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This queue is for tickets about the bioperl CPAN distribution.

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The Basics
Id: 12802
Status: resolved
Priority: 0/
Queue: bioperl

People
Owner: Nobody in particular
Requestors: SAPER [...] cpan.org
Cc:
AdminCc:

Bug Information
Severity: Unimportant
Broken in: (no value)
Fixed in: (no value)



Subject: Documentation patch
Download (untitled) / with headers
text/plain 161b
Hello, Here is a documentation patch that corrects the module names as they appear in the documentation, because there were a few inconsistenties. Regards
Download bioperl-1.4.patch
text/x-diff 5.4k
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
Applied, courtesy of Chris Fields


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