cleanup

[jalview.git] / forester / java / src / org / forester / tools / PhylogenyDecorator.java

diff --git a/forester/java/src/org/forester/tools/PhylogenyDecorator.java b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
index 9d865e1..57ef9f0 100644 (file)
--- a/forester/java/src/org/forester/tools/PhylogenyDecorator.java
+++ b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
@@ -251,6 +251,9 @@ public final class PhylogenyDecorator {
                             if ( ParserUtils.TAXOMONY_CODE_PATTERN_4.matcher( new_value ).find() ) {
                                 new_value = extractBracketedTaxCodes( node, new_value );
                             }
+                            else if ( ParserUtils.TAXOMONY_CODE_PATTERN_6.matcher( new_value ).find() ) {
+                                new_value = extractBracketedTaxCodes6( node, new_value );
+                            }
                             else if ( picky ) {
                                 throw new IllegalArgumentException( " could not get taxonomy from \"" + new_value
                                         + "\"" );
@@ -264,7 +267,7 @@ public final class PhylogenyDecorator {
                                 if ( !node.getNodeData().isHasSequence() ) {
                                     node.getNodeData().setSequence( new Sequence() );
                                 }
-                                final Annotation annotation = new Annotation( "?" );
+                                final Annotation annotation = new Annotation();
                                 annotation.setDesc( new_value );
                                 node.getNodeData().getSequence().addAnnotation( annotation );
                                 break;
@@ -479,6 +482,30 @@ public final class PhylogenyDecorator {
         return new_value; //TODO //FIXME
     }
 
+    private static String extractBracketedTaxCodes6( final PhylogenyNode node, final String new_value ) {
+        final Matcher m = ParserUtils.TAXOMONY_CODE_PATTERN_6.matcher( new_value );
+        String tc = "?";
+        if ( m.find() ) {
+            tc = m.group( 1 );
+        }
+        ForesterUtil.ensurePresenceOfTaxonomy( node );
+        try {
+            if ( tc.length() == 6 ) {
+                final String t = tc.substring( 0, 5 );
+                System.out.println( "WARNING: taxonomy code " + tc + " -> " + t );
+                tc = t;
+            }
+            else {
+                throw new IllegalArgumentException();
+            }
+            node.getNodeData().getTaxonomy().setTaxonomyCode( tc );
+        }
+        catch ( final PhyloXmlDataFormatException e ) {
+            throw new IllegalArgumentException( "illegal format for taxonomy code: " + tc );
+        }
+        return new_value; //TODO //FIXME
+    }
+
     private static String extractIntermediate( final Map<String, String> intermediate_map, final String name ) {
         String new_name = null;
         if ( PhylogenyDecorator.VERBOSE ) {