From 58eec3dbd8522a2af4e7da68311621bfc06c6534 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 2 Apr 2014 23:59:51 +0000
Subject: [PATCH] inprogress

---
 .../io/parsers/phyloxml/PhyloXmlHandler.java       |   15 ++++--
 .../forester/phylogeny/data/NodeVisualData.java    |   53 +++++++++++++++++++-
 2 files changed, 63 insertions(+), 5 deletions(-)

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
index d33cb74..4eed70c 100644
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
@@ -59,6 +59,7 @@ import org.forester.phylogeny.data.NodeVisualData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.PropertiesMap;
 import org.forester.phylogeny.data.Property;
+import org.forester.phylogeny.data.Property.AppliesTo;
 import org.forester.phylogeny.data.Reference;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.SequenceRelation;
@@ -325,11 +326,17 @@ public final class PhyloXmlHandler extends DefaultHandler {
             else if ( qualified_name.equals( PhyloXmlMapping.PROPERTY ) ) {
                 final Property prop = ( Property ) PropertyParser.getInstance().parse( element );
                 if ( prop.getRef().startsWith( NodeVisualData.APTX_VISUALIZATION_REF ) ) {
-                    if ( node.getNodeData().getNodeVisualData() == null ) {
-                        node.getNodeData().setNodeVisualData( new NodeVisualData() );
+                    if ( prop.getAppliesTo() == AppliesTo.NODE ) {
+                        if ( node.getNodeData().getNodeVisualData() == null ) {
+                            node.getNodeData().setNodeVisualData( new NodeVisualData() );
+                        }
+                        final NodeVisualData vd = node.getNodeData().getNodeVisualData();
+                        vd.parseProperty( prop );
+                    }
+                    else {
+                        System.err.println( "Do not know how to handle " + NodeVisualData.APTX_VISUALIZATION_REF
+                                + " property applied to " + prop.getAppliesTo() );
                     }
-                    final NodeVisualData vd = node.getNodeData().getNodeVisualData();
-                    vd.parseProperty( prop );
                 }
                 else {
                     if ( !node.getNodeData().isHasProperties() ) {
diff --git a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
index a2018a2..4ef6adc 100644
--- a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java
@@ -215,6 +215,43 @@ public final class NodeVisualData implements PhylogenyData {
                 return;
             }
         }
+        //
+        else if ( prop.getRef().equals( NODE_SIZE_REF ) ) {
+            int s = -1;
+            try {
+                s = Integer.parseInt( prop.getValue() );
+            }
+            catch ( final NumberFormatException e ) {
+                return;
+            }
+            if ( s >= 0 ) {
+                setSize( s );
+            }
+        }
+        else if ( prop.getRef().equals( NODE_FILL_COLOR_REF ) ) {
+            try {
+                setFillColor( Color.decode( prop.getValue() ) );
+            }
+            catch ( final NumberFormatException e ) {
+                return;
+            }
+        }
+        else if ( prop.getRef().equals( NODE_BORDER_COLOR_REF ) ) {
+            try {
+                setBorderColor( Color.decode( prop.getValue() ) );
+            }
+            catch ( final NumberFormatException e ) {
+                return;
+            }
+        }
+        else if ( prop.getRef().equals( NODE_SHAPE_REF ) ) {
+            try {
+                setShape( prop.getValue() );
+            }
+            catch ( final NumberFormatException e ) {
+                return;
+            }
+        }
     }
 
     public final void setBorderColor( final Color border_color ) {
@@ -293,7 +330,22 @@ public final class NodeVisualData implements PhylogenyData {
         _shape = shape;
     }
 
+    public final void setShape( final String shape ) {
+        if ( shape.equalsIgnoreCase( NODE_SHAPE_CIRCLE ) ) {
+            setShape( NodeShape.CIRCLE );
+        }
+        else if ( shape.equalsIgnoreCase( NODE_SHAPE_RECTANGLE ) ) {
+            setShape( NodeShape.RECTANGLE );
+        }
+        else {
+            setShape( NodeShape.DEFAULT );
+        }
+    }
+
     public final void setSize( final float size ) {
+        if ( ( size != DEFAULT_SIZE ) && ( size < 0 ) ) {
+            throw new IllegalArgumentException( "negative size: " + size );
+        }
         _size = size;
     }
 
@@ -371,7 +423,6 @@ public final class NodeVisualData implements PhylogenyData {
                                           FONT_COLOR_TYPE,
                                           AppliesTo.NODE ) );
         }
-        //
         if ( getShape() != NodeShape.DEFAULT ) {
             String shape = null;
             if ( getShape() == NodeShape.RECTANGLE ) {
-- 
1.7.10.2