Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 192d82a..96fea6e 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -59,6 +59,7 @@ import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
@@ -451,17 +452,17 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * returns the visible column regions of the alignment
+   * Returns an iterator over the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
    *          true to just return the contigs intersecting with the selected
    *          area
    * @return
    */
-  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
   {
-    int[] viscontigs = null;
-    int start = 0, end = 0;
+    int start = 0;
+    int end = 0;
     if (selectedRegionOnly && selectionGroup != null)
     {
       start = selectionGroup.getStartRes();
@@ -471,9 +472,9 @@ public class AlignViewport extends AlignmentViewport
     {
       end = getAlignment().getWidth();
     }
-    viscontigs = getAlignment().getHiddenColumns().getVisibleContigs(start,
-            end);
-    return viscontigs;
+
+    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+            end, false);
   }
 
   /**
@@ -587,58 +588,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  /**
-   * 
-   * @param pdbEntries
-   * @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)
-  {
-    List<SequenceI[]> seqvectors = new ArrayList<>();
-    for (PDBEntry pdb : pdbEntries)
-    {
-      List<SequenceI> choosenSeqs = new ArrayList<>();
-      for (SequenceI sq : getAlignment().getSequences())
-      {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
-                .getAllPDBEntries();
-        if (pdbRefEntries == null)
-        {
-          continue;
-        }
-        for (PDBEntry pdbRefEntry : pdbRefEntries)
-        {
-          if (pdbRefEntry.getId().equals(pdb.getId()))
-          {
-            if (pdbRefEntry.getChainCode() != null
-                    && pdb.getChainCode() != null)
-            {
-              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
-                      pdb.getChainCode()) && !choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-            else
-            {
-              if (!choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-
-          }
-        }
-      }
-      seqvectors
-              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
-    }
-    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
-  }
-
   @Override
   public boolean isNormaliseSequenceLogo()
   {