From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sun, 20 Jan 2013 05:24:13 +0000 (+0000)
Subject: keep tilde annotation
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=10aba63f0733a9f81c39a68d09538fd79e4b6f13;p=jalview.git

keep tilde annotation
---

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index ba79613..d0197aa 100644
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -71,8 +71,8 @@ public final class decorator {
     final static private String MAPPING_FILE_SEPARATOR_OPTION           = "s";
     final static private String MAPPING_FILE_SEPARATOR_DEFAULT          = ": ";
     final static private String PRG_NAME                                = "decorator";
-    final static private String PRG_VERSION                             = "1.12";
-    final static private String PRG_DATE                                = "2012.12.21";
+    final static private String PRG_VERSION                             = "1.13";
+    final static private String PRG_DATE                                = "2013.01.19";
 
     public static void main( final String args[] ) {
         ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
diff --git a/forester/java/src/org/forester/tools/PhylogenyDecorator.java b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
index f4f6c1a..1502146 100644
--- a/forester/java/src/org/forester/tools/PhylogenyDecorator.java
+++ b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
@@ -218,8 +218,11 @@ public final class PhylogenyDecorator {
         for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             String name = node.getName();
+            String tilde_annotation = null;
             if ( trim_after_tilde && ( name.indexOf( '~' ) > 0 ) ) {
-                name = name.substring( 0, name.indexOf( '~' ) );
+                final int ti = name.indexOf( '~' );
+                name = name.substring( 0, ti );
+                tilde_annotation = name.substring( ti );
             }
             if ( !ForesterUtil.isEmpty( name ) ) {
                 if ( intermediate_map != null ) {
@@ -279,6 +282,9 @@ public final class PhylogenyDecorator {
                                 node.getNodeData().getTaxonomy().setScientificName( new_value );
                                 break;
                             case SEQUENCE_NAME:
+                                if ( trim_after_tilde ) {
+                                    new_value = addTildeAnnotation( tilde_annotation, new_value );
+                                }
                                 if ( PhylogenyDecorator.VERBOSE ) {
                                     System.out.println( name + ": " + new_value );
                                 }
@@ -312,6 +318,9 @@ public final class PhylogenyDecorator {
                                 if ( PhylogenyDecorator.SANITIZE ) {
                                     new_value = PhylogenyDecorator.sanitize( new_value );
                                 }
+                                if ( trim_after_tilde ) {
+                                    new_value = addTildeAnnotation( tilde_annotation, new_value );
+                                }
                                 if ( PhylogenyDecorator.VERBOSE ) {
                                     System.out.println( new_value );
                                 }
@@ -329,6 +338,13 @@ public final class PhylogenyDecorator {
         }
     }
 
+    private final static String addTildeAnnotation( final String tilde_annotation, final String new_value ) {
+        if ( ForesterUtil.isEmpty( tilde_annotation ) ) {
+            return new_value;
+        }
+        return new_value + tilde_annotation;
+    }
+
     public static void decorate( final Phylogeny[] phylogenies,
                                  final Map<String, Map<String, String>> map,
                                  final boolean picky,
@@ -438,7 +454,10 @@ public final class PhylogenyDecorator {
 
     private static String extractBracketedTaxCodes( final PhylogenyNode node, final String new_value ) {
         final int i = new_value.lastIndexOf( "[" );
-        final String tc = new_value.substring( i + 1, new_value.length() - 1 );
+        String tc = new_value.substring( i + 1, new_value.length() - 1 );
+        if ( tc.length() == 6 ) {
+            tc = tc.substring( 0, 5 );
+        }
         ForesterUtil.ensurePresenceOfTaxonomy( node );
         try {
             node.getNodeData().getTaxonomy().setTaxonomyCode( tc );