in progress

[jalview.git] / forester / java / src / org / forester / phylogeny / data / NodeData.java

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index 7e180d4..08b3e2c 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -38,20 +38,6 @@ import org.forester.util.ForesterUtil;
 
 public class NodeData implements PhylogenyData {
 
-    public enum NODE_DATA {
-        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;
@@ -184,7 +170,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Distribution.
-     *  
+     *
      * @return Distribution
      */
     public Distribution getDistribution() {
@@ -209,9 +195,9 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Reference.
-     * 
+     *
      *  @return Reference
-     *  
+     *
      */
     public Reference getReference() {
         return getReference( 0 );
@@ -227,7 +213,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Sequence.
-     * 
+     *
      * @return Sequence
      */
     public Sequence getSequence() {
@@ -248,9 +234,9 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Taxonomy.
-     * 
+     *
      * @return  Taxonomy
-     * 
+     *
      */
     public Taxonomy getTaxonomy() {
         return getTaxonomy( 0 );
@@ -272,7 +258,7 @@ public class NodeData implements PhylogenyData {
     public boolean isEmpty() {
         return ( ForesterUtil.isEmpty( _node_name ) && !isHasSequence() && !isHasTaxonomy() && !isHasBinaryCharacters()
                 && !isHasDate() && !isHasDistribution() && !isHasEvent() && !isHasProperties() && !isHasReference() && ( ( _vector == null ) || _vector
-                .isEmpty() ) );
+                        .isEmpty() ) );
     }
 
     public boolean isHasDate() {
@@ -286,7 +272,7 @@ public class NodeData implements PhylogenyData {
         return ( ( ( getDistributions() != null ) && ( getDistributions().size() > 0 ) ) && ( ( !ForesterUtil
                 .isEmpty( getDistribution().getDesc() ) )
                 || ( ( getDistribution().getPoints() != null ) && ( getDistribution().getPoints().size() > 0 ) ) || ( ( getDistribution()
-                .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) );
+                        .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) );
     }
 
     public boolean isHasEvent() {
@@ -300,7 +286,7 @@ public class NodeData implements PhylogenyData {
     public boolean isHasReference() {
         return ( ( getReferences() != null ) && ( getReferences().size() > 0 ) )
                 && ( !ForesterUtil.isEmpty( getReference().getDoi() ) || !ForesterUtil.isEmpty( getReference()
-                        .getDescription() ) );
+                                                                                                .getDescription() ) );
     }
 
     public boolean isHasSequence() {
@@ -321,7 +307,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Distribution.
-     * 
+     *
      */
     public void setDistribution( final Distribution distribution ) {
         if ( _distributions == null ) {
@@ -363,7 +349,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Reference.
-     * 
+     *
      */
     public void setReference( final Reference reference ) {
         if ( _references == null ) {
@@ -390,7 +376,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Sequence.
-     * 
+     *
      */
     public void setSequence( final Sequence sequence ) {
         if ( _sequences == null ) {
@@ -421,7 +407,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Taxonomy.
-     * 
+     *
      */
     public void setTaxonomy( final Taxonomy taxonomy ) {
         if ( _taxonomies == null ) {
@@ -488,6 +474,9 @@ public class NodeData implements PhylogenyData {
         if ( isHasProperties() ) {
             getProperties().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
         }
+        if ( ( level == 0 ) && ( getNodeVisualData() != null ) && !getNodeVisualData().isEmpty() ) {
+            getNodeVisualData().toPhyloXML( writer, level, indentation.substring( 0, indentation.length() - 2 ) );
+        }
         if ( ( getVector() != null )
                 && !getVector().isEmpty()
                 && ( ( getProperties() == null ) || getProperties()