Added getValues and write to DistanceMatrix interface for broader use

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

diff --git a/forester/java/src/org/forester/phylogeny/data/Accession.java b/forester/java/src/org/forester/phylogeny/data/Accession.java
index 069978b..fe11d8d 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Accession.java
+++ b/forester/java/src/org/forester/phylogeny/data/Accession.java
@@ -32,20 +32,74 @@ import org.forester.io.parsers.nhx.NHXtags;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.util.ForesterUtil;
 
-public final class Accession implements PhylogenyData {
+public final class Accession implements PhylogenyData, Comparable<Accession> {
 
-    final private String _value;
+    final private String _comment;
     final private String _source;
-    final private String _value_source;
+    final private String _source_value;
+    final private String _value;
+
+    public enum Source {
+        NCBI, REFSEQ, UNIPROT, GI, EMBL, ENSEMBL, UNKNOWN;
+
+        @Override
+        public String toString() {
+            switch ( this ) {
+                case NCBI:
+                    return "ncbi";
+                case REFSEQ:
+                    return "refseq";
+                case UNIPROT:
+                    return "uniprot";
+                case GI:
+                    return "gi";
+                case EMBL:
+                    return "embl";
+                case ENSEMBL:
+                    return "ensembl";
+                case UNKNOWN:
+                    return "unknown";
+                default:
+                    throw new IllegalArgumentException();
+            }
+        }
+    }
+
+    public Accession( final String value ) {
+        _value = value;
+        _source = "";
+        _comment = "";
+        _source_value = value;
+    }
 
     public Accession( final String value, final String source ) {
         _value = value;
         _source = source;
+        _comment = "";
+        if ( source != null ) {
+            _source_value = source + value;
+        }
+        else {
+            _source_value = value;
+        }
+    }
+
+    public Accession( final String value, final Source source ) {
+        _value = value;
+        _source = source.toString();
+        _comment = "";
+        _source_value = source + value;
+    }
+
+    public Accession( final String value, final String source, final String comment ) {
+        _value = value;
+        _source = source;
+        _comment = comment;
         if ( source != null ) {
-            _value_source = value + source;
+            _source_value = source + value;
         }
         else {
-            _value_source = value;
+            _source_value = value;
         }
     }
 
@@ -58,15 +112,27 @@ public final class Accession implements PhylogenyData {
     public StringBuffer asText() {
         final StringBuffer sb = new StringBuffer();
         if ( !ForesterUtil.isEmpty( getSource() ) ) {
-            sb.append( "[" );
             sb.append( getSource() );
-            sb.append( "] " );
+            sb.append( ": " );
         }
         sb.append( getValue() );
+        if ( !ForesterUtil.isEmpty( getComment() ) ) {
+            sb.append( " (" );
+            sb.append( getComment() );
+            sb.append( ")" );
+        }
         return sb;
     }
 
     @Override
+    public int compareTo( final Accession o ) {
+        if ( equals( o ) ) {
+            return 0;
+        }
+        return _source_value.compareTo( o._source_value );
+    }
+
+    @Override
     public PhylogenyData copy() {
         return new Accession( getValue(), getSource() );
     }
@@ -88,6 +154,10 @@ public final class Accession implements PhylogenyData {
         }
     }
 
+    public String getComment() {
+        return _comment;
+    }
+
     public String getSource() {
         return _source;
     }
@@ -98,10 +168,7 @@ public final class Accession implements PhylogenyData {
 
     @Override
     public int hashCode() {
-        //if ( getSource() != null ) {
-        //    return ( getSource() + getValue() ).hashCode();
-        // }
-        return _value_source.hashCode();
+        return _source_value.hashCode();
     }
 
     @Override
@@ -131,20 +198,44 @@ public final class Accession implements PhylogenyData {
     @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         if ( ForesterUtil.isEmpty( getSource() ) ) {
-            PhylogenyDataUtil.appendElement( writer,
-                                             PhyloXmlMapping.ACCESSION,
-                                             getValue(),
-                                             PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
-                                             "unknown",
-                                             indentation );
+            if ( ForesterUtil.isEmpty( getComment() ) ) {
+                PhylogenyDataUtil.appendElement( writer,
+                                                 PhyloXmlMapping.ACCESSION,
+                                                 getValue(),
+                                                 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+                                                 "unknown",
+                                                 indentation );
+            }
+            else {
+                PhylogenyDataUtil.appendElement( writer,
+                                                 PhyloXmlMapping.ACCESSION,
+                                                 getValue(),
+                                                 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+                                                 "unknown",
+                                                 PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
+                                                 getComment(),
+                                                 indentation );
+            }
         }
         else {
-            PhylogenyDataUtil.appendElement( writer,
-                                             PhyloXmlMapping.ACCESSION,
-                                             getValue(),
-                                             PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
-                                             getSource(),
-                                             indentation );
+            if ( ForesterUtil.isEmpty( getComment() ) ) {
+                PhylogenyDataUtil.appendElement( writer,
+                                                 PhyloXmlMapping.ACCESSION,
+                                                 getValue(),
+                                                 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+                                                 getSource(),
+                                                 indentation );
+            }
+            else {
+                PhylogenyDataUtil.appendElement( writer,
+                                                 PhyloXmlMapping.ACCESSION,
+                                                 getValue(),
+                                                 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+                                                 getSource(),
+                                                 PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
+                                                 getComment(),
+                                                 indentation );
+            }
         }
     }