| Subject: | Documentation patch |
Hello,
Here is a documentation patch that corrects the module names
as they appear in the documentation, because there were a few
inconsistenties.
Regards
diff -Naur bioperl-1.4/Bio/Graphics/Glyph/arrow.pm bioperl-1.4-new/Bio/Graphics/Glyph/arrow.pm
--- bioperl-1.4/Bio/Graphics/Glyph/arrow.pm 2003-10-17 01:14:24.000000000 +0200
+++ bioperl-1.4-new/Bio/Graphics/Glyph/arrow.pm 2005-05-15 11:57:52.639391339 +0200
@@ -229,11 +229,11 @@
=head1 NAME
-Ace::Graphics::Glyph::arrow - The "arrow" glyph
+Bio::Graphics::Glyph::arrow - The "arrow" glyph
=head1 SYNOPSIS
- See L<Ace::Graphics::Panel> and L<Ace::Graphics::Glyph>.
+ See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
diff -Naur bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm bioperl-1.4-new/Bio/Graphics/Glyph/redgreen_segment.pm
--- bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm 2003-06-04 10:36:40.000000000 +0200
+++ bioperl-1.4-new/Bio/Graphics/Glyph/redgreen_segment.pm 2005-05-15 11:59:34.976348187 +0200
@@ -74,7 +74,7 @@
=head1 NAME
-Bio::Graphics::Glyph::redgreen_segments - The "redgreen_segments" glyph
+Bio::Graphics::Glyph::redgreen_segment - The "redgreen_segments" glyph
=head1 SYNOPSIS
diff -Naur bioperl-1.4/Bio/IdCollectionI.pm bioperl-1.4-new/Bio/IdCollectionI.pm
--- bioperl-1.4/Bio/IdCollectionI.pm 2002-10-22 09:38:24.000000000 +0200
+++ bioperl-1.4-new/Bio/IdCollectionI.pm 2005-05-15 12:01:04.829262057 +0200
@@ -7,7 +7,7 @@
=head1 NAME
-Bio::IdcollectionI - interface for objects with multiple identifiers
+Bio::IdCollectionI - interface for objects with multiple identifiers
=head1 SYNOPSIS
diff -Naur bioperl-1.4/Bio/Location/SplitLocationI.pm bioperl-1.4-new/Bio/Location/SplitLocationI.pm
--- bioperl-1.4/Bio/Location/SplitLocationI.pm 2002-12-01 01:05:20.000000000 +0100
+++ bioperl-1.4-new/Bio/Location/SplitLocationI.pm 2005-05-15 12:11:24.554034588 +0200
@@ -10,7 +10,7 @@
=head1 NAME
-Bio::SplitLocationI - Abstract interface of a Location on a Sequence
+Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence
which has multiple locations (start/end points)
=head1 SYNOPSIS
@@ -21,9 +21,8 @@
my $count = 1;
# print the start/end points of the sub locations
- foreach my $location ( sort { $a->start <=> $b->start }
- @sublocs ) {
- printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
+ foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) {
+ printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
$count++;
}
diff -Naur bioperl-1.4/Bio/Matrix/Generic.pm bioperl-1.4-new/Bio/Matrix/Generic.pm
--- bioperl-1.4/Bio/Matrix/Generic.pm 2003-09-08 14:17:12.000000000 +0200
+++ bioperl-1.4-new/Bio/Matrix/Generic.pm 2005-05-15 12:02:11.560800592 +0200
@@ -12,12 +12,12 @@
=head1 NAME
-Bio::Matrix::GenericMatrix - A generic matrix implementation
+Bio::Matrix::Generic - A generic matrix implementation
=head1 SYNOPSIS
# A matrix has columns and rows
- my $matrix = new Bio::Matrix::GenericMatrix();
+ my $matrix = new Bio::Matrix::Generic();
$matrix->add_column_num(1,$column1);
$matrix->add_column_num(2,$column2);
diff -Naur bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm bioperl-1.4-new/Bio/Matrix/PSM/IO/meme.pm
--- bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm 2003-12-12 18:01:42.000000000 +0100
+++ bioperl-1.4-new/Bio/Matrix/PSM/IO/meme.pm 2005-05-15 12:04:14.711494233 +0200
@@ -3,7 +3,7 @@
=head1 NAME
-Bio::Matrix::PSM::meme - PSM meme parser implementation
+Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
=head1 SYNOPSIS
@@ -142,7 +142,7 @@
my $seq=$db->get_Seq_by_acc($id);
#Do something with the sequence
}
- where $db might be Bio::DB:GenBank object, see
+ where $db might be Bio::DB::GenBank object, see
Returns : Hash with three keys: instances, weights and lengths, which
should be self-explenatory. Each value is an array
reference. Each array element corresponds to the same
diff -Naur bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm bioperl-1.4-new/Bio/Matrix/PSM/IO/transfac.pm
--- bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm 2003-12-18 19:59:24.000000000 +0100
+++ bioperl-1.4-new/Bio/Matrix/PSM/IO/transfac.pm 2005-05-15 12:05:07.885151572 +0200
@@ -3,7 +3,7 @@
=head1 NAME
-Bio::Matrix::PSM::transfac - PSM transfac parser
+Bio::Matrix::PSM::IO::transfac - PSM transfac parser
=head1 SYNOPSIS
diff -Naur bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm bioperl-1.4-new/Bio/SeqFeature/Gene/Poly_A_site.pm
--- bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm 2002-10-22 09:45:20.000000000 +0200
+++ bioperl-1.4-new/Bio/SeqFeature/Gene/Poly_A_site.pm 2005-05-15 12:06:37.693056035 +0200
@@ -12,7 +12,7 @@
=head1 NAME
-Bio::SeqFeature::Gene::poly_A_site - DESCRIPTION of Object
+Bio::SeqFeature::Gene::Poly_A_site - DESCRIPTION of Object
=head1 SYNOPSIS
diff -Naur bioperl-1.4/Bio/SeqIO/genbank.pm bioperl-1.4-new/Bio/SeqIO/genbank.pm
--- bioperl-1.4/Bio/SeqIO/genbank.pm 2003-12-22 19:33:15.000000000 +0100
+++ bioperl-1.4-new/Bio/SeqIO/genbank.pm 2005-05-15 12:08:33.529875666 +0200
@@ -12,7 +12,7 @@
=head1 NAME
-Bio::SeqIO::GenBank - GenBank sequence input/output stream
+Bio::SeqIO::genbank - GenBank sequence input/output stream
=head1 SYNOPSIS
diff -Naur bioperl-1.4/Bio/SeqIO/qual.pm bioperl-1.4-new/Bio/SeqIO/qual.pm
--- bioperl-1.4/Bio/SeqIO/qual.pm 2002-12-27 20:42:32.000000000 +0100
+++ bioperl-1.4-new/Bio/SeqIO/qual.pm 2005-05-15 12:09:30.921868275 +0200
@@ -12,7 +12,7 @@
=head1 NAME
-Bio::SeqIO::Qual - .qual file input/output stream
+Bio::SeqIO::qual - .qual file input/output stream
=head1 SYNOPSIS