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 c341108..a65de7c 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -33,7 +33,9 @@ import java.util.List;
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
 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;
@@ -41,9 +43,7 @@ import org.forester.util.ForesterUtil;
 
 public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
 
-    /** Value of -99.0 is used as default value. */
-    public final static double       DISTANCE_DEFAULT = -1024.0;
-    private static int               _node_count      = 0;
+    private static int               _node_count = 0;
     private byte                     _indicator;
     private int                      _id;
     private int                      _sum_ext_nodes;
@@ -413,28 +413,47 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
 
     public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
         //TODO work on me ~~
-        if ( isInternal() ) {
-            throw new UnsupportedOperationException( "attempt to get next external node of an internal node" );
+        if ( isInternal() && !isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
         }
-        else if ( isLastExternalNode() ) {
+        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.getNumberOfDescendants() == 1 ) || previous_node.isLastChildNode() ) ) {
+                && ( current_node.isCollapse() || ( current_node.getNumberOfDescendants() == 1 ) || previous_node
+                        .isLastChildNode() ) ) {
             index = current_node.getChildNodeIndex();
             previous_node = current_node;
             current_node = current_node.getParent();
         }
-        current_node = current_node.getChildNode( index + 1 );
-        while ( current_node.isInternal() ) {
+        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();
@@ -576,7 +595,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         _x = 0;
         _y = 0;
         //_node_name = "";
-        _distance_parent = PhylogenyNode.DISTANCE_DEFAULT;
+        _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
         _collapse = false;
         _link = null;
         _branch_data = null;
@@ -904,7 +923,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     // ---------------------------------------------------------
     // Writing of Nodes to Strings
     // ---------------------------------------------------------
-    final public String toNewHampshire( final boolean simple_nh, final boolean write_distance_to_parent ) {
+    final public String toNewHampshire( final boolean simple_nh,
+                                        final boolean write_distance_to_parent,
+                                        final boolean write_support_values_in_brackets ) {
         final StringBuilder sb = new StringBuilder();
         String data = "";
         if ( !ForesterUtil.isEmpty( getName() ) ) {
@@ -943,10 +964,16 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 sb.append( data );
             }
         }
-        if ( ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) && write_distance_to_parent ) {
+        if ( write_distance_to_parent && ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
             sb.append( ":" );
             sb.append( getDistanceToParent() );
         }
+        if ( write_support_values_in_brackets && !isExternal()
+                && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+            sb.append( "[" );
+            sb.append( getBranchData().getConfidence( 0 ).getValue() );
+            sb.append( "]" );
+        }
         return sb.toString();
     }
 
@@ -968,7 +995,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 sb.append( name );
             }
         }
-        if ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+        if ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
             sb.append( ":" );
             sb.append( getDistanceToParent() );
         }
@@ -1030,24 +1057,24 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
-        return new PhylogenyNode( nhx, ForesterUtil.TAXONOMY_EXTRACTION.NO, false );
+        return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction )
+                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
             throws NHXFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                             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 ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+                           final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
                            final boolean replace_underscores ) throws NHXFormatException {
         init();
         NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );