X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=0c8afaa6bba9d3c7fa8a0eb7a30afdd75d3c245a;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=617800b6c7e22b41114b31d03d890343728f428b;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 617800b..0c8afaa 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -214,15 +214,18 @@ public abstract class AlignmentViewport implements AlignViewportI
     // calculation till later or to do all calculations in thread.
     // via changecolour
     globalColourScheme = cs;
-    boolean recalc=false;
-    if (cs!=null)
+    boolean recalc = false;
+    if (cs != null)
     {
       cs.setConservationApplied(recalc = getConservationSelected());
-      if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+      if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+              || cs instanceof Blosum62ColourScheme)
       {
         recalc = true;
         cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
-      } else {
+      }
+      else
+      {
         cs.setThreshold(0, ignoreGapsInConsensusCalculation);
       }
       if (recalc)
@@ -247,7 +250,7 @@ public abstract class AlignmentViewport implements AlignViewportI
                 || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
-          recalc=true;
+          recalc = true;
         }
         else
         {
@@ -257,16 +260,19 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (getConservationSelected())
         {
           sg.cs.setConservationApplied(true);
-          recalc=true;
+          recalc = true;
         }
         else
         {
           sg.cs.setConservation(null);
           // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
         }
-        if (recalc) {
+        if (recalc)
+        {
           sg.recalcConservation();
-        } else {
+        }
+        else
+        {
           sg.cs.alignmentChanged(sg, hiddenRepSequences);
         }
       }
@@ -302,13 +308,15 @@ public abstract class AlignmentViewport implements AlignViewportI
    * view
    */
   protected Hashtable[] hStrucConsensus = null;
-  
+
   protected Conservation hconservation = null;
+
   @Override
   public void setConservation(Conservation cons)
   {
     hconservation = cons;
   }
+
   /**
    * percentage gaps allowed in a column before all amino acid properties should
    * be considered unconserved
@@ -1373,15 +1381,15 @@ public abstract class AlignmentViewport implements AlignViewportI
       {
         conservation = new AlignmentAnnotation("Conservation",
                 "Conservation of total alignment less than "
-                        + getConsPercGaps() + "% gaps",
-                new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
+                        + getConsPercGaps() + "% gaps", new Annotation[1],
+                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
       }
     }
   }
+
   private void initQuality()
   {
     if (showQuality)
@@ -1390,21 +1398,20 @@ public abstract class AlignmentViewport implements AlignViewportI
       {
         quality = new AlignmentAnnotation("Quality",
                 "Alignment Quality based on Blosum62 scores",
-                new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
         alignment.addAnnotation(quality);
       }
     }
   }
+
   private void initRNAStructure()
   {
-    if (alignment.hasRNAStructure() && strucConsensus==null)
+    if (alignment.hasRNAStructure() && strucConsensus == null)
     {
       strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-              new Annotation[1], 0f, 100f,
-              AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       strucConsensus.hasText = true;
       strucConsensus.autoCalculated = true;