searhc of domains only when domains are shown!

[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 8dedcd2..651bbbc 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -32,16 +32,21 @@ import java.util.List;
 
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 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;
 
+/**
+ * Warning. Implementation of method 'compareTo' only looks at 
+ * node name. Thus, use of this class in SortedSets might lead
+ * to unexpected behavior.
+ *
+ */
 public final class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
 
     private static int               _node_count      = 0;
@@ -70,12 +75,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
     }
 
-    public void reset() {
+    public void removeConnections() {
         _parent = null;
         _link = null;
         _descendants = null;
-        _node_data = null;
-        _branch_data = null;
     }
 
     /**
@@ -105,6 +108,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     @Override
+    // this is poor, as it only compares on names!
     final public int compareTo( final PhylogenyNode o ) {
         final PhylogenyNode n = o;
         if ( ( getName() == null ) || ( n.getName() == null ) ) {
@@ -195,12 +199,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) && this_data.getSequence()
                         .isEqual( other_data.getSequence() ) );
             }
-            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
-                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
-            }
             else if ( this_data.isHasTaxonomy() && other_data.isHasTaxonomy() ) {
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) );
             }
+            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
+                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
+            }
             else if ( getName().length() > 0 ) {
                 // Node name is not empty, and equal.
                 return true;
@@ -496,6 +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;
@@ -744,13 +752,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     // ---------------------------------------------------------
-    // Iterator
-    // ---------------------------------------------------------
-    final public PhylogenyNodeIterator iterateChildNodesForward() {
-        return new ChildNodeIteratorForward( this );
-    }
-
-    // ---------------------------------------------------------
     // Basic printing
     // ---------------------------------------------------------
     /**
@@ -1059,17 +1060,13 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     @Override
     final public String toString() {
-        StringBuilder sb = new StringBuilder();
-        if ( ForesterUtil.isEmpty( getName() ) ) {
-            sb.append( getName() );
-            sb.append( " " );
-        }
+        final StringBuilder sb = new StringBuilder();
         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( " " );
             }
@@ -1083,15 +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() );
@@ -1130,26 +1131,27 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         PhylogenyNode._node_count = i;
     }
 
-    public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
+    public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException,
+            PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
                                                              final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
-            throws NHXFormatException {
+            throws NHXFormatException, PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
                                                              final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
                                                              final boolean replace_underscores )
-            throws NHXFormatException {
+            throws NHXFormatException, PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
     }
 
     private PhylogenyNode( final String nhx,
                            final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
-                           final boolean replace_underscores ) throws NHXFormatException {
+                           final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException {
         //  init();
         NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );
         setId( PhylogenyNode.getNodeCount() );