X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=9f8fb82bde033a6fa1b46bb906fef830489b91e7;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=7b06a710ad1f1695434b4491f345ce7c76ce4274;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 7b06a71..9f8fb82 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 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;
@@ -79,9 +81,10 @@ public class DBRefFetcher implements Runnable
   private SequenceI[] alseqs;
 
   /**
-   * when true - retrieved sequences will be trimmed to cover longest derived alignment sequence 
+   * when true - retrieved sequences will be trimmed to cover longest derived
+   * alignment sequence
    */
-  private boolean trimDsSeqs=true;
+  private boolean trimDsSeqs = true;
 
   public DBRefFetcher()
   {
@@ -129,7 +132,8 @@ 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 
+    // set default behaviour for transferring excess sequence data to the
+    // dataset
     trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
     if (sources == null)
     {
@@ -279,11 +283,11 @@ public class DBRefFetcher implements Runnable
   {
     if (dbSources == null)
     {
-      throw new Error("Implementation error. Must initialise dbSources");
+      throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar("Fetching db refs", startTime);
+    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -379,7 +383,7 @@ public class DBRefFetcher implements Runnable
             if (retrieved != null)
             {
               transferReferences(sdataset, dbsource.getDbSource(),
-                      retrieved,trimDsSeqs);
+                      retrieved, trimDsSeqs);
             }
           }
           else
@@ -458,15 +462,20 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.
     if (sbuffer.length() > 0)
     {
-      output.setText(MessageManager.getString("label.your_sequences_have_been_verified")
+      output.setText(MessageManager
+              .getString("label.your_sequences_have_been_verified")
               + sbuffer.toString());
-      Desktop.addInternalFrame(output, MessageManager.getString("label.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(MessageManager.getString("label.dbref_search_completed"), startTime);
+    af.setProgressBar(
+            MessageManager.getString("label.dbref_search_completed"),
+            startTime);
     // promptBeforeBlast();
 
     running = false;
@@ -476,14 +485,15 @@ public class DBRefFetcher implements Runnable
   /**
    * Verify local sequences in seqRefs against the retrieved sequence database
    * records.
-   * @param trimDatasetSeqs 
+   * 
+   * @param trimDatasetSeqs
    * 
    */
   void transferReferences(Vector sdataset, String dbSource,
           AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
   // file)
   {
-    System.out.println("trimming ? "+trimDatasetSeqs);
+    System.out.println("trimming ? " + trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
       return;
@@ -658,7 +668,8 @@ public class DBRefFetcher implements Runnable
         // unknownSequences.remove(sequence);
         int absEnd = absStart + nonGapped.length();
         absStart += 1;
-        if (!trimDatasetSeqs) {
+        if (!trimDatasetSeqs)
+        {
           // insert full length sequence from record
           sequence.setSequence(entry.getSequenceAsString());
           sequence.setStart(entry.getStart());
@@ -666,7 +677,8 @@ public class DBRefFetcher implements Runnable
         if (updateRefFrame)
         {
           // finally, update local sequence reference frame if we're allowed
-          if (trimDatasetSeqs) {
+          if (trimDatasetSeqs)
+          {
             // just fix start/end
             sequence.setStart(absStart);
             sequence.setEnd(absEnd);