debian/changelog

+libbio-graphics-perl (2.40-5) unstable; urgency=medium
+
+  * Team upload.
+  * debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789)
+  * debian/patches/spelling: fix typos
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 23 Nov 2019 09:23:09 +0100
+
 libbio-graphics-perl (2.40-4) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -28,6 +28,8 @@ Depends: ${perl:Depends},
          ${misc:Depends},
          bioperl,
          libgd-gd2-perl
+Breaks: libbio-perl-perl (<< 1.7.3)
+Replaces: libbio-perl-perl (<< 1.7.3)
 Recommends: libbio-scf-perl,
             perl,
             libberkeleydb-perl,

debian/patches/series

 unescaped_left_brace.patch
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix a few typos
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Feature.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Feature.pm
+@@ -260,7 +260,7 @@
+            called the accession_number. For sequences from established
+            databases, the implementors should try to use the correct
+            accession number. Notice that primary_id() provides the
+-           unique id for the implemetation, allowing multiple objects
++           unique id for the implementation, allowing multiple objects
+            to have the same accession number in a particular implementation.
+ 
+            For sequences with no accession number, this method should return
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/FeatureFile.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/FeatureFile.pm
+@@ -314,7 +314,7 @@
+ 
+    -safe_world     If the -safe option is not set, and -safe_world
+                    is set to a true value, then Bio::Graphics::FeatureFile
+-                   will evalute "sub {}" options in a L<Safe::World>
++                   will evaluate "sub {}" options in a L<Safe::World>
+                    environment with minimum permissions. Subroutines
+                    will be able to access and interrogate 
+                    Bio::DB::SeqFeature objects and perform basic Perl
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/decorated_transcript.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/decorated_transcript.pm
+@@ -17,7 +17,7 @@
+ sub my_descripton {
+   return <<END;
+ This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript glyph 
+-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
++and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
+ on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes 
+ inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level 
+ in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. 
+@@ -201,7 +201,7 @@
+ 	return $feature->get_tag_values(DECORATION_TAG_NAME);
+ }
+ 
+-# allows to retrieve additional decorations via callback
++# allows one to retrieve additional decorations via callback
+ sub additional_decorations {
+ 	my $self    = shift;
+ 	my $feature = $self->feature;
+@@ -948,7 +948,7 @@
+ =head1 DESCRIPTION
+ 
+ This glyph extends the functionality of the L<Bio::Graphics::Glyph::processed_transcript> glyph 
+-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
++and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
+ on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes 
+ inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level 
+ in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. 
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/fb_shmiggle.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/fb_shmiggle.pm
+@@ -611,7 +611,7 @@
+ <br>
+ <br>
+ 
+-Setting 'subsetsnames' allows to rename subsets (very important as in most cases
++Setting 'subsetsnames' allows one to rename subsets (very important as in most cases
+ workflow names of subsets are unsutable for intelligent data display to end users).
+ If setting omitted, initial subsets names will be used for display.
+ 
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/heat_map.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/heat_map.pm
+@@ -522,7 +522,7 @@
+ white->red.
+ 
+ For the start_color and end_color options, 140 named webcolors
+-and their corresponsing RGB hex codes (listed below) are supported.
++and their corresponding RGB hex codes (listed below) are supported.
+ 
+  steelblue           	#4682B4
+  royalblue           	#041690
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/ideogram.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/ideogram.pm
+@@ -298,7 +298,7 @@
+   $self->wipe(@_);
+ 
+   # For single, unaggregated bands, make the terminal band
+-  # a bit wider to accomodate the arc
++  # a bit wider to accommodate the arc
+   if ($self->{single}) {
+     $x1 -= 5 if $state == 1;
+     $x2 += 5 if $state == 0;
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/segments.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/segments.pm
+@@ -1136,7 +1136,7 @@
+ hit() method, and both the source and the target DNA must be
+ available.  If you pass the glyph a series of
+ Bio::SeqFeature::SimilarityPair objects, then these criteria will be
+-satisified.
++satisfied.
+ 
+ Without additional help, this glyph cannot display gapped alignments
+ correctly.  To display gapped alignments, you can use the
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/trace.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/trace.pm
+@@ -733,7 +733,7 @@
+ installed).
+ 
+ Until an alignment feature is added to this glyph, the feature start and end
+-must correspond exactly with the begining and end of the called sequence.
++must correspond exactly with the beginning and end of the called sequence.
+ Meaning that even if the starting sequence is poor and doesn't match the
+ sequence, it must still be included.
+ 
+@@ -883,7 +883,7 @@
+ 
+ =head1 BUGS AND LIMITATIONS
+ 
+-See the L<DESCRIPTION> for an explaination of how to align the trace with the
++See the L<DESCRIPTION> for an explanation of how to align the trace with the
+ reference.
+ 
+ The trace looks a little off when the feature is on the negative strand of the
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Panel.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Panel.pm
+@@ -1710,7 +1710,7 @@
+   -auto_pad    If "left" or "right" keys are in use  true
+                then setting auto_pad to a true value
+                will allow the panel to adjust its
+-               width in order to accomodate the
++               width in order to accommodate the
+                length of the longest key.
+ 
+   -empty_tracks What to do when a track is empty.    suppress
+@@ -1758,7 +1758,7 @@
+                Useful when working with the
+                "image" glyph.
+ 
+-  -truetype    Render text using scaleable vector    false
++  -truetype    Render text using scalable vector    false
+                fonts rather than bitmap fonts.
+ 
+   -image_class To create output in scalable vector
+--- libbio-graphics-perl.orig/lib/Bio/Graphics/Wiggle/Loader.pm
++++ libbio-graphics-perl/lib/Bio/Graphics/Wiggle/Loader.pm
+@@ -101,7 +101,7 @@
+ 
+ =back
+ 
+-Example entended track declaration:
++Example intended track declaration:
+ 
+  track type=wiggle_0 name="example" description="20 degrees, 2 hr"  \
+        trim=stdev2 transform=logsquared