[med-svn] [SCM] libbio-graphics-perl branch, master, updated. debian/2.33-1-11-g28d7223
Olivier Sallou
olivier.sallou at debian.org
Mon Jul 29 07:22:56 UTC 2013
The following commit has been merged in the master branch:
commit dcba51ef5f2734324b42ebc8eadece79b6cddf4b
Merge: affe3a42d70ee060615d07c3e0970c1cd69b06e6 8bbcdcf663e989da0838c17994e91f4a93252bb7
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Mon Jul 29 08:41:07 2013 +0200
fix merges
diff --combined Changes
index 1c4b45e,779759e..c7b5fc1
--- a/Changes
+++ b/Changes
@@@ -1,8 -1,28 +1,31 @@@
Revision history for Perl extension Bio::Graphics.
+ 2.37
+ - Merge fix for incorrect parsing of feature_file sections (issue #6)
+ - Added decorated_transcript glyph
+ - Added nathanweeks fix for broken heatmap glyph
+
+ 2.36
+ - Fix regression in glyph parent_feature() method so that it once again returns
+ the parent of the current feature.
+ - Remove recommended prerequisite of Bio::SCF, which is hardly used now.
+
+ 2.35
+ - Change Glyph/segments.pm to work with both variants of CIGAR strings.
+ - Workaround for broken useFontConfig() support in versions of GD prior to 2.50.
+ - Fix "gdTinyFont doesn't support height() method error in xyplot".
+
+ 2.34 Thu May 16 15:42:25 CDT 2013
+ - Fixed silent crashes when rendering with the GD::SVG class.
+
+ 2.33 Fri Feb 22 15:58:10 EST 2013
+ - Add truetype support. Enable by passing -truetype=>1 to Bio::Graphics::Panel->new()
+
+ 2.32 Mon Dec 10 05:47:45 EST 2012
+ - Clean up appearance of crossbox to avoid odd black bar in the middle.
+2.33 Fri Feb 22 15:58:10 EST 2013
+ - Add truetype support. Enable by passing -truetype=>1 to Bio::Graphics::Panel->new()
+
2.32 Mon Dec 10 05:47:45 EST 2012
- Clean up appearance of crossbox to avoid odd black bar in the middle.
diff --combined META.json
index 212de8c,e1bd058..ce1d237
--- a/META.json
+++ b/META.json
@@@ -4,7 -4,7 +4,7 @@@
"Lincoln Stein <lincoln.stein at oicr.on.ca>"
],
"dynamic_config" : 1,
- "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.110440",
+ "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.112150",
"license" : [
"perl_5"
],
@@@ -21,7 -21,6 +21,6 @@@
},
"runtime" : {
"recommends" : {
- "Bio::SCF" : "1.01",
"GD::SVG" : "0.32",
"Text::ParseWords" : "3.26"
},
@@@ -35,7 -34,7 +34,7 @@@
"provides" : {
"Bio::Graphics" : {
"file" : "lib/Bio/Graphics.pm",
- "version" : "2.33"
+ "version" : "2.37"
},
"Bio::Graphics::ConfiguratorI" : {
"file" : "lib/Bio/Graphics/ConfiguratorI.pm",
@@@ -125,6 -124,14 +124,14 @@@
"file" : "lib/Bio/Graphics/Glyph/dashed_line.pm",
"version" : 0
},
+ "Bio::Graphics::Glyph::decorated_gene" : {
+ "file" : "lib/Bio/Graphics/Glyph/decorated_gene.pm",
+ "version" : 0
+ },
+ "Bio::Graphics::Glyph::decorated_transcript" : {
+ "file" : "lib/Bio/Graphics/Glyph/decorated_transcript.pm",
