X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=15c09718475cae787b8974c5ca9f071010bf708a;hb=1b0f0d6c0a343e67453ed4f7e1ca3f9c2a7a6ff2;hp=90271c8e4a6ac604e052eddb51074482f61ca228;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 90271c8..15c0971 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -36,7 +35,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
@@ -58,10 +56,9 @@ import java.awt.Dimension;
 import java.awt.Font;
 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;
 
 import javax.swing.JInternalFrame;
 
@@ -257,9 +254,11 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-
+    if (Cache.getDefault("NORMALISE_GAPS", true))
+    {
+      alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(
+              0));
+    }
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
     if (hconsensus == null && !isDataset)
@@ -453,10 +452,10 @@ public class AlignViewport extends AlignmentViewport
    *          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();
@@ -466,8 +465,8 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
-    return viscontigs;
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**
@@ -583,58 +582,6 @@ 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<SequenceI[]>();
-    for (PDBEntry pdb : pdbEntries)
-    {
-      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
-      for (SequenceI sq : alignment.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()
   {
@@ -656,7 +603,7 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {