removed lineage

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

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java
index 6c0a849..23df0da 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java
@@ -21,17 +21,17 @@
 // 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.data;
 
 import java.util.HashMap;
 import java.util.Map;
 
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlHandler;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.io.parsers.phyloxml.XmlElement;
-import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Sequence;
@@ -46,29 +46,29 @@ public class SequenceRelationParser implements PhylogenyDataPhyloXmlParser {
     }
 
     @Override
-    public SequenceRelation parse( final XmlElement element ) throws PhylogenyParserException {
+    public SequenceRelation parse( final XmlElement element ) throws PhyloXmlDataFormatException {
         final SequenceRelation seqRelation = new SequenceRelation();
         if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_RELATION_TYPE ) ) {
             final String sType = element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_TYPE );
             seqRelation.setType( SequenceRelation.SEQUENCE_RELATION_TYPE.valueOf( sType ) );
         }
         if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF0 ) && ( _phylogeny != null ) ) {
-            final Sequence ref = PhyloXmlHandler.getSequenceMapByIdForPhylogeny( _phylogeny ).get( element
-                    .getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF0 ) );
+            final Sequence ref = PhyloXmlHandler.getSequenceMapByIdForPhylogeny( _phylogeny )
+                    .get( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF0 ) );
             if ( ref != null ) {
                 seqRelation.setRef0( ref );
             }
         }
         if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF1 ) && ( _phylogeny != null ) ) {
-            final Sequence ref = PhyloXmlHandler.getSequenceMapByIdForPhylogeny( _phylogeny ).get( element
-                    .getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF1 ) );
+            final Sequence ref = PhyloXmlHandler.getSequenceMapByIdForPhylogeny( _phylogeny )
+                    .get( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_ID_REF1 ) );
             if ( ref != null ) {
                 seqRelation.setRef1( ref );
             }
         }
         if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) {
-            seqRelation.setDistance( Double
-                    .valueOf( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) );
+            seqRelation
+            .setDistance( Double.valueOf( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) );
         }
         for( int i = 0; i < element.getNumberOfChildElements(); ++i ) {
             final XmlElement child_element = element.getChildElement( i );