From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 30 Aug 2014 01:49:23 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dc91a2ae1088da367adffb2401b18d285d328b47;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 23eeec1..979fafe 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -971,6 +971,12 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
     @Override
     final public String toString() {
         final StringBuilder sb = new StringBuilder();
+        
+        if ( !ForesterUtil.isEmpty( getName() ) ) {
+            sb.append( getName() );
+            sb.append( " " );
+        }
+        
         if ( getNodeData().isHasTaxonomy() ) {
             if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) {
                 sb.append( getNodeData().getTaxonomy().getScientificName() );
@@ -1003,10 +1009,7 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
                 sb.append( " " );
             }
         }
-        if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) {
-            sb.append( getName() );
-            sb.append( " " );
-        }
+       
         if ( sb.length() <= 1 ) {
             sb.append( "[" );
             sb.append( getId() );
diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index da16246..fde5351 100644
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -65,6 +65,7 @@ public final class SequenceDbWsTools {
     private final static boolean DEBUG                   = true;
     private final static String  URL_ENC                 = "UTF-8";
     private final static int     SLEEP                   = 200;
+    private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = true;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
                                                                            final int max_taxonomies_return )
@@ -383,7 +384,7 @@ public final class SequenceDbWsTools {
             }
             if ( ( db_entry.getMolecularSequence() != null )
                     && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
-                    && seq.getMolecularSequence().isEmpty() ) {
+                    && ( ALLOW_TO_OVERWRITE_MOL_SEQ || seq.getMolecularSequence().isEmpty() ) ) {
                 seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() );
                 seq.setMolecularSequenceAligned( false );
                 if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) {