From: jprocter <Jim Procter>
Date: Mon, 8 Jun 2009 10:53:26 +0000 (+0000)
Subject: minor optimization. apply gpl development license
X-Git-Tag: Release_2_5~292
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a8401d0452aac399083c1a89fb614adbfaa98ff8;p=jalview.git

minor optimization. apply gpl development license
---

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 34219b4..fe971d9 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -259,16 +259,19 @@ public class VamsasAppDatastore
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
+      jalview.datamodel.AlignmentI jds = jal.getDataset();
       boolean nw = false;
       VAMSAS root = null; // will be resolved based on Dataset Parent.
       // /////////////////////////////////////////
       // SAVE THE DATASET
       DataSet dataset = null;
-      if (jal.getDataset() == null)
+      if (jds == null)
       {
         Cache.log.warn("Creating new dataset for an alignment.");
         jal.setDataset(null);
+        jds = jal.getDataset();
       }
+      
       // try and get alignment and association for sequence set id
 
       Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId());
@@ -277,7 +280,7 @@ public class VamsasAppDatastore
         dataset = (DataSet) alignment.getV_parent();
       } else {
       	// is the dataset already registered
-	dataset = (DataSet) getjv2vObj(jal.getDataset());
+	dataset = (DataSet) getjv2vObj(jds);
       }
       
       if (dataset == null)
@@ -285,8 +288,7 @@ public class VamsasAppDatastore
         // it might be that one of the dataset sequences does actually have a
         // binding, so search for it indirectly. If it does, then the local jalview dataset
         // must be merged with the existing vamsas dataset.
-        jalview.datamodel.SequenceI[] jdatset = jal.getDataset()
-                .getSequencesArray();
+        jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray();
         for (int i = 0; i < jdatset.length; i++)
         {
           Vobject vbound = getjv2vObj(jdatset[i]);
@@ -321,7 +323,7 @@ public class VamsasAppDatastore
         root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
         dataset = new DataSet();
         root.addDataSet(dataset);
-        bindjvvobj(jal.getDataset(), dataset);
+        bindjvvobj(jds, dataset);
         dataset.setProvenance(dummyProvenance());
         // dataset.getProvenance().addEntry(provEntry);
         nw = true;