POD fixes

svn path=/bioperl-run/trunk/; revision=13426
bioperl · May 12, 2003 · d82b771 · d82b771
1 parent 6bf2c8b
commit d82b771
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Showing 12 changed files with 46 additions and 50 deletions.
diff --git a/Bio/Tools/Run/Alignment/TCoffee.pm b/Bio/Tools/Run/Alignment/TCoffee.pm
@@ -661,9 +661,6 @@ sub version {
            -profile  => profile to align to, if this is an array ref
                         will specify the first two entries as the two
                         profiles to align to each other
-       
-          
-
 
 =cut
 

diff --git a/Bio/Tools/Run/Analysis.pm b/Bio/Tools/Run/Analysis.pm
@@ -31,7 +31,7 @@ Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis t
 		          });
   # ...and after a while
   $job->result ('outseq');
-    
+
   # get all results in the same invocation (as a hash reference
   # with result names as keys) - let the module decide which
   # results are binary (images in this examples) and save those
@@ -246,6 +246,7 @@ parameter.
 
 It indicates what lower-level module to load.  Default is 'soap'.
 Other (but future) possibilities are:
+
    -access => 'novella'
    -access => 'local'
 
@@ -266,7 +267,7 @@ no default value (which usually means that this parameter is mandatory
 unless your I<-location> parameter includes also the name (but it is
 then access-dependent).
 
-=item -destroy_on_exit => '0'
+=item -destroy_on_exit =E<gt> '0'
 
 Default value is '1' which means that all Bio::Tools::Run::Analysis::Job
 objects - when being finalised - will send a request

diff --git a/Bio/Tools/Run/Analysis/soap.pm b/Bio/Tools/Run/Analysis/soap.pm
@@ -174,7 +174,7 @@ There is no default value (which usually means that this parameter is
 mandatory unless your I<-location> parameter includes also the Web
 Service name).
 
-=item -destroy_on_exit => '0'
+=item -destroy_on_exit =E<gt> '0'
 
 Default value is '1' which means that all Bio::Tools::Run::Analysis::Job
 objects - when being finalised - will send a request

diff --git a/Bio/Tools/Run/AnalysisFactory.pm b/Bio/Tools/Run/AnalysisFactory.pm
@@ -189,6 +189,7 @@ parameter.
 
 It indicates what lower-level module to load.  Default is 'soap'.
 Other (but future) possibilities are:
+
    -access => 'novella'
    -access => 'local'
 

diff --git a/Bio/Tools/Run/PiseApplication/clustalw_convert.pm b/Bio/Tools/Run/PiseApplication/clustalw_convert.pm
@@ -19,7 +19,7 @@ Bio::Tools::Run::PiseApplication::clustalw_convert
 
 
 		clustalw_convert (String)
-			
+
 
 		seqfile (Sequence)
 			Alignment to convert (-infile)
@@ -29,22 +29,18 @@ Bio::Tools::Run::PiseApplication::clustalw_convert
 			Output format (-output)
 
 		gdefile (Results)
-			
+
 
 		clufile (Results)
-			
 			pipe: readseq_ok_alig
 
 		phyfile (Results)
-			
 			pipe: readseq_ok_alig
 
 		gcgfile (Results)
-			
 			pipe: readseq_ok_alig
 
 		pirfile (Results)
-			
 			pipe: readseq_ok_alig
 
 =cut

diff --git a/Bio/Tools/Run/PiseApplication/dialign2.pm b/Bio/Tools/Run/PiseApplication/dialign2.pm
@@ -24,7 +24,7 @@ Bio::Tools::Run::PiseApplication::dialign2
 
 
 		dialign2 (String)
-			
+
 
 		sequence (Sequence)
 			Sequences
@@ -52,7 +52,7 @@ Bio::Tools::Run::PiseApplication::dialign2
 			Alignment in fasta format
 
 		ali (Results)
-			
+
 
 =cut
 

diff --git a/Bio/Tools/Run/PiseApplication/grailclnt.pm b/Bio/Tools/Run/PiseApplication/grailclnt.pm
@@ -24,7 +24,7 @@ Bio::Tools::Run::PiseApplication::grailclnt
 
 
 		grailclnt (String)
-			
+
 
 		seq (Sequence)
 			Sequence
@@ -95,19 +95,19 @@ Bio::Tools::Run::PiseApplication::grailclnt
 			Strand
 
 		rpttv_organism (String)
-			
+
 
 		start_seq (String)
-			
+
 
 		end_seq (String)
-			
+
 
 		end_request (String)
-			
+
 
 		input_file (Results)
-			
+
 
 		outfile (OutFile)
 			Result file

diff --git a/Bio/Tools/Run/PiseApplication/neighbor.pm b/Bio/Tools/Run/PiseApplication/neighbor.pm
@@ -26,7 +26,7 @@ Bio::Tools::Run::PiseApplication::neighbor
 
 
 		neighbor (String)
-			
+
 
 		distance_method (Excl)
 			Distance method
@@ -60,16 +60,16 @@ Bio::Tools::Run::PiseApplication::neighbor
 			Compute a consensus tree
 
