From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 4 Dec 2012 22:33:17 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dfb728ba91a9112309c510d032464446cecc273e;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index a8c58ee..89184ef 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -60,7 +60,7 @@ import org.forester.archaeopteryx.tools.ProcessPool;
 import org.forester.archaeopteryx.tools.ProcessRunning;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 80a315b..e6be588 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -91,7 +91,7 @@ import org.forester.msa.MsaFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index f388e14..abbc7c7 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -27,7 +27,7 @@ package org.forester.archaeopteryx;
 
 import java.awt.Font;
 
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.NodeVisualization;
diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index 512921e..7e03ef3 100644
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -41,7 +41,7 @@ import org.forester.io.parsers.nexus.NexusConstants;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PostOrderStackObject;
diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 8c7cf82..d3095aa 100644
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -39,7 +39,7 @@ import java.util.NoSuchElementException;
 import java.util.Vector;
 
 import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Identifier;
diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index b41da60..625cf19 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -47,8 +47,11 @@ import org.forester.util.ForesterUtil;
  * to unexpected behavior.
  *
  */
-public final class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
+public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
+    public enum NH_CONVERSION_SUPPORT_VALUE_STYLE {
+        NONE, IN_SQUARE_BRACKETS, AS_INTERNAL_NODE_NAMES;
+    }
     private static int               _node_count      = 0;
     private byte                     _indicator;
     private int                      _id;
@@ -88,9 +91,8 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * @param n
      *            the PhylogenyNode to add
      */
-    @Override
-    final public void addAsChild( final PhylogenyNodeI node ) {
-        final PhylogenyNode n = ( PhylogenyNode ) node;
+    final public void addAsChild( final PhylogenyNode node ) {
+        final PhylogenyNode n = node;
         addChildNode( n );
         n.setParent( this );
     }
@@ -281,7 +283,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * @throws IllegalArgumentException
      *             if n is out of bounds
      */
-    @Override
     final public PhylogenyNode getChildNode( final int i ) {
         if ( isExternal() ) {
             throw new UnsupportedOperationException( "attempt to get the child node of an external node." );
@@ -356,7 +357,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Returns the length of the branch leading to the _parent of this
      * PhylogenyNode (double).
      */
-    @Override
     final public double getDistanceToParent() {
         return _distance_parent;
     }
@@ -487,12 +487,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * Returns the ID (int) of this PhylogenyNode.
      */
-    @Override
     final public int getId() {
         return _id;
     }
 
-    @Override
     final public String getName() {
         return getNodeData().getNodeName();
     }
@@ -860,7 +858,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Sets the length of the branch leading to the _parent of this
      * PhylogenyNode to double d.
      */
-    @Override
     final public void setDistanceToParent( final double d ) {
         _distance_parent = d;
     }
@@ -897,7 +894,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * Sets the name of this node.
      */
-    @Override
     final public void setName( final String node_name ) {
         getNodeData().setNodeName( node_name );
     }
@@ -917,7 +913,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * Sets the _parent PhylogenyNode of this PhylogenyNode to n.
      */
-    @Override
     final public void setParent( final PhylogenyNode n ) {
         _parent = n;
     }
diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNodeI.java b/forester/java/src/org/forester/phylogeny/PhylogenyNodeI.java
deleted file mode 100644
index 86863b0..0000000
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNodeI.java
+++ /dev/null
@@ -1,51 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// Copyright (C) 2000-2001 Washington University School of Medicine
-// and Howard Hughes Medical Institute
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.phylogeny;
-
-public interface PhylogenyNodeI {
-
-    public enum NH_CONVERSION_SUPPORT_VALUE_STYLE {
-        NONE, IN_SQUARE_BRACKETS, AS_INTERNAL_NODE_NAMES;
-    }
-
-    public void addAsChild( PhylogenyNodeI node );
-
-    public PhylogenyNode getChildNode( int i );
-
-    public double getDistanceToParent();
-
-    public int getId();
-
-    public String getName();
-
-    public void setDistanceToParent( double d );
-
-    public void setName( String name );
-
-    public void setParent( PhylogenyNode phylogenyNode );
-}
diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 6b3639f..6c036fd 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -69,7 +69,7 @@ import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 1ca9fe0..547d9cd 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -66,7 +66,7 @@ import org.forester.phylogeny.PhylogenyBranch;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyMethods.TAXONOMY_EXTRACTION;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;