perldoc edits

svn path=/; revision=152

diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl
index c01ec1bac2213117d97262a6abb25d1f0d8dcf5b..4c8e4a1eda7f80adfe763709f6f28ec65dfddc39 100644 (file)
--- a/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -10,7 +10,7 @@ Pathway Gene Swapper
 
 =head1 DESCRIPTION
 
-Swap out one set of genes (or gene representation) for another in an 
+Swap out one set of genes (or gene representations) for another in an 
 existing PathVisio GPML file. Optionally removes literature references.
 
 If multiple replacement genes map to a single original gene,
@@ -32,7 +32,7 @@ of cards).
 
 =head1 USAGE
 
-pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -v -G -d
+pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -L -v -G -d
 
 =head1 OPTIONS
 
@@ -136,6 +136,7 @@ $Data::Dumper::Pad = "... ";
 
 # ---------------------------------------------------------------------------
 =item B<hash config($file_path)>
+Accepts a config file path.
 Reads a configuration file and sets config values.
 Returns a hash with config values set.
 =cut
@@ -355,7 +356,10 @@ sub show_input
 }
 
 # ---------------------------------------------------------------------------
-=item B<string create_unique_hex_id()>
+=item B<string create_unique_hex_id($hash_ref, $string_id_type)>
+Accepts a reference to a hash of existing hex ids and a string as 
+the "type" of ID (e.g. "Group.GraphId"). The latter is currently for 
+documentary purposes only.
 Generates a "random" 5-digit hexadecimal id, checks to see if it 
 already exists in the hex list, and if not, adds it to the list
 of hex ids already present in the GPML doc. Otherwise, generates