added TODOs

svn path=/; revision=146

diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl
index c205efa9c2598a8b9fe0daa07f51de7851dff481..65b41eed0731b546d45104c551a95420d91187c2 100644 (file)
--- a/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -453,6 +453,9 @@ sub swap_genes
             # for new nodes ary
             for (@new_nodes)
             {
+                # TODO: check for new group ref to use
+                # TODO: integrate attr settings into the if..else below 
+                
                 if ($is_first_paralog) 
                 {
                     # print "first paralog...\n";
@@ -462,8 +465,12 @@ sub swap_genes
                 {
                     # print "add'l paralog...\n";
                     # SUB: generate a new DataNode hex id not already in use
+                    # update add'l nodes w/ special attributes:
+                        # decrement the Z-order
+                        # decrement CenterX and CenterY by 10px each
                 }                
-                # update new nodes w/ attributes:
+                # update all new nodes w/ attributes...
+
                 # rename TextLabel (prefix (config), suffix: -alpha or numeric, based on regex)
                 $_->setAttribute("TextLabel",
                     $configs{"LabelPrefix"} 
@@ -477,15 +484,14 @@ sub swap_genes
                 $_->insertBefore($new_comment,$_->getFirstChild); # assumes other child nodes  
                 
                 # edit <Xref Database="JGI" ID="Egrandis..." />
-                # decrement the Z-order
-                # decrement CenterX and CenterY by 10px each
-                # change box Width if needed
+                # change box Width
                 # color the box (<Graphics...Color="4488ff" />)
             }
             
+            # TODO: roll these node statments into the loop above
             # replace old node w/ new node(s); do this in place
             for (@new_nodes) {
-                # replace one
+                # replace one...
                 $pathway_node->replaceChild($_,$curr_old_gene_node);
                 # ...and add the others immediately preceding
                 #insertBefore();
@@ -500,7 +506,7 @@ sub swap_genes
     
     # [later]
     # .After PathVisio sanity check, before communication:
-    #   .remove back-ref TAIR comments
+    #   .remove added back-ref TAIR comments (just rerun w/o added <Comment>?)
     
     # [usage example]
     # my $nodes = $gpml_doc->getElementsByTagName("DataNode");