JAL-1925 update source version in license

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index e8494e4..a2526a9 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -81,9 +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()
   {
@@ -124,14 +125,19 @@ public class DBRefFetcher implements Runnable
     {
       alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
+      {
         ds[i] = seqs[i].getDatasetSequence();
+      }
       else
+      {
         ds[i] = seqs[i];
+      }
     }
     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)
     {
@@ -281,11 +287,14 @@ 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))
@@ -381,7 +390,7 @@ public class DBRefFetcher implements Runnable
             if (retrieved != null)
             {
               transferReferences(sdataset, dbsource.getDbSource(),
-                      retrieved,trimDsSeqs);
+                      retrieved, trimDsSeqs);
             }
           }
           else
@@ -391,8 +400,8 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(), new String[]
-                      { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+                      sequence.getDBRef(),
+                      new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
               if (uprefs != null && uprefs.length > 0)
@@ -460,15 +469,20 @@ 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;
@@ -478,14 +492,15 @@ 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;
@@ -509,8 +524,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[]
-              { dbSource });
+              entry.getDBRef(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -586,9 +600,9 @@ public class DBRefFetcher implements Runnable
                 sequence.getSequenceAsString()).toUpperCase();
 
         int absStart = entrySeq.indexOf(nonGapped);
-        int mapStart = entry.getStart();
-        jalview.datamodel.Mapping mp;
+        Mapping mp;
 
+        final int sequenceStart = sequence.getStart();
         if (absStart == -1)
         {
           // Is local sequence contained in dataset sequence?
@@ -608,12 +622,10 @@ public class DBRefFetcher implements Runnable
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
-          mp = new Mapping(null, new int[]
-          { sequence.getStart() + absStart,
-              sequence.getStart() + absStart + entrySeq.length() - 1 },
-                  new int[]
-                  { entry.getStart(),
-                      entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+          mp = new Mapping(null, new int[] { sequenceStart + absStart,
+              sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+          { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+                  1, 1);
           updateRefFrame = false; // mapping is based on current start/end so
           // don't modify start and end
         }
@@ -636,7 +648,7 @@ public class DBRefFetcher implements Runnable
             if (sequence.getSequenceFeatures() != null)
             {
               SequenceFeature[] sf = sequence.getSequenceFeatures();
-              int start = sequence.getStart();
+              int start = sequenceStart;
               int end = sequence.getEnd();
               int startShift = 1 - absStart - start; // how much the features
                                                      // are
@@ -658,9 +670,10 @@ public class DBRefFetcher implements Runnable
                 + " from " + dbSource + " sequence : " + entry.getName());
         sequence.transferAnnotation(entry, mp);
         // unknownSequences.remove(sequence);
-        int absEnd = absStart + nonGapped.length();
-        absStart += 1;
-        if (!trimDatasetSeqs) {
+        absStart += entry.getStart();
+        int absEnd = absStart + nonGapped.length() - 1;
+        if (!trimDatasetSeqs)
+        {
           // insert full length sequence from record
           sequence.setSequence(entry.getSequenceAsString());
           sequence.setStart(entry.getStart());
@@ -668,7 +681,8 @@ 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);