X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=f46779b226f09f2fbcf0537b9a0725a14a020232;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=6fe1466484ace6787e94c32359b0fedaaf0feb08;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 6fe1466..f46779b 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws;
 
@@ -30,10 +31,10 @@ import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
+import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -77,6 +78,11 @@ public class DBRefFetcher implements Runnable
 
   private SequenceI[] alseqs;
 
+  /**
+   * when true - retrieved sequences will be trimmed to cover longest derived alignment sequence 
+   */
+  private boolean trimDsSeqs=true;
+
   public DBRefFetcher()
   {
   }
@@ -123,6 +129,8 @@ public class DBRefFetcher implements Runnable
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
     sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+    // set default behaviour for transferring excess sequence data to the dataset 
+    trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
     if (sources == null)
     {
       // af.featureSettings_actionPerformed(null);
@@ -137,10 +145,13 @@ public class DBRefFetcher implements Runnable
       {
         jalviewSourceI src = en.nextElement();
         List<DbSourceProxy> sp = src.getSequenceSourceProxies();
-        selsources.addAll(sp);
-        if (sp.size() > 1)
+        if (sp != null)
         {
-          Cache.log.debug("Added many Db Sources for :" + src.getTitle());
+          selsources.addAll(sp);
+          if (sp.size() > 1)
+          {
+            Cache.log.debug("Added many Db Sources for :" + src.getTitle());
+          }
         }
       }
       // select appropriate databases based on alignFrame context.
@@ -368,7 +379,7 @@ public class DBRefFetcher implements Runnable
             if (retrieved != null)
             {
               transferReferences(sdataset, dbsource.getDbSource(),
-                      retrieved);
+                      retrieved,trimDsSeqs);
             }
           }
           else
@@ -447,17 +458,15 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.
     if (sbuffer.length() > 0)
     {
-      output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
-              + "altered, most likely the start/end residue will have been updated.\n"
-              + "Save your alignment to maintain the updated id.\n\n"
+      output.setText(MessageManager.getString("label.your_sequences_have_been_verified")
               + sbuffer.toString());
-      Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
+      Desktop.addInternalFrame(output, MessageManager.getString("label.sequence_names_updated"), 600, 300);
       // The above is the dataset, we must now find out the index
       // of the viewed sequence
 
     }
 
-    af.setProgressBar("DBRef search completed", startTime);
+    af.setProgressBar(MessageManager.getString("label.dbref_search_completed"), startTime);
     // promptBeforeBlast();
 
     running = false;
@@ -467,12 +476,14 @@ public class DBRefFetcher implements Runnable
   /**
    * Verify local sequences in seqRefs against the retrieved sequence database
    * records.
+   * @param trimDatasetSeqs 
    * 
    */
   void transferReferences(Vector sdataset, String dbSource,
-          AlignmentI retrievedAl) // File
+          AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
   // file)
   {
+    System.out.println("trimming ? "+trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
       return;
@@ -566,6 +577,7 @@ public class DBRefFetcher implements Runnable
         // mappings are made (but content matches retrieved set)
         boolean updateRefFrame = sequence.getDBRef() == null
                 || sequence.getDBRef().length == 0;
+        // TODO:
         // verify sequence against the entry sequence
 
         String nonGapped = AlignSeq.extractGaps("-. ",
@@ -646,11 +658,19 @@ public class DBRefFetcher implements Runnable
         // unknownSequences.remove(sequence);
         int absEnd = absStart + nonGapped.length();
         absStart += 1;
+        if (!trimDatasetSeqs) {
+          // insert full length sequence from record
+          sequence.setSequence(entry.getSequenceAsString());
+          sequence.setStart(entry.getStart());
+        }
         if (updateRefFrame)
         {
           // finally, update local sequence reference frame if we're allowed
-          sequence.setStart(absStart);
-          sequence.setEnd(absEnd);
+          if (trimDatasetSeqs) {
+            // just fix start/end
+            sequence.setStart(absStart);
+            sequence.setEnd(absEnd);
+          }
           // search for alignment sequences to update coordinate frame for
           for (int alsq = 0; alsq < alseqs.length; alsq++)
           {