in progress

[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 851398a..b724a79 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
@@ -120,6 +120,9 @@ public final class PhyloXmlHandler extends DefaultHandler {
                 catch ( final PhylogenyParserException ex ) {
                     throw new SAXException( ex.getMessage() );
                 }
+                catch ( final PhyloXmlDataFormatException e ) {
+                    throw new SAXException( e.getMessage() );
+                }
             }
             else if ( local_name.equals( PhyloXmlMapping.SEQUENCE_RELATION ) ) {
                 try {
@@ -173,7 +176,7 @@ public final class PhyloXmlHandler extends DefaultHandler {
                         }
                     }
                 }
-                catch ( final PhylogenyParserException ex ) {
+                catch ( final PhyloXmlDataFormatException ex ) {
                     throw new SAXException( ex.getMessage() );
                 }
             }
@@ -181,8 +184,11 @@ public final class PhyloXmlHandler extends DefaultHandler {
                 try {
                     PhyloXmlHandler.mapElementToPhylogeny( getCurrentXmlElement(), getCurrentPhylogeny() );
                 }
-                catch ( final PhylogenyParserException ex ) {
-                    throw new SAXException( ex.getMessage() );
+                catch ( final PhylogenyParserException e ) {
+                    throw new SAXException( e.getMessage() );
+                }
+                catch ( final PhyloXmlDataFormatException e ) {
+                    throw new SAXException( e.getMessage() );
                 }
                 finishPhylogeny();
                 reset();
@@ -245,7 +251,7 @@ public final class PhyloXmlHandler extends DefaultHandler {
     }
 
     private void mapElementToPhylogenyNode( final XmlElement xml_element, final PhylogenyNode node )
-            throws PhylogenyParserException {
+            throws PhylogenyParserException, PhyloXmlDataFormatException {
         if ( xml_element.isHasAttribute( PhyloXmlMapping.BRANCH_LENGTH ) ) {
             double d = 0;
             try {
@@ -257,6 +263,12 @@ public final class PhyloXmlHandler extends DefaultHandler {
             }
             node.setDistanceToParent( d );
         }
+        if ( xml_element.isHasAttribute( PhyloXmlMapping.NODE_COLLAPSE ) ) {
+            final String collapse_str = xml_element.getAttribute( PhyloXmlMapping.NODE_COLLAPSE );
+            if ( !ForesterUtil.isEmpty( collapse_str ) && collapse_str.trim().equalsIgnoreCase( "true" ) ) {
+                node.setCollapse( true );
+            }
+        }
         for( int i = 0; i < xml_element.getNumberOfChildElements(); ++i ) {
             final XmlElement element = xml_element.getChildElement( i );
             final String qualified_name = element.getQualifiedName();
@@ -434,7 +446,7 @@ public final class PhyloXmlHandler extends DefaultHandler {
     }
 
     private static void mapElementToPhylogeny( final XmlElement xml_element, final Phylogeny phylogeny )
-            throws PhylogenyParserException {
+            throws PhylogenyParserException, PhyloXmlDataFormatException {
         for( int i = 0; i < xml_element.getNumberOfChildElements(); ++i ) {
             final XmlElement element = xml_element.getChildElement( i );
             final String qualified_name = element.getQualifiedName();