+ "version" : 0
+ },
"Bio::Graphics::Glyph::diamond" : {
"file" : "lib/Bio/Graphics/Glyph/diamond.pm",
"version" : 0
@@@ -476,5 -483,5 +483,5 @@@
"http://dev.perl.org/licenses/"
]
},
- "version" : "2.33"
+ "version" : "2.37"
}
diff --combined META.yml
index eb14f35,343d703..38f04e0
--- a/META.yml
+++ b/META.yml
@@@ -6,7 -6,7 +6,7 @@@ build_requires: {
configure_requires:
Module::Build: 0.38
dynamic_config: 1
-generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.110440'
+generated_by: 'Module::Build version 0.38, CPAN::Meta::Converter version 2.112150'
license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@@ -15,7 -15,7 +15,7 @@@ name: Bio-Graphic
provides:
Bio::Graphics:
file: lib/Bio/Graphics.pm
- version: 2.33
+ version: 2.37
Bio::Graphics::ConfiguratorI:
file: lib/Bio/Graphics/ConfiguratorI.pm
version: 0
@@@ -82,6 -82,12 +82,12 @@@
Bio::Graphics::Glyph::dashed_line:
file: lib/Bio/Graphics/Glyph/dashed_line.pm
version: 0
+ Bio::Graphics::Glyph::decorated_gene:
+ file: lib/Bio/Graphics/Glyph/decorated_gene.pm
+ version: 0
+ Bio::Graphics::Glyph::decorated_transcript:
+ file: lib/Bio/Graphics/Glyph/decorated_transcript.pm
+ version: 0
Bio::Graphics::Glyph::diamond:
file: lib/Bio/Graphics/Glyph/diamond.pm
version: 0
@@@ -341,7 -347,6 +347,6 @@@
file: lib/Bio/Graphics/Wiggle/Loader.pm
version: 0
recommends:
- Bio::SCF: 1.01
GD::SVG: 0.32
Text::ParseWords: 3.26
requires:
@@@ -350,4 -355,4 +355,4 @@@
Statistics::Descriptive: 2.6
resources:
license: http://dev.perl.org/licenses/
- version: 2.33
+ version: 2.37
diff --combined lib/Bio/Graphics/Glyph.pm
index 16af62c,b6d2587..9e8739f
--- a/lib/Bio/Graphics/Glyph.pm
+++ b/lib/Bio/Graphics/Glyph.pm
@@@ -780,23 -780,9 +780,29 @@@ sub getfont
my $font = $self->option($option) || $default;
return unless $font;
++<<<<<<< HEAD
+ my $img_class = $self->image_class;
+
+ if (!UNIVERSAL::isa($font,$img_class . '::Font') && $font =~ /^(gd|sanserif)/) {
+ my $ref = {
+ gdTinyFont => $img_class->gdTinyFont(),
+ gdSmallFont => $img_class->gdSmallFont(),
+ gdMediumBoldFont => $img_class->gdMediumBoldFont(),
+ gdLargeFont => $img_class->gdLargeFont(),
+ gdGiantFont => $img_class->gdGiantFont(),
+ sanserif => $img_class->gdSmallFont(),
+ };
+
+ my $gdfont = $ref->{$font} || $ref->{gdSmallFont};
+ $self->configure($option => $gdfont);
+ return $gdfont;
+ }
+ return $font;
++=======
+ my $gdfont = $self->panel->gdfont($font);
+ $self->configure($option => $gdfont);
+ return $gdfont;
++>>>>>>> upstream/2.37
}
sub tkcolor { # "track color"
@@@ -1095,7 -1081,7 +1101,7 @@@ sub draw
my $fake_x = $x;
$fake_x-- if defined $last_x && $parts[$i]->left - $last_x == 1;
$parts[$i]->draw_highlight($gd,$fake_x,$y);
- $parts[$i]->draw($gd,$fake_x,$y,$i,scalar(@parts));
+ $parts[$i]->draw_it($gd,$fake_x,$y,$i,scalar(@parts));
$last_x = $parts[$i]->right;
}
}
diff --combined lib/Bio/Graphics/Glyph/xyplot.pm
index 99829cb,754461b..5fd03df
--- a/lib/Bio/Graphics/Glyph/xyplot.pm
+++ b/lib/Bio/Graphics/Glyph/xyplot.pm
@@@ -107,8 -107,8 +107,8 @@@ sub point_radius
sub pad_top {
my $self = shift;
my $pad = $self->Bio::Graphics::Glyph::generic::pad_top(@_);
- if ($pad < $self->font_height('gdTinyFont')+8) {
- $pad = $self->font_height('gdTinyFont')+8; # extra room for the scale
+ if ($pad < $self->font_height($self->getfont('gdTinyFont'))+8) {
+ $pad = $self->font_height($self->getfont('gdTinyFont'))+8; # extra room for the scale
}
$pad;
}
@@@ -116,8 -116,8 +116,13 @@@
sub pad_bottom {
my $self = shift;
my $pad = $self->Bio::Graphics::Glyph::generic::pad_bottom(@_);
++<<<<<<< HEAD
+ if ($pad < $self->font_height('gdTinyFont')/4) {
+ $pad = $self->font_height('gdTinyFont')/4; # extra room for the scale
++=======
+ if ($pad < $self->font_height($self->getfont('gdTinyFont'))/4) {
+ $pad = $self->font_height($self->getfont('gdTinyFont'))/4; # extra room for the scale
++>>>>>>> upstream/2.37
}
$pad;
}
diff --combined lib/Bio/Graphics/Panel.pm
index 48e5789,bab836f..8c28ba0
--- a/lib/Bio/Graphics/Panel.pm
+++ b/lib/Bio/Graphics/Panel.pm
@@@ -520,7 -520,8 +520,8 @@@ sub gd
my $gd = $existing_gd || $pkg->new($width,$height,
($self->{truecolor} && $pkg->can('isTrueColor') ? 1 : ())
);
- $self->{gd} = $gd;
+ $gd->{debug} = 0 if $gd->isa('GD::SVG::Image'); # hack
+ $self->{gd} = $gd;
if ($self->{truecolor}
&& $pkg->can('saveAlpha')) {
@@@ -535,8 -536,8 +536,13 @@@
}
$self->{translations} = \%translation_table;
++<<<<<<< HEAD
+ $self->{gd} = $gd->isa('GD::SVG') ? $gd
+ : $self->truetype ? Bio::Graphics::GDWrapper->new($gd,$self->truetype)
++=======
+ $self->{gd} = $gd->isa('GD::SVG::Image') ? $gd
+ : $self->truetype ? Bio::Graphics::GDWrapper->new($gd,$self->truetype)
++>>>>>>> upstream/2.37
: $gd;
eval {$gd->alphaBlending(0)};
@@@ -619,6 -620,26 +625,29 @@@
return $self->{gd} = $self->rotate ? $gd->copyRotate90 : $gd;
}
++<<<<<<< HEAD
++=======
+ sub gdfont {
+ my $self = shift;
+ my $font = shift;
+ my $img_class = $self->image_class;
+
+ if (!UNIVERSAL::isa($font,$img_class . '::Font') && $font =~ /^(gd|sanserif)/) {
+ my $ref = $self->{gdfonts} ||= {
+ gdTinyFont => $img_class->gdTinyFont(),
+ gdSmallFont => $img_class->gdSmallFont(),
+ gdMediumBoldFont => $img_class->gdMediumBoldFont(),
+ gdLargeFont => $img_class->gdLargeFont(),
+ gdGiantFont => $img_class->gdGiantFont(),
+ sanserif => $img_class->gdSmallFont(),
+ };
+ return $ref->{$font} || $ref->{gdSmallFont};
+ } else {
+ return $font;
+ }
+ }
+
++>>>>>>> upstream/2.37
sub string_width {
my $self = shift;
my ($font,$string) = @_;
--
Generate GD images of Bio::Seq objects.
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