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[jalview.git] / forester / java / src / org / forester / io / parsers / phyloxml / PhyloXmlHandler.java

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..3e2f6a7 100644 (file)
--- 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;
@@ -308,7 +309,7 @@ public final class PhyloXmlHandler extends DefaultHandler {
             }
             else if ( qualified_name.equals( PhyloXmlMapping.BINARY_CHARACTERS ) ) {
                 node.getNodeData().setBinaryCharacters( ( BinaryCharacters ) BinaryCharactersParser.getInstance()
-                        .parse( element ) );
+                                                        .parse( element ) );
             }
             else if ( qualified_name.equals( PhyloXmlMapping.COLOR ) ) {
                 node.getBranchData().setBranchColor( ( BranchColor ) ColorParser.getInstance().parse( element ) );
@@ -324,12 +325,12 @@ 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 ( prop.getRef().startsWith( NodeVisualData.APTX_VISUALIZATION_REF )
+                        && ( prop.getAppliesTo() == AppliesTo.NODE ) ) {
                     if ( node.getNodeData().getNodeVisualData() == null ) {
                         node.getNodeData().setNodeVisualData( new NodeVisualData() );
                     }
-                    final NodeVisualData vd = node.getNodeData().getNodeVisualData();
-                    vd.parseProperty( prop );
+                    node.getNodeData().getNodeVisualData().parseProperty( prop );
                 }
                 else {
                     if ( !node.getNodeData().isHasProperties() ) {
@@ -405,15 +406,15 @@ public final class PhyloXmlHandler extends DefaultHandler {
                 final XmlElement element = new XmlElement( namespace_uri, local_name, local_name, attributes );
                 if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) {
                     getCurrentPhylogeny().setRerootable( Boolean.parseBoolean( element
-                            .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) );
+                                                                               .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) );
                 }
                 if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) ) {
                     getCurrentPhylogeny()
-                            .setDistanceUnit( element.getAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) );
+                    .setDistanceUnit( element.getAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) );
                 }
                 if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) {
                     getCurrentPhylogeny().setRooted( Boolean.parseBoolean( element
-                            .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) );
+                                                                           .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) );
                 }
                 if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_TYPE_ATTR ) ) {
                     getCurrentPhylogeny().setType( ( element.getAttribute( PhyloXmlMapping.PHYLOGENY_TYPE_ATTR ) ) );