X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Fphyloxml%2FPhyloXmlHandler.java;h=ec05952809070ceeafcbe1d0a78cb04064e2bdef;hb=a648fae3c8d0402dbdafa379ff3d42bbea96633d;hp=c4c5be2f390b4503389ab9443e1fc84a214a3f76;hpb=f6de7e66f71bf840d3d68ed70dda9946ad2e0faa;p=jalview.git

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 c4c5be2..ec05952 100644
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.io.parsers.phyloxml;
 
@@ -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 {
@@ -440,7 +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();