Merge branch 'develop' into developtomchmmer

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 192d82a..847084d 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -35,7 +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;
@@ -57,10 +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;
 
@@ -81,7 +79,7 @@ public class AlignViewport extends AlignmentViewport
 
   private Rectangle explodedGeometry;
 
-  String viewName;
+  private String viewName;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -263,7 +261,11 @@ public class AlignViewport extends AlignmentViewport
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
     AlignmentI al = getAlignment();
-    al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+
+    if (Cache.getDefault("NORMALISE_GAPS", true))
+    {
+      al.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
@@ -281,6 +283,10 @@ public class AlignViewport extends AlignmentViewport
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
 
@@ -300,7 +306,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(al, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -314,6 +320,7 @@ public class AlignViewport extends AlignmentViewport
     {
       residueShading.setConsensus(consensusProfiles);
     }
+    setColourAppliesToAllGroups(true);
   }
 
   /**
@@ -451,17 +458,17 @@ 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 +478,9 @@ public class AlignViewport extends AlignmentViewport
     {
       end = getAlignment().getWidth();
     }
-    viscontigs = getAlignment().getHiddenColumns().getVisibleContigs(start,
-            end);
-    return viscontigs;
+
+    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+            end, false);
   }
 
   /**
@@ -589,75 +596,6 @@ public class AlignViewport extends AlignmentViewport
 
   /**
    * 
-   * @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()
-  {
-    return normaliseSequenceLogo;
-  }
-
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
-  public void setNormaliseHMMSequenceLogo(boolean state)
-  {
-    normaliseHMMSequenceLogo = state;
-  }
-
-  /**
-   * 
    * @return true if alignment characters should be displayed
    */
   @Override
@@ -858,7 +796,7 @@ public class AlignViewport extends AlignmentViewport
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
     newAlignFrame.setTitle(title);
-    newAlignFrame.statusBar.setText(MessageManager
+    newAlignFrame.setStatus(MessageManager
             .formatMessage("label.successfully_loaded_file", new Object[]
             { title }));
 
@@ -1096,10 +1034,13 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
-  @Override
-  public boolean isNormaliseHMMSequenceLogo()
+  public String getViewName()
   {
-    return normaliseHMMSequenceLogo;
+    return viewName;
   }
 
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }