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pod tweaks

svn path=/bioperl-dev/trunk/; revision=15953
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1 parent f274a41 commit 7902c1fc91543d16ce17b947ed5b66756bcf9be7 maj committed Aug 17, 2009
Showing with 26 additions and 14 deletions.
  1. +3 −4 Bio/AlignIO/nexml.pm
  2. +17 −6 Bio/NexmlIO.pm
  3. +3 −2 Bio/SeqIO/nexml.pm
  4. +3 −2 Bio/TreeIO/nexml.pm
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@@ -9,17 +9,16 @@
=head1 NAME
-Bio::AlignIO::nexml - nexml sequence input/output stream
+Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
=head1 SYNOPSIS
-Do not use this module directly. Use it via the L<Bio::AlignIO>
-class.
+Do not use this module directly. Use it via the L<Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform L<Bio::SimpleAlign> objects to and from
-nexml files.
+NeXML format. For more information on NeXML, visit L<http://www.nexml.org>.
=head1 FEEDBACK
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@@ -16,7 +16,7 @@
=head1 NAME
-Bio::NexmlIO - stream handler for nexml documents
+Bio::NexmlIO - stream handler for NeXML documents
=head1 SYNOPSIS
@@ -39,11 +39,22 @@ Bio::NexmlIO - stream handler for nexml documents
=head1 DESCRIPTION
-Bio::NexmlIO is a handler for a Nexml document. A Nexml document can represent three different data types: simple sequences, alignments, and trees. NexmlIO has four main methods next_tree, next_seq, next_aln, and write. NexmlIO returns bioperl seq, tree, and aln objects which can be manipulated then passed to the write method of a new NexmlIO instance to allow the creation of a nexml document.
-
-Each bioperl object contains all the information necessary to recreate a Bio::Phylo::Taxa object, so each time a bioperl object is converted to a biophylo object I check to see if its associated taxa has already been created (with a hash using the NexmlIO_ID and Taxa_ID to create a unique string). If not I create it; if so, I just use that taxa object to link the Bio::Phylo tree or matrix to.
-
-For more information on the Nexml format, see L<http://www.nexml.org>.
+Bio::NexmlIO is an I/O handler for a NeXML document. A NeXML document can
+represent three different data types: simple sequences, alignments,
+and trees. NexmlIO has four main methods next_tree, next_seq,
+next_aln, and write. NexmlIO returns bioperl seq, tree, and aln
+objects which can be manipulated then passed to the write method of a
+new NexmlIO instance to allow the creation of a NeXML document.
+
+Each bioperl object contains all the information necessary to recreate
+a Bio::Phylo::Taxa object, so each time a bioperl object is converted
+to a biophylo object, the bioperl object is checked to see if its
+associated taxa has already been created (against a hash using the
+NexmlIO_ID and Taxa_ID to create a unique string). If not, it is
+created; if so, that taxa object is used to link the Bio::Phylo tree
+or matrix.
+
+For more information on the NeXML format, see L<http://www.nexml.org>.
=head1 FEEDBACK
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@@ -15,15 +15,16 @@
=head1 NAME
-Bio::SeqIO::nexml - nexml sequence input/output stream
+Bio::SeqIO::nexml - NeXML sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
-This object can transform Bio::Seq objects to and from nexml xml files.
+This object can transform Bio::Seq objects to and from NeXML format.
+For more information on the NeXML standard, visit L<http://www.nexml.org>.
=head1 FEEDBACK
View
@@ -14,7 +14,7 @@
=head1 NAME
-Bio::TreeIO::nexml - A TreeIO driver module for parsing Nexml tree files
+Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files
=head1 SYNOPSIS
@@ -25,7 +25,8 @@ Bio::TreeIO::nexml - A TreeIO driver module for parsing Nexml tree files
=head1 DESCRIPTION
-This is a driver module for parsing tree data in a Nexml format.
+This is a driver module for parsing tree data in a NeXML format. For
+more information on NeXML, visit L<http://www.nexml.org>.
=head1 FEEDBACK

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