Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cf12145..2224021 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -44,6 +44,7 @@ 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;
 
@@ -54,6 +55,7 @@ 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;
@@ -83,7 +85,7 @@ import jalview.ws.params.AutoCalcSetting;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, AlignViewportI, CommandListener
+        SelectionSource, CommandListener
 {
   Font font;
 
@@ -95,6 +97,9 @@ public class AlignViewport extends AlignmentViewport implements
 
   private Rectangle explodedGeometry;
 
+  private FeatureRenderer featureRenderer;
+
+  private boolean includeHiddenRegion = true;
   String viewName;
 
   /*
@@ -656,35 +661,32 @@ 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;
           }
         }
       }
@@ -1038,4 +1040,26 @@ public class AlignViewport extends AlignmentViewport implements
       complementPanel.scrollToCentre(sr, seqOffset);
     }
   }
+
+  @Override
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return featureRenderer;
+  }
+
+  @Override
+  public void setFeatureRenderer(FeatureRenderer featureRenderer)
+  {
+    this.featureRenderer = featureRenderer;
+  }
+
+  public boolean isIncludeHiddenRegion()
+  {
+    return includeHiddenRegion;
+  }
+
+  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  {
+    this.includeHiddenRegion = includeHiddenRegion;
+  }
 }