inprogress

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

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index db6804a..115e885 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -38,6 +38,7 @@ import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
+import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BranchData;
@@ -47,6 +48,8 @@ import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.SequenceRelation;
 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.ExternalForwardIterator;
 import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@ -304,6 +307,11 @@ public class Phylogeny {
         return _distance_unit;
     }
 
+    public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
+        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+        return factory.create( nhx, new NHXParser() )[ 0 ];
+    }
+
     /**
      * 
      * Warning. The order of the returned nodes is random
@@ -489,6 +497,20 @@ public class Phylogeny {
         return nodes;
     }
 
+    public List<PhylogenyNode> getNodesViaGeneName( final String seq_name ) {
+        if ( isEmpty() ) {
+            return null;
+        }
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+        for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
+                nodes.add( n );
+            }
+        }
+        return nodes;
+    }
+
     public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
         if ( isEmpty() ) {
             return null;
@@ -830,35 +852,6 @@ public class Phylogeny {
     }
 
     /**
-     * Places the root of this Phylogeny on Branch b. The new root is always
-     * placed on the middle of the branch b.
-     * 
-     */
-    public void reRoot( final PhylogenyBranch b ) {
-        final PhylogenyNode n1 = b.getFirstNode();
-        final PhylogenyNode n2 = b.getSecondNode();
-        if ( n1.isExternal() ) {
-            reRoot( n1 );
-        }
-        else if ( n2.isExternal() ) {
-            reRoot( n2 );
-        }
-        else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
-            reRoot( n2 );
-        }
-        else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
-            reRoot( n1 );
-        }
-        else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
-                && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
-            reRoot( n1 );
-        }
-        else {
-            throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
-        }
-    }
-
-    /**
      * Places the root of this Phylogeny on the parent branch PhylogenyNode n.
      * The new root is always placed on the middle of the branch.
      * <p>
@@ -1105,14 +1098,12 @@ public class Phylogeny {
     }
 
     public String toNewHampshire() {
-        return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+        return toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
     }
 
-    public String toNewHampshire( final boolean simple_nh,
-                                  final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+    public String toNewHampshire( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
         try {
-            return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
-                    .toString();
+            return new PhylogenyWriter().toNewHampshire( this, true, nh_conversion_support_style ).toString();
         }
         catch ( final IOException e ) {
             throw new Error( "this should not have happend: " + e.getMessage() );