Merge branch 'develop' into features/filetypeEnum

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7d8d4fe..d4d2054 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -507,17 +507,6 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param tree
    *          DOCUMENT ME!
    */
@@ -663,39 +652,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * synthesize a column selection if none exists so it covers the given
-   * selection group. if wholewidth is false, no column selection is made if the
-   * selection group covers the whole alignment width.
-   * 
-   * @param sg
-   * @param wholewidth
-   */
-  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
-  {
-    int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
-            && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
-    {
-      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
-      {
-        // do nothing
-        return;
-      }
-      if (colSel == null)
-      {
-        colSel = new ColumnSelection();
-      }
-      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
-      {
-        colSel.addElement(cspos);
-      }
-    }
-  }
-
-  /**
    * Returns the (Desktop) instance of the StructureSelectionManager
    */
   @Override
@@ -716,27 +672,42 @@ public class AlignViewport extends AlignmentViewport implements
     List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
     for (PDBEntry pdb : pdbEntries)
     {
-      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
-        if (pdbs == null)
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+        if (pdbRefEntries == null)
         {
           continue;
         }
-        for (PDBEntry p1 : pdbs)
+        for (PDBEntry pdbRefEntry : pdbRefEntries)
         {
-          if (p1.getId().equals(pdb.getId()))
+          if (pdbRefEntry.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq))
+            if (pdbRefEntry.getChainCode() != null
+                    && pdb.getChainCode() != null)
+            {
+              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+                      pdb.getChainCode())
+                      && !choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+            else
             {
-              seqs.add(sq);
-              continue;
+              if (!choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
             }
+
           }
         }
       }
-      seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+      seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
@@ -961,7 +932,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     // TODO if we want this (e.g. to enable reload of the alignment from file),
     // we will need to add parameters to the stack.
-    // if (!protocol.equals(AppletFormatAdapter.PASTE))
+    // if (!protocol.equals(DataSourceType.PASTE))
     // {
     // alignFrame.setFileName(file, format);
     // }
@@ -1136,6 +1107,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @param featureSettings
    */
+  @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
     if (featureSettings == null)