X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=0b40abd1992115f2fe2faf940511d3f97e3dc7d0;hb=d64df47a7e363e2415d2de43353accf523393e56;hp=ef2401160f3cc8afb07f5823dbda24f77eb0ad20;hpb=1d0f5219658cdf6ad5e1a1cbe6e1bb8cd12e6d85;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ef24011..0b40abd 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -79,7 +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
@@ -254,14 +254,13 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+		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)
+		if (hconsensus == null && !isDataset)
     {
-      if (!alignment.isNucleotide())
+			if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -273,13 +272,19 @@ 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);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    String colourProperty = alignment.isNucleotide()
+    // initInformation();
+
+		String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -302,10 +307,11 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(hconsensus);
+			residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
-
+  
   boolean validCharWidth;
 
   /**
@@ -390,7 +396,7 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+		if (alignment != null && align != null)
     {
       alignment.setCodonFrames(align.getCodonFrames());
     }
@@ -443,7 +449,7 @@ 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
@@ -463,8 +469,9 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
+
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -514,7 +521,7 @@ public class AlignViewport extends AlignmentViewport
   }
 
   public boolean followSelection = true;
-
+  
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -579,18 +586,20 @@ public class AlignViewport extends AlignmentViewport
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
   }
-
+  
   @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
 
-  public void setNormaliseSequenceLogo(boolean state)
+  @Override
+public void setNormaliseSequenceLogo(boolean state)
   {
     normaliseSequenceLogo = state;
   }
 
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -600,7 +609,7 @@ public class AlignViewport extends AlignmentViewport
   {
     return validCharWidth;
   }
-
+  
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
@@ -795,7 +804,7 @@ 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 }));
 
@@ -1032,4 +1041,14 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
+
+  public String getViewName()
+  {
+    return viewName;
+  }
+
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }