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..3a4c670 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;
@@ -59,7 +45,7 @@ public class NodeData implements PhylogenyData {
     private List<Distribution> _distributions;
     private Date               _date;
     private BinaryCharacters   _binary_characters;
-    private PropertiesMap      _properties;
+    private PropertiesList      _properties;
     private List<Reference>    _references;
     private List<Double>       _vector;
     private NodeVisualData     _node_visual_data;
@@ -169,7 +155,7 @@ public class NodeData implements PhylogenyData {
             new_data.setDate( ( Date ) getDate().copy() );
         }
         if ( isHasProperties() ) {
-            new_data.setProperties( ( PropertiesMap ) getProperties().copy() );
+            new_data.setProperties( ( PropertiesList ) getProperties().copy() );
         }
         return new_data;
     }
@@ -184,7 +170,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Distribution.
-     *  
+     *
      * @return Distribution
      */
     public Distribution getDistribution() {
@@ -192,6 +178,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Distribution getDistribution( final int index ) {
+        if ( _distributions == null ) {
+            return null;
+        }
         return _distributions.get( index );
     }
 
@@ -203,21 +192,24 @@ public class NodeData implements PhylogenyData {
         return _event;
     }
 
-    public PropertiesMap getProperties() {
+    public PropertiesList getProperties() {
         return _properties;
     }
 
     /**
      * Convenience method -- always returns the first Reference.
-     * 
+     *
      *  @return Reference
-     *  
+     *
      */
     public Reference getReference() {
         return getReference( 0 );
     }
 
     public Reference getReference( final int index ) {
+        if ( _references == null ) {
+            return null;
+        }
         return _references.get( index );
     }
 
@@ -227,7 +219,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Sequence.
-     * 
+     *
      * @return Sequence
      */
     public Sequence getSequence() {
@@ -235,6 +227,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Sequence getSequence( final int index ) {
+        if ( _sequences == null ) {
+            return null;
+        }
         return _sequences.get( index );
     }
 
@@ -248,15 +243,18 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always returns the first Taxonomy.
-     * 
+     *
      * @return  Taxonomy
-     * 
+     *
      */
     public Taxonomy getTaxonomy() {
         return getTaxonomy( 0 );
     }
 
     public Taxonomy getTaxonomy( final int index ) {
+        if ( _taxonomies == null ) {
+            return null;
+        }
         return _taxonomies.get( index );
     }
 
@@ -272,7 +270,7 @@ 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 +284,7 @@ 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 +298,7 @@ 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 +319,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Distribution.
-     * 
+     *
      */
     public void setDistribution( final Distribution distribution ) {
         if ( _distributions == null ) {
@@ -350,7 +348,7 @@ public class NodeData implements PhylogenyData {
         _event = event;
     }
 
-    public void setProperties( final PropertiesMap custom_data ) {
+    public void setProperties( final PropertiesList custom_data ) {
         _properties = custom_data;
     }
 
@@ -363,7 +361,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Reference.
-     * 
+     *
      */
     public void setReference( final Reference reference ) {
         if ( _references == null ) {
@@ -390,7 +388,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Sequence.
-     * 
+     *
      */
     public void setSequence( final Sequence sequence ) {
         if ( _sequences == null ) {
@@ -421,7 +419,7 @@ public class NodeData implements PhylogenyData {
 
     /**
      * Convenience method -- always sets the first Taxonomy.
-     * 
+     *
      */
     public void setTaxonomy( final Taxonomy taxonomy ) {
         if ( _taxonomies == null ) {
@@ -488,6 +486,9 @@ 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()