X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2Fdata%2FNodeData.java;h=c5c5d40f042e23f2b128be18780d8b3a856f3c60;hb=a1e88a27d4df0836cd947b7140b37bb7a0b16077;hp=bc7e8b97985b50055d74928cd2fb52ef18cd60ba;hpb=a07102813fbac79ba1a534dc9954a8500dc5e5ff;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index bc7e8b9..c5c5d40 100644
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -23,7 +23,7 @@
 // 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.phylogeny.data;
 
@@ -42,17 +42,19 @@ public class NodeData implements PhylogenyData {
         NODE_NAME,
         EVENT,
         SEQUENCE_NAME,
+        GENE_NAME,
         SEQUENCE_SYMBOL,
         SEQUENCE_MOL_SEQ,
+        SEQUENCE_MOL_SEQ_FASTA,
         SEQUENCE_ACC,
         TAXONOMY_SCIENTIFIC_NAME,
+        TAXONOMY_COMM0N_NAME,
         TAXONOMY_CODE,
         UNKNOWN;
     }
     private String                  _node_name;
     private Event                   _event;
     private List<Sequence>          _sequences;
-    private Identifier              _node_identifier;
     private List<Taxonomy>          _taxonomies;
     private List<Distribution>      _distributions;
     private Date                    _date;
@@ -123,9 +125,6 @@ public class NodeData implements PhylogenyData {
         if ( isHasEvent() ) {
             new_data.setEvent( ( Event ) getEvent().copy() );
         }
-        if ( isHasNodeIdentifier() ) {
-            new_data.setNodeIdentifier( ( Identifier ) getNodeIdentifier().copy() );
-        }
         if ( ( getTaxonomies() != null ) && ( getTaxonomies().size() > 0 ) ) {
             new_data.setTaxonomies( new ArrayList<Taxonomy>() );
             for( final Taxonomy t : getTaxonomies() ) {
@@ -199,10 +198,6 @@ public class NodeData implements PhylogenyData {
         return _event;
     }
 
-    public Identifier getNodeIdentifier() {
-        return _node_identifier;
-    }
-
     public PropertiesMap getProperties() {
         return _properties;
     }
@@ -262,13 +257,19 @@ public class NodeData implements PhylogenyData {
 
     @Override
     public boolean isEqual( final PhylogenyData data ) {
-        throw new UnsupportedOperationException();
+        throw new NoSuchMethodError();
     }
 
     public boolean isHasBinaryCharacters() {
         return getBinaryCharacters() != null;
     }
 
+    public boolean isEmpty() {
+        return ( ForesterUtil.isEmpty( _node_name ) && !isHasSequence() && !isHasTaxonomy() && !isHasBinaryCharacters()
+                && !isHasDate() && !isHasDistribution() && !isHasEvent() && !isHasProperties() && !isHasReference() && ( ( _vector == null ) || _vector
+                .isEmpty() ) );
+    }
+
     public boolean isHasDate() {
         return ( getDate() != null )
                 && ( !ForesterUtil.isEmpty( getDate().getDesc() ) || !ForesterUtil.isNull( getDate().getMax() )
@@ -287,10 +288,6 @@ public class NodeData implements PhylogenyData {
         return getEvent() != null;
     }
 
-    public boolean isHasNodeIdentifier() {
-        return getNodeIdentifier() != null;
-    }
-
     public boolean isHasProperties() {
         return ( getProperties() != null ) && ( getProperties().size() > 0 );
     }
@@ -348,10 +345,6 @@ public class NodeData implements PhylogenyData {
         _event = event;
     }
 
-    public void setNodeIdentifier( final Identifier node_identifier ) {
-        _node_identifier = node_identifier;
-    }
-
     public void setProperties( final PropertiesMap custom_data ) {
         _properties = custom_data;
     }
@@ -440,9 +433,6 @@ public class NodeData implements PhylogenyData {
     @Override
     public StringBuffer toNHX() {
         final StringBuffer sb = new StringBuffer();
-        if ( isHasNodeIdentifier() ) {
-            sb.append( getNodeIdentifier().toNHX() );
-        }
         if ( isHasTaxonomy() ) {
             sb.append( getTaxonomy().toNHX() );
         }
@@ -452,26 +442,11 @@ public class NodeData implements PhylogenyData {
         if ( isHasEvent() ) {
             sb.append( getEvent().toNHX() );
         }
-        if ( isHasProperties() ) {
-            sb.append( getProperties().toNHX() );
-        }
         return sb;
     }
 
     @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
-        if ( isHasNodeIdentifier() ) {
-            writer.write( ForesterUtil.LINE_SEPARATOR );
-            writer.write( indentation );
-            //  if ( !org.forester.util.ForesterUtil.isEmpty( getNodeIdentifier().getProvider() ) ) {
-            //     PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.NODE_IDENTIFIER, getNodeIdentifier()
-            //             .getValue(), PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR, getNodeIdentifier().getProvider() );
-            // }
-            // else {
-            //     PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.NODE_IDENTIFIER, getNodeIdentifier()
-            //             .getValue() );
-            // }
-        }
         if ( isHasTaxonomy() ) {
             for( final Taxonomy t : getTaxonomies() ) {
                 if ( !t.isEmpty() ) {