From 9794a064aff842558c2afd65c884127f33b2fd5e Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 8 Jun 2012 17:01:13 +0000
Subject: [PATCH] phylotastic hackathon at NESCENT 120608

---
 .../src/org/forester/phylogeny/PhylogenyNode.java  |   42 +++++++++++++++++---
 forester/java/src/org/forester/sdi/GSDI.java       |   38 ++++++++++--------
 2 files changed, 58 insertions(+), 22 deletions(-)

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 71dec09..4045537 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -1051,15 +1051,45 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     @Override
     final public String toString() {
-        final StringBuilder sb = new StringBuilder();
-        if ( !ForesterUtil.isEmpty( getName() ) ) {
+        StringBuilder sb = new StringBuilder();
+        if ( ForesterUtil.isEmpty( getName() ) ) {
             sb.append( getName() );
             sb.append( " " );
         }
-        sb.append( "[" );
-        sb.append( getId() );
-        sb.append( "]" );
-        return sb.toString();
+        if ( getNodeData().isHasTaxonomy() ) {
+            if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) {
+                sb.append( getNodeData().getTaxonomy().getScientificName() );
+                sb.append( " " );
+            }
+            else if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                sb.append( getNodeData().getTaxonomy().getTaxonomyCode() );
+                sb.append( " " );
+            }
+            else if ( getNodeData().getTaxonomy().getIdentifier() != null ) {
+                sb.append( getNodeData().getTaxonomy().getIdentifier().toString() );
+                sb.append( " " );
+            }
+        }
+        if ( getNodeData().isHasSequence() ) {
+            if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getName() ) ) {
+                sb.append( getNodeData().getSequence().getName() );
+                sb.append( " " );
+            }
+            else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) {
+                sb.append( getNodeData().getSequence().getSymbol() );
+                sb.append( " " );
+            }
+            else if ( getNodeData().getSequence().getAccession() != null ) {
+                sb.append( getNodeData().getTaxonomy().getIdentifier().toString() );
+                sb.append( " " );
+            }
+        }
+        if ( sb.length() <= 1 ) {
+            sb.append( "[" );
+            sb.append( getId() );
+            sb.append( "]" );
+        }
+        return sb.toString().trim();
     }
 
     /**
diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 46453e2..bbdbb74 100644
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -274,22 +274,10 @@ public final class GSDI extends SDI {
             }
         }
         if ( _strip_gene_tree ) {
-            final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
-            for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
-                final PhylogenyNode g = iter.next();
-                if ( !g.getNodeData().isHasTaxonomy() ) {
-                    throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
-                }
-                final PhylogenyNode s = speciestree_ext_nodes.get( g.getNodeData().getTaxonomy() );
-                if ( s == null ) {
-                    // throw new IllegalArgumentException( "species " + g.getNodeData().getTaxonomy()
-                    //         + " not present in species tree" );
-                    to_delete.add( g );
-                }
-            }
-            for( final PhylogenyNode n : to_delete ) {
-                _gene_tree.deleteSubtree( n, true );
-                System.out.println( "deleted" + n );
+            stripGeneTree( speciestree_ext_nodes );
+            if ( ( _gene_tree == null ) || ( _gene_tree.getNumberOfExternalNodes() < 2 ) ) {
+                throw new IllegalArgumentException( "species tree does not contain any"
+                        + " nodes matching species in the gene tree" );
             }
         }
         // Retrieve the reference to the PhylogenyNode with a matching species.
@@ -307,6 +295,24 @@ public final class GSDI extends SDI {
         }
     }
 
+    private final void stripGeneTree( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
+        final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
+        for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode g = iter.next();
+            if ( !g.getNodeData().isHasTaxonomy() ) {
+                throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
+            }
+            final PhylogenyNode s = speciestree_ext_nodes.get( g.getNodeData().getTaxonomy() );
+            if ( s == null ) {
+                to_delete.add( g );
+            }
+        }
+        for( final PhylogenyNode n : to_delete ) {
+            _gene_tree.deleteSubtree( n, true );
+            System.out.println( "deleted node from gene tree: " + n );
+        }
+    }
+
     @Override
     public final String toString() {
         final StringBuffer sb = new StringBuffer();
-- 
1.7.10.2