 		consense_confirm (String)
-			
+
 
 		consense_terminal_type (String)
-			
+
 
 		consense_outfile (Results)
-			
+
 
 		consense_treefile (Results)
-			
+
 			pipe: phylip_tree
 
 		output (Paragraph)
@@ -97,26 +97,25 @@ Bio::Tools::Run::PiseApplication::neighbor
 			Matrix format
 
 		outfile (Results)
-			
+
 
 		treefile (Results)
-			
 			pipe: phylip_tree
 
 		indented_treefile (Results)
-			
+
 
 		params (Results)
-			
+
 
 		confirm (String)
-			
+
 
 		terminal_type (String)
-			
+
 
 		tmp_params (Results)
-			
+
 
 =cut
 

diff --git a/Bio/Tools/Run/PiseApplication/pdbsearch.pm b/Bio/Tools/Run/PiseApplication/pdbsearch.pm
@@ -19,7 +19,7 @@ Bio::Tools::Run::PiseApplication::pdbsearch
 
 
 		pdbsearch (String)
-			
+
 
 		query (String)
 			query (4 letters)
@@ -28,7 +28,6 @@ Bio::Tools::Run::PiseApplication::pdbsearch
 			Extracts sequence? (-i)
 
 		outfile (OutFile)
-			
 			pipe: pdbfile
 			pipe: seqfile
 

diff --git a/Bio/Tools/Run/PiseApplication/prot_nucml.pm b/Bio/Tools/Run/PiseApplication/prot_nucml.pm
@@ -5,6 +5,8 @@ Bio::Tools::Run::PiseApplication::prot_nucml
 
 =head1 SYNOPSIS
 
+  #
+
 =head1 DESCRIPTION
 
 Bio::Tools::Run::PiseApplication::prot_nucml
@@ -20,17 +22,15 @@ Bio::Tools::Run::PiseApplication::prot_nucml
 			Program
 
 		interleaved (String)
-			
+
 
 		tee (String)
-			
+
 
 		results (OutFile)
-			
 			pipe: phylip_dist
 
 		outtree (OutFile)
-			
 			pipe: phylip_tree
 
 		sequences (Sequence)
@@ -59,7 +59,8 @@ Bio::Tools::Run::PiseApplication::prot_nucml
 			Strategy or Mode
 
 		topology (InFile)
-			Topology File (if Users Tree mode or Exhaustive	      search or local Rearrangement search)
+			Topology File (if Users Tree mode or Exhaustive
+                        search or local Rearrangement search)
 
 		output (Paragraph)
 			Output Parameters

diff --git a/Bio/Tools/Run/PiseJobParser.pm b/Bio/Tools/Run/PiseJobParser.pm
@@ -7,6 +7,8 @@ Bio::Tools::Run::PiseJobParser
 
 =head1 SYNOPSIS
 
+  #
+
 =head1 DESCRIPTION
 
    Parsing of Pise XHTML output to extract results files and piping menus.

diff --git a/Bio/Tools/Run/Promoterwise.pm b/Bio/Tools/Run/Promoterwise.pm
@@ -19,7 +19,7 @@ promoterwise
   my  $factory = Bio::Tools::Run::Promoterwise->new(@params);
 
   my (@fp)= $factory->run($seq1,$seq2);
-  
+
   #each feature pair is a group of hsps
   foreach my $fp(@fp){
     print "Hit Length: ".$fp->feature1->length."\n";
@@ -43,32 +43,32 @@ promoterwise
 
 =head1 DESCRIPTION
 
-Promoterwise is an alignment algorithm that relaxes the constraint that         
-local alignments have to be co-linear. Otherwise it provides a similar      
-model to DBA, which is designed for promoter sequence alignments by Ewan Birney. 
-It is part of the wise2 package available at:
-http://www.sanger.ac.uk/software/wise2.
+Promoterwise is an alignment algorithm that relaxes the constraint
+that local alignments have to be co-linear. Otherwise it provides a
+similar model to DBA, which is designed for promoter sequence
+alignments by Ewan Birney.  It is part of the wise2 package available
+at: http://www.sanger.ac.uk/software/wise2.
 
 =head1 FEEDBACK
 
 =head2 Mailing Lists
-    irint "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";
 
 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to one
 of the Bioperl mailing lists.  Your participation is much appreciated.
 
-  bioperl-l@bioperl.org          - General discussion
-  http://bio.perl.org/MailList.html             - About the mailing lists
-d2 Reporting Bugs
+  bioperl-l@bioperl.org                       - General discussion
+  http://bio.perl.org/MailList.html           - About the mailing lists
+
+=head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
  the bugs and their resolution.  Bug reports can be submitted via
  the web:
 
   http://bugzilla.bioperl.org/
 
-=head1 AUTHOR - Shawn Hoon 
+=head1 AUTHOR - Shawn Hoon
 
 Email: shawnh@fugu-sg.org