in progress

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyNode.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 58dd0a3..651bbbc 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -38,8 +38,6 @@ import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterUtil;
 
@@ -502,6 +500,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return getNodeData().getNodeName();
     }
 
+    final public List<PhylogenyNode> getAllDescendants() {
+        return _descendants;
+    }
+
     final public int getNumberOfDescendants() {
         if ( _descendants == null ) {
             return 0;
@@ -750,13 +752,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     // ---------------------------------------------------------
-    // Iterator
-    // ---------------------------------------------------------
-    final public PhylogenyNodeIterator iterateChildNodesForward() {
-        return new ChildNodeIteratorForward( this );
-    }
-
-    // ---------------------------------------------------------
     // Basic printing
     // ---------------------------------------------------------
     /**
@@ -1066,16 +1061,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     @Override
     final public String toString() {
         final StringBuilder sb = new StringBuilder();
-        if ( !ForesterUtil.isEmpty( getName() ) ) {
-            sb.append( getName() );
-            sb.append( " " );
-        }
         if ( getNodeData().isHasTaxonomy() ) {
             if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) {
                 sb.append( getNodeData().getTaxonomy().getScientificName() );
                 sb.append( " " );
             }
-            else if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+            else if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
                 sb.append( getNodeData().getTaxonomy().getTaxonomyCode() );
                 sb.append( " " );
             }
@@ -1089,15 +1080,19 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 sb.append( getNodeData().getSequence().getName() );
                 sb.append( " " );
             }
-            else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) {
+            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() );
+            if ( getNodeData().getSequence().getAccession() != null ) {
+                sb.append( getNodeData().getSequence().getAccession().toString() );
                 sb.append( " " );
             }
         }
+        if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) {
+            sb.append( getName() );
+            sb.append( " " );
+        }
         if ( sb.length() <= 1 ) {
             sb.append( "[" );
             sb.append( getId() );