Merge branch 'develop' into features/JAL-892varnaToProject

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e32e910..b275186 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -42,7 +42,6 @@ import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -71,6 +70,7 @@ import java.awt.Font;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Set;
 import java.util.Vector;
 
@@ -96,8 +96,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   private Rectangle explodedGeometry;
 
-  private FeatureRenderer featureRenderer;
-
   String viewName;
 
   /*
@@ -659,35 +657,32 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * 
    * @param pdbEntries
-   * @return a series of SequenceI arrays, one for each PDBEntry, listing which
-   *         sequence in the alignment holds a reference to it
+   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+   *         sequences in the alignment hold a reference to it
    */
   public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
   {
-    ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
     for (PDBEntry pdb : pdbEntries)
     {
-      ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
-      for (int i = 0; i < alignment.getHeight(); i++)
+      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      for (SequenceI sq : alignment.getSequences())
       {
-        Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
-                .getPDBId();
+        Vector<PDBEntry> pdbs = sq
+                .getDatasetSequence().getPDBId();
         if (pdbs == null)
         {
           continue;
         }
-        SequenceI sq;
-        for (int p = 0; p < pdbs.size(); p++)
+        for (PDBEntry p1 : pdbs)
         {
-          PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
           if (p1.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+            if (!seqs.contains(sq))
             {
               seqs.add(sq);
+              continue;
             }
-
-            continue;
           }
         }
       }
@@ -804,7 +799,7 @@ public class AlignViewport extends AlignmentViewport implements
      * If any cDNA/protein mappings can be made between the alignments, offer to
      * open a linked alignment with split frame option.
      */
-    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
       if (AlignmentUtils.isMappable(al, getAlignment()))
       {
@@ -1042,15 +1037,4 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  @Override
-  public FeatureRenderer getFeatureRenderer()
-  {
-    return featureRenderer;
-  }
-
-  @Override
-  public void setFeatureRenderer(FeatureRenderer featureRenderer)
-  {
-    this.featureRenderer = featureRenderer;
-  }
 }