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[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 da0ab5d..25b33d7 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -86,7 +86,23 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
     private PhylogenyNode( final String nhx,
                            final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
                            final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException {
-        NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false );
+        NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false, false );
+        setId( PhylogenyNode.getNodeCount() );
+        PhylogenyNode.increaseNodeCount();
+        setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!).
+    }
+    
+    private PhylogenyNode( final String nhx,
+                           final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
+                           final boolean replace_underscores,
+                           final boolean parse_extended_tags ) throws NHXFormatException, PhyloXmlDataFormatException {
+        NHXParser.parseNHX( nhx,
+                            this,
+                            taxonomy_extraction,
+                            replace_underscores,
+                            false,
+                            false,
+                            parse_extended_tags );
         setId( PhylogenyNode.getNodeCount() );
         PhylogenyNode.increaseNodeCount();
         setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!).
@@ -232,10 +248,7 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
         }
     }
 
-    final public List<PhylogenyNode> getAllDescendants() {
-        return _descendants;
-    }
-
+ 
     /**
      * Returns a List containing references to all external children of this
      * PhylogenyNode.
@@ -452,12 +465,12 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
     public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
         //TODO work on me ~~
-        if ( isInternal() && !isCollapse() ) {
-            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
-        }
         if ( isRoot() ) {
             return null;
         }
+        if ( isInternal() && !isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
+        }
         if ( getParent().isCollapse() ) {
             throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
         }
@@ -499,6 +512,10 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
         }
         return _node_data;
     }
+    
+    public final boolean isHasNodeData() {
+        return ( !( _node_data == null || _node_data.isEmpty() ) );
+    }
 
     final public int getNumberOfDescendants() {
         if ( _descendants == null ) {
@@ -597,9 +614,10 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
     /**
      * Returns whether this PhylogenyNode should be drawn as collapsed.
+     * Root can not be collapsed.
      */
     final public boolean isCollapse() {
-        return _collapse;
+        return _collapse && _parent != null;
     }
 
     /**
@@ -620,10 +638,7 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
      * @return true if this PhylogenyNode is external, false otherwise
      */
     final public boolean isExternal() {
-        if ( _descendants == null ) {
-            return true;
-        }
-        return ( getNumberOfDescendants() < 1 );
+        return ( _descendants == null ) || ( _descendants.size() == 0 );
     }
 
     final public boolean isFirstChildNode() {
@@ -768,14 +783,14 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
     }
 
     /**
-     * Inserts PhylogenyNode n at the specified position i into the list of
+     * Inserts PhylogenyNode node at the specified position i into the list of
      * child nodes. This does not allow null slots in the list of child nodes:
-     * If i is larger than the number of child nodes, n is just added to the
-     * list, not place at index i.
+     * If i is larger than the number of child nodes, node is just added to the
+     * list, not placed at index i.
      *
      * @param i
      *            the index of position where to add the child
-     * @param n
+     * @param node
      *            the PhylogenyNode to add
      */
     final public void setChildNode( final int i, final PhylogenyNode node ) {
@@ -1006,10 +1021,6 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
                 sb.append( getNodeData().getSequence().getAccession().toString() );
                 sb.append( " " );
             }
-            if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getMolecularSequence() ) ) {
-                sb.append( getNodeData().getSequence().getMolecularSequence() );
-                sb.append( " " );
-            }
         }
         if ( sb.length() <= 1 ) {
             sb.append( "[" );
@@ -1086,6 +1097,14 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
                                                                      throws NHXFormatException, PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
     }
+    
+    public static PhylogenyNode createInstanceFromNhxString( final String nhx,
+                                                             final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                             final boolean replace_underscores,
+                                                             final boolean parse_extended_tags )
+                                                                     throws NHXFormatException, PhyloXmlDataFormatException {
+        return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores, parse_extended_tags );
+    }
 
     /**
      * Returns the total number of all Nodes created so far.