JAL-2798 tree frame is now added to active views when added to Jalview

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ea6c5f2..c01b99c 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -26,7 +26,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.DasSourceBrowser;
@@ -118,7 +117,7 @@ public class DBRefFetcher implements Runnable
           DbSourceProxy[] sources, FeatureSettings featureSettings,
           boolean isNucleotide)
   {
-    listeners = new ArrayList<FetchFinishedListenerI>();
+    listeners = new ArrayList<>();
     this.progressWindow = progressIndicatorFrame;
     alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
@@ -164,7 +163,7 @@ public class DBRefFetcher implements Runnable
   {
     // af.featureSettings_actionPerformed(null);
     String[] defdb = null;
-    List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> selsources = new ArrayList<>();
     Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
             ? featureSettings.getSelectedSources()
             : new DasSourceBrowser().getSelectedSources();
@@ -190,7 +189,7 @@ public class DBRefFetcher implements Runnable
     {
       defdb = DBRefSource.PROTEINDBS;
     }
-    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> srces = new ArrayList<>();
     for (String ddb : defdb)
     {
       List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
@@ -268,7 +267,7 @@ public class DBRefFetcher implements Runnable
     // TODO can we not simply write
     // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
 
-    Thread thread = new Thread(this);
+    Thread thread = new Thread(this, "FetchDBRef");
     thread.start();
     running = true;
 
@@ -310,14 +309,14 @@ public class DBRefFetcher implements Runnable
       }
       else if (seqs == null)
       {
-        seqs = new Vector<SequenceI>();
+        seqs = new Vector<>();
         seqs.addElement(seq);
       }
 
     }
     else
     {
-      seqs = new Vector<SequenceI>();
+      seqs = new Vector<>();
       seqs.addElement(seq);
     }
 
@@ -356,9 +355,9 @@ public class DBRefFetcher implements Runnable
       e.printStackTrace();
     }
 
-    Vector<SequenceI> sdataset = new Vector<SequenceI>(
+    Vector<SequenceI> sdataset = new Vector<>(
             Arrays.asList(dataset));
-    List<String> warningMessages = new ArrayList<String>();
+    List<String> warningMessages = new ArrayList<>();
 
     int db = 0;
     while (sdataset.size() > 0 && db < dbSources.length)
@@ -370,8 +369,8 @@ public class DBRefFetcher implements Runnable
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
       sdataset.copyInto(currSeqs);// seqs that are to be validated against
       // dbSources[db]
-      Vector<String> queries = new Vector<String>(); // generated queries curSeq
-      seqRefs = new Hashtable<String, Vector<SequenceI>>();
+      Vector<String> queries = new Vector<>(); // generated queries curSeq
+      seqRefs = new Hashtable<>();
 
       int seqIndex = 0;
 
@@ -573,7 +572,7 @@ public class DBRefFetcher implements Runnable
     {
       // Work out which sequences this sequence matches,
       // taking into account all accessionIds and names in the file
-      Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
+      Vector<SequenceI> sequenceMatches = new Vector<>();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = DBRefUtils
               .selectRefs(retrievedSeq.getDBRefs(), new String[]
@@ -706,28 +705,13 @@ public class DBRefFetcher implements Runnable
 
           if (updateRefFrame)
           {
-            SequenceFeature[] sfs = sequence.getSequenceFeatures();
-            if (sfs != null)
+            /*
+             * relocate existing sequence features by offset
+             */
+            int startShift = absStart - sequenceStart + 1;
+            if (startShift != 0)
             {
-              /*
-               * relocate existing sequence features by offset
-               */
-              int start = sequenceStart;
-              int end = sequence.getEnd();
-              int startShift = 1 - absStart - start;
-
-              if (startShift != 0)
-              {
-                for (SequenceFeature sf : sfs)
-                {
-                  if (sf.getBegin() >= start && sf.getEnd() <= end)
-                  {
-                    sf.setBegin(sf.getBegin() + startShift);
-                    sf.setEnd(sf.getEnd() + startShift);
-                    modified = true;
-                  }
-                }
-              }
+              modified |= sequence.getFeatures().shiftFeatures(startShift);
             }
           }
         }
@@ -840,7 +824,7 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-    Vector<SequenceI> nseq = new Vector<SequenceI>();
+    Vector<SequenceI> nseq = new Vector<>();
     for (int i = 0; sequencesArray != null
             && i < sequencesArray.length; i++)
     {