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 253c4c3..7bf60ef 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -32,7 +32,6 @@ import java.util.List;
 
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
-import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
@@ -70,39 +69,6 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
     }
 
-    public PhylogenyNode( final String nhx ) throws NHXFormatException {
-        this( nhx, ForesterUtil.TAXONOMY_EXTRACTION.NO );
-    }
-
-    public PhylogenyNode( final String nhx, final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction )
-            throws NHXFormatException {
-        init();
-        NHXParser.parseNHX( nhx, this, taxonomy_extraction, false );
-        setId( PhylogenyNode.getNodeCount() );
-        PhylogenyNode.increaseNodeCount();
-        setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
-    }
-
-    /**
-     * Constructor for PhylogenyNode.
-     * <p>
-     * 
-     * @param s
-     *            String representing one PhylogenyNode in New Hampshire (NH) or
-     *            New Hampshire X (NHX) format.
-     * @throws NHXFormatException
-     * @throws PhylogenyParserException
-     */
-    public PhylogenyNode( final String nhx,
-                          final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
-                          final boolean replace_underscores ) throws NHXFormatException {
-        init();
-        NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );
-        setId( PhylogenyNode.getNodeCount() );
-        PhylogenyNode.increaseNodeCount();
-        setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
-    }
-
     /**
      * Adds PhylogenyNode n to the list of child nodes and sets the _parent of n
      * to this.
@@ -445,6 +411,49 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         return current_node;
     }
 
+    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 ( getParent().isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
+        }
+        // This checks if last node.
+        PhylogenyNode n = this;
+        boolean last = true;
+        while ( !n.isRoot() ) {
+            if ( !n.isLastChildNode() ) {
+                last = false;
+                break;
+            }
+            n = n.getParent();
+        }
+        if ( last ) {
+            return null;
+        }
+        int index = getChildNodeIndex();
+        PhylogenyNode previous_node = this;
+        PhylogenyNode current_node = getParent();
+        while ( !current_node.isRoot()
+                && ( current_node.isCollapse() || ( current_node.getNumberOfDescendants() == 1 ) || previous_node
+                        .isLastChildNode() ) ) {
+            index = current_node.getChildNodeIndex();
+            previous_node = current_node;
+            current_node = current_node.getParent();
+        }
+        if ( index < current_node.getNumberOfDescendants() - 1 ) {
+            current_node = current_node.getChildNode( index + 1 );
+        }
+        while ( current_node.isInternal() && !current_node.isCollapse() ) {
+            current_node = current_node.getFirstChildNode();
+        }
+        return current_node;
+    }
+
     public final NodeData getNodeData() {
         if ( _node_data == null ) {
             _node_data = new NodeData();
@@ -1038,4 +1047,31 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     synchronized final static void setNodeCount( final int i ) {
         PhylogenyNode._node_count = i;
     }
+
+    public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
+        return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
+    }
+
+    public static PhylogenyNode createInstanceFromNhxString( final String nhx,
+                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
+            throws NHXFormatException {
+        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 {
+        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 {
+        init();
+        NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );
+        setId( PhylogenyNode.getNodeCount() );
+        PhylogenyNode.increaseNodeCount();
+        setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
+    }
 }