update spikes/mungo from JAL-3076 patch branch

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 862c4fb..7e77bec 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -92,12 +92,6 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  boolean validCharWidth;
-
-  public boolean followSelection = true;
-
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
   /**
    * Creates a new AlignViewport object.
    * 
@@ -260,14 +254,14 @@ 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));
+    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 (consensusProfiles == null && !isDataset)
+    if (hconsensus == null && !isDataset)
     {
-      if (!al.isNucleotide())
+      if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -279,19 +273,13 @@ 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();
-    // initInformation();
-
-    String colourProperty = al.isNucleotide()
+    String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -302,7 +290,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(al, schemeName);
+            .getColourScheme(alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -314,10 +302,12 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(consensusProfiles);
+      residueShading.setConsensus(hconsensus);
     }
   }
 
+  boolean validCharWidth;
+
   /**
    * {@inheritDoc}
    */
@@ -400,9 +390,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (getAlignment() != null && align != null)
+    if (alignment != null && align != null)
     {
-      getAlignment().setCodonFrames(align.getCodonFrames());
+      alignment.setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -453,7 +443,7 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * Returns an iterator over the visible column regions of the alignment
+   * returns the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
    *          true to just return the contigs intersecting with the selected
@@ -471,11 +461,10 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = getAlignment().getWidth();
+      end = alignment.getWidth();
     }
-
-    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
-            end, false);
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**
@@ -524,6 +513,8 @@ public class AlignViewport extends AlignmentViewport
     return false;
   }
 
+  public boolean followSelection = true;
+
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -589,6 +580,17 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -599,6 +601,8 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);
@@ -1028,5 +1032,4 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
-
 }