTypedSource ctor by rvalue

diff --git a/src/libsigfile/source.cc b/src/libsigfile/source.cc
index d825123..f5ffe73 100644
--- a/src/libsigfile/source.cc
+++ b/src/libsigfile/source.cc
@@ -64,10 +64,10 @@ CTypedSource (CTypedSource&& rv)
 {
switch ( _type = rv._type ) {
case TType::ascii:
-   _obj = new CTSVFile( move(*static_cast(rv._obj)));
+   _obj = static_cast (rv._obj);
break;
case TType::edf:
-   _obj = new CEDFFile( move(*static_cast(rv._obj)));
+   _obj = static_cast (rv._obj);
break;
 
case TType::bin:
@@ -78,7 +78,6 @@ CTypedSource (CTypedSource&& rv)
throw invalid_argument ("Bad source type");
}
 
-   delete rv._obj;
rv._obj = nullptr;
 }
 

-- 
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[med-svn] [SCM] aghermann branch, master, updated. 3603e7ef1289f9ec79a3eb415b6d141166e9498a

[Andrei Zavada]

The following commit has been merged in the master branch:
commit 3f722ca94c61af48b4251e5092f5874683dd2e53
Author: Andrei Zavada 
Date:   Thu Jul 11 02:03:17 2013 +0300

don't call save_ancillary_files() from CSource dtor

diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 281cb3e..827c7ab 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -370,6 +370,9 @@ CEDFFile (CEDFFile&& rv)
 CEDFFile::
 ~CEDFFile ()
 {
+   if ( not (_flags & no_ancillary_files) )
+   save_ancillary_files();
+
if ( _mmapping != (void*)-1 ) {
munmap( _mmapping, _fsize);
close( _fd);
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index 98df897..c35bc5a 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -247,8 +247,9 @@ class CSource {
CSource( CSource&&);
virtual ~CSource()
{
-   if ( not (_flags & no_ancillary_files) )
-   save_ancillary_files();
+   // if ( not (_flags & no_ancillary_files) )
+   //  save_ancillary_files();
+   /// for similar reasons, some methods will revert to 
pure when called from CSource dtor
}
 
int status()const { return _status; }

-- 
Sleep experiment manager

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[med-svn] Produse pentru sanatatea ta!

[Vox Magnum SRL]

Title: cumparaturi-ieftine-10_iulie




Versiune online | Viziteaza site




















Daca nu doriti sa primiti
ofertele noastre, un singur click este de ajuns.  Click aici pentru dezabonare.



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[med-svn] r14161 - trunk/packages/epigrass/branches/2.2.2-1/debian

[Thorsten Alteholz]

Author: alteholz
Date: 2013-07-14 16:00:51 + (Sun, 14 Jul 2013)
New Revision: 14161

Modified:
   trunk/packages/epigrass/branches/2.2.2-1/debian/changelog
Log:
line too long

Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog
===
--- trunk/packages/epigrass/branches/2.2.2-1/debian/changelog   2013-07-14 
15:46:54 UTC (rev 14160)
+++ trunk/packages/epigrass/branches/2.2.2-1/debian/changelog   2013-07-14 
16:00:51 UTC (rev 14161)
@@ -1,6 +1,6 @@
 epigrass (2.2.2-2) unstable; urgency=low
 
-  * rebuild package and remove dependency on python-sqlalchemy<0.8 (Closes: 
#715433) 
+  * rebuild and remove dependency on python-sqlalchemy<0.8 (Closes: #715433) 
 
  -- Thorsten Alteholz   Sun, 14 Jul 2013 17:00:00 +0200
 


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[med-svn] r14160 - in trunk/packages/epigrass: . branches branches/2.2.2-1 branches/2.2.2-1/debian

[Thorsten Alteholz]

Author: alteholz
Date: 2013-07-14 15:46:54 + (Sun, 14 Jul 2013)
New Revision: 14160

Added:
   trunk/packages/epigrass/branches/
   trunk/packages/epigrass/branches/2.2.2-1/
   trunk/packages/epigrass/branches/2.2.2-1/debian/
Modified:
   trunk/packages/epigrass/branches/2.2.2-1/debian/changelog
Log:
add 2.2.2-1-branch and close  #715433

Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog
===
--- trunk/packages/epigrass/trunk/debian/changelog  2013-05-16 15:15:39 UTC 
(rev 13605)
+++ trunk/packages/epigrass/branches/2.2.2-1/debian/changelog   2013-07-14 
15:46:54 UTC (rev 14160)
@@ -1,3 +1,9 @@
+epigrass (2.2.2-2) unstable; urgency=low
+
+  * rebuild package and remove dependency on python-sqlalchemy<0.8 (Closes: 
#715433) 
+
+ -- Thorsten Alteholz   Sun, 14 Jul 2013 17:00:00 +0200
+
 epigrass (2.2.2-1) unstable; urgency=low
 
   * new upstream version


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[med-svn] r14159 - trunk/packages/epigrass/tags

[Thorsten Alteholz]

Author: alteholz
Date: 2013-07-14 15:45:49 + (Sun, 14 Jul 2013)
New Revision: 14159

Added:
   trunk/packages/epigrass/tags/2.2.2-1/
Log:
add tag for 2.2.2-1


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[med-svn] r14158 - in trunk/packages/t-coffee/tags: . 9.03.r1318-1/debian 9.03.r1318-1/debian/patches

[Charles Plessy]

Author: plessy
Date: 2013-07-14 10:26:29 + (Sun, 14 Jul 2013)
New Revision: 14158

Added:
   trunk/packages/t-coffee/tags/9.03.r1318-1/
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/changelog
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/compat
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/control
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/copyright
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/patches/probconsrna.patch
Removed:
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/README.test
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/changelog
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/compat
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/control
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/copyright
   trunk/packages/t-coffee/tags/9.03.r1318-1/debian/patches/probconsrna.patch
Log:
[svn-buildpackage] Tagging t-coffee 9.03.r1318-1

Deleted: trunk/packages/t-coffee/tags/9.03.r1318-1/debian/README.test
===
--- trunk/packages/t-coffee/trunk/debian/README.test2013-07-13 07:50:35 UTC 
(rev 14148)
+++ trunk/packages/t-coffee/tags/9.03.r1318-1/debian/README.test
2013-07-14 10:26:29 UTC (rev 14158)
@@ -1,4 +0,0 @@
-T-COFFEE is tested at build time by running the Perl ‘bin/test.pl’.
-Results can be seen in the build logs at the following URL.
-
-https://buildd.debian.org/t-coffee

Deleted: trunk/packages/t-coffee/tags/9.03.r1318-1/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-13 07:50:35 UTC 
(rev 14148)
+++ trunk/packages/t-coffee/tags/9.03.r1318-1/debian/changelog  2013-07-14 
10:26:29 UTC (rev 14158)
@@ -1,178 +0,0 @@
-t-coffee (9.03.r1318-1ubuntu2) precise; urgency=low
-
-  * Rebuild for Ubuntu with new upstream
-  * Removed the -doc package as it is empty - docs are no longer in
-tarball but online:
- http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
-  * Rejigged the rules file to use DH, not CDBS 
-  * Avoid compressing files under t-coffee-examples
-  * Remove TMalign binary on clean (should avoid building it at all)
-  * Fix minor typo flagged by Lintian
-
- -- Tim Booth   Wed, 22 Aug 2012 17:33:25 +0100
-
-t-coffee (9.02.r1228-3) UNRELEASED; urgency=low
-
-  * debian/upstream: Single Reference field instead of Reference-*
-
- -- Andreas Tille   Wed, 07 Mar 2012 23:35:03 +0100
-
-t-coffee (9.02.r1228-2) unstable; urgency=low
-
-  * Recommend tm-align instead of distributing local copy
-(debian/control, debian/t-coffee.install, Closes: #661516).
-
- -- Charles Plessy   Fri, 02 Mar 2012 14:04:20 +0900
-
-t-coffee (9.02.r1228-1) unstable; urgency=low
-
-  * New upstream release (Closes: #649263).
-  * Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install)
-  * Corrected debian/rules as upstream test suite was removed.
-  * Complies with Policy 3.9.3 (debian/control, no other changes needed).
-  * Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and
-debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream.
-
- -- Charles Plessy   Mon, 27 Feb 2012 13:09:36 +0900
-
-t-coffee (8.99-1) unstable; urgency=low
-
-  * New upstream release in Debian.
-  * Converted and validated debian/copyright to DEP 5 machine-readable format.
-  * Using debhelper 8 (debian/control, debian/compat).
-  * Incremented Standards-Version to reflect conformance with Policy 3.9.2.
-(debian/control, no change needed).
-  * Corrected VCS URLs in debian/control.
-  * Run upstream tests at build time (debian/rules, debian/README.test).
-
- -- Charles Plessy   Tue, 21 Jun 2011 14:14:10 +0900
-
-t-coffee (8.99-0ubuntu1) lucid; urgency=low
-
-  * Rebuild for new upstream release.
-  * There is no changelog from upstream to read.
-
- -- Tim Booth   Sat, 29 Jan 2011 15:18:01 +
-
-t-coffee (8.97-0ubuntu2) lucid; urgency=low
-
-  * New upstream release, changed watch file and auto rebuild using uupdate
-  * Cleared out old patch - apparently unneeded or else needs total re-write
-
- -- Tim Booth   Tue, 23 Nov 2010 14:01:22 +
-
-t-coffee (8.95-1) lucid; urgency=low
-
-  * New upstream version, rebuild by Tim for Bio-Linux/Lucid
-
- -- Tim Booth   Mon, 01 Nov 2010 15:05:07 +
-
-t-coffee (8.84-1) unstable; urgency=low
-
-  * New upstream version
-
- -- Andreas Tille   Thu, 24 Jun 2010 14:46:16 +0200
-
-t-coffee (8.47-1) unstable; urgency=low
-
-  [ Charles Plessy ]
-  * Collected Upstream information in debian/upstream-metadata.yaml.
-
-  [ Andreas Tille ]
-  * New upstream version
-  * Source format 3.0 (quilt)
-  * Standards-Version: 3.8.4 (no changes needed)
-
- -- Andreas Tille   Fri, 09 Apr 2010 21:08:32 +0200
-
-t-coffee (8.14-1) unstable; urgency=low
-
-  * New upstream version
-
- -- Andreas Tille   Tue, 03 Nov 2009 13:56:33 +0100
-
-t-coffee (8.13-1) unstable; urgency=low
-
-  * New upstream version
-
- -- Andr

[med-svn] r14157 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 10:24:53 + (Sun, 14 Jul 2013)
New Revision: 14157

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
Log:
t-coffee (9.03.r1318-1) unstable; urgency=low

  * New upstream release.

  [ Tim Booth ]
  * Removed the -doc package as it is empty (Closes: #688630).
docs are no longer in tarball but online:
 http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
  * Rejigged the rules file to use DH, not CDBS 
  * Avoid compressing files under t-coffee-examples
  * Remove TMalign binary on clean (should avoid building it at all)
  * Fix minor typo flagged by Lintian

  [ Charles Plessy ]
  * Normalised debian/control with config-model-edit.
  * Normalised VCS URLs.
  * Using Debhelper 9.
  * Complies with Policy 3.9.4.

  [Andreas Tille]
  * debian/upstream: Single Reference field instead of Reference-*

 -- Charles Plessy   Sun, 14 Jul 2013 19:03:20 +0900



Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 10:02:59 UTC 
(rev 14156)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 10:24:53 UTC 
(rev 14157)
@@ -1,4 +1,4 @@
-t-coffee (9.03.r1318-1) UNRELEASED; urgency=low
+t-coffee (9.03.r1318-1) unstable; urgency=low
 
   * New upstream release.
 
@@ -20,7 +20,7 @@
   [Andreas Tille]
   * debian/upstream: Single Reference field instead of Reference-*
 
- -- Charles Plessy   Sun, 14 Jul 2013 18:46:44 +0900
+ -- Charles Plessy   Sun, 14 Jul 2013 19:03:20 +0900
 
 t-coffee (9.02.r1228-2) unstable; urgency=low
 


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[med-svn] r14156 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 10:02:59 + (Sun, 14 Jul 2013)
New Revision: 14156

Removed:
   trunk/packages/t-coffee/trunk/debian/README.test
Log:
Removed README.test as no regression tests are ran anymore.


Deleted: trunk/packages/t-coffee/trunk/debian/README.test
===
--- trunk/packages/t-coffee/trunk/debian/README.test2013-07-14 09:51:32 UTC 
(rev 14155)
+++ trunk/packages/t-coffee/trunk/debian/README.test2013-07-14 10:02:59 UTC 
(rev 14156)
@@ -1,4 +0,0 @@
-T-COFFEE is tested at build time by running the Perl ‘bin/test.pl’.
-Results can be seen in the build logs at the following URL.
-
-https://buildd.debian.org/t-coffee


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[med-svn] r14155 - trunk/packages/t-coffee/trunk/debian/patches

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:51:32 + (Sun, 14 Jul 2013)
New Revision: 14155

Modified:
   trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
Log:
Added trivial header to probconsrna patch.


Modified: trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
===
--- trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch  
2013-07-14 09:47:35 UTC (rev 14154)
+++ trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch  
2013-07-14 09:51:32 UTC (rev 14155)
@@ -1,3 +1,6 @@
+Description: Debian-specific adjustment.
+ The program "probconsRNA" is called "probcons-RNA" in Debian.
+Forwarded: not-needed
 --- a/t_coffee_source/define_header.h
 +++ b/t_coffee_source/define_header.h
 @@ -592,7 +592,7 @@


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[med-svn] r14154 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:47:35 + (Sun, 14 Jul 2013)
New Revision: 14154

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
Log:
Consolidated changelog.


Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:42:41 UTC 
(rev 14153)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:47:35 UTC 
(rev 14154)
@@ -1,30 +1,26 @@
 t-coffee (9.03.r1318-1) UNRELEASED; urgency=low
 
-  * Normalised debian/control with config-model-edit.
-  * Normalised VCS URLs.
-  * Using Debhelper 9.
-  * Complies with Policy 3.9.4.
+  * New upstream release.
 
- -- Charles Plessy   Sun, 14 Jul 2013 18:03:36 +0900
-
-t-coffee (9.03.r1318-1ubuntu2) precise; urgency=low
-
-  * Rebuild for Ubuntu with new upstream
-  * Removed the -doc package as it is empty - docs are no longer in
-tarball but online:
+  [ Tim Booth ]
+  * Removed the -doc package as it is empty (Closes: #688630).
+docs are no longer in tarball but online:
  http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
   * Rejigged the rules file to use DH, not CDBS 
   * Avoid compressing files under t-coffee-examples
   * Remove TMalign binary on clean (should avoid building it at all)
   * Fix minor typo flagged by Lintian
 
- -- Tim Booth   Wed, 22 Aug 2012 17:33:25 +0100
+  [ Charles Plessy ]
+  * Normalised debian/control with config-model-edit.
+  * Normalised VCS URLs.
+  * Using Debhelper 9.
+  * Complies with Policy 3.9.4.
 
-t-coffee (9.02.r1228-3) UNRELEASED; urgency=low
-
+  [Andreas Tille]
   * debian/upstream: Single Reference field instead of Reference-*
 
- -- Andreas Tille   Wed, 07 Mar 2012 23:35:03 +0100
+ -- Charles Plessy   Sun, 14 Jul 2013 18:46:44 +0900
 
 t-coffee (9.02.r1228-2) unstable; urgency=low
 


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[med-svn] r14153 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:42:41 + (Sun, 14 Jul 2013)
New Revision: 14153

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/control
Log:
Complies with Policy 3.9.4.


Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:37:30 UTC 
(rev 14152)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:42:41 UTC 
(rev 14153)
@@ -3,6 +3,7 @@
   * Normalised debian/control with config-model-edit.
   * Normalised VCS URLs.
   * Using Debhelper 9.
+  * Complies with Policy 3.9.4.
 
  -- Charles Plessy   Sun, 14 Jul 2013 18:03:36 +0900
 

Modified: trunk/packages/t-coffee/trunk/debian/control
===
--- trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:37:30 UTC 
(rev 14152)
+++ trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:42:41 UTC 
(rev 14153)
@@ -7,7 +7,7 @@
 Priority: optional
 Build-Depends: debhelper (>= 9),
gfortran
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/t-coffee/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/t-coffee/trunk/
 Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html


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[med-svn] r14152 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:37:30 + (Sun, 14 Jul 2013)
New Revision: 14152

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/compat
   trunk/packages/t-coffee/trunk/debian/control
Log:
Using Debhelper 9.

Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:36:32 UTC 
(rev 14151)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:37:30 UTC 
(rev 14152)
@@ -2,6 +2,7 @@
 
   * Normalised debian/control with config-model-edit.
   * Normalised VCS URLs.
+  * Using Debhelper 9.
 
  -- Charles Plessy   Sun, 14 Jul 2013 18:03:36 +0900
 

Modified: trunk/packages/t-coffee/trunk/debian/compat
===
--- trunk/packages/t-coffee/trunk/debian/compat 2013-07-14 09:36:32 UTC (rev 
14151)
+++ trunk/packages/t-coffee/trunk/debian/compat 2013-07-14 09:37:30 UTC (rev 
14152)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/t-coffee/trunk/debian/control
===
--- trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:36:32 UTC 
(rev 14151)
+++ trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:37:30 UTC 
(rev 14152)
@@ -5,7 +5,7 @@
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 8),
+Build-Depends: debhelper (>= 9),
gfortran
 Standards-Version: 3.9.3
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/t-coffee/trunk/


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[med-svn] r14151 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:36:32 + (Sun, 14 Jul 2013)
New Revision: 14151

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/control
Log:
Normalised VCS URLs.

Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:34:26 UTC 
(rev 14150)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:36:32 UTC 
(rev 14151)
@@ -1,6 +1,7 @@
 t-coffee (9.03.r1318-1) UNRELEASED; urgency=low
 
   * Normalised debian/control with config-model-edit.
+  * Normalised VCS URLs.
 
  -- Charles Plessy   Sun, 14 Jul 2013 18:03:36 +0900
 

Modified: trunk/packages/t-coffee/trunk/debian/control
===
--- trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:34:26 UTC 
(rev 14150)
+++ trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:36:32 UTC 
(rev 14151)
@@ -8,8 +8,8 @@
 Build-Depends: debhelper (>= 8),
gfortran
 Standards-Version: 3.9.3
-Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/
+Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/t-coffee/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/t-coffee/trunk/
 Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
 
 Package: t-coffee


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[med-svn] r14150 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:34:26 + (Sun, 14 Jul 2013)
New Revision: 14150

Modified:
   trunk/packages/t-coffee/trunk/debian/copyright
Log:
New upstream release (no new copyright nor license statements).


Modified: trunk/packages/t-coffee/trunk/debian/copyright
===
--- trunk/packages/t-coffee/trunk/debian/copyright  2013-07-14 09:04:18 UTC 
(rev 14149)
+++ trunk/packages/t-coffee/trunk/debian/copyright  2013-07-14 09:34:26 UTC 
(rev 14150)
@@ -1,5 +1,5 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: 
http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_9.02.r1228.tar.gz
+Source: 
http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_9.03.r1318.tar.gz
 
 Files: *
 Copyright: Centre National de la Recherche Scientifique (CNRS)


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[med-svn] r14149 - trunk/packages/t-coffee/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2013-07-14 09:04:18 + (Sun, 14 Jul 2013)
New Revision: 14149

Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/control
Log:
Normalised debian/control with config-model-edit.


Modified: trunk/packages/t-coffee/trunk/debian/changelog
===
--- trunk/packages/t-coffee/trunk/debian/changelog  2013-07-13 07:50:35 UTC 
(rev 14148)
+++ trunk/packages/t-coffee/trunk/debian/changelog  2013-07-14 09:04:18 UTC 
(rev 14149)
@@ -1,3 +1,9 @@
+t-coffee (9.03.r1318-1) UNRELEASED; urgency=low
+
+  * Normalised debian/control with config-model-edit.
+
+ -- Charles Plessy   Sun, 14 Jul 2013 18:03:36 +0900
+
 t-coffee (9.03.r1318-1ubuntu2) precise; urgency=low
 
   * Rebuild for Ubuntu with new upstream

Modified: trunk/packages/t-coffee/trunk/debian/control
===
--- trunk/packages/t-coffee/trunk/debian/control2013-07-13 07:50:35 UTC 
(rev 14148)
+++ trunk/packages/t-coffee/trunk/debian/control2013-07-14 09:04:18 UTC 
(rev 14149)
@@ -1,12 +1,12 @@
 Source: t-coffee
+Maintainer: Debian Med Packaging Team 

+Uploaders: Steffen Moeller ,
+   Charles Plessy ,
+   Andreas Tille 
 Section: science
 Priority: optional
-Maintainer: Debian Med Packaging Team 

-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller ,
- Charles Plessy ,
- Andreas Tille 
-Build-Depends: debhelper (>= 8), gfortran
+Build-Depends: debhelper (>= 8),
+   gfortran
 Standards-Version: 3.9.3
 Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/
@@ -14,11 +14,23 @@
 
 Package: t-coffee
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align
-Suggests: boxshade, seaview, t-coffee-examples,
-  dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw,
-  amap-align, proda
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: libsoap-lite-perl,
+libxml-simple-perl,
+tm-align
+Suggests: boxshade,
+  seaview,
+  t-coffee-examples,
+  dialign-tx,
+  kalign,
+  mafft,
+  muscle,
+  poa,
+  probcons,
+  clustalw,
+  amap-align,
+  proda
 Description: Multiple Sequence Alignment
  T-Coffee is a multiple sequence alignment package. Given a set of
  sequences (Proteins or DNA), T-Coffee generates a multiple sequence
@@ -40,9 +52,10 @@
 
 Package: t-coffee-examples
 Architecture: all
+Depends: ${misc:Depends}
 Recommends: t-coffee
-Depends: ${misc:Depends}
 Description: annotated examples for the use of T-Coffee
  To help increasing the proficiency in the use of T-Coffee, this
  package provides examples for input sequences and their proper
  alignment.
+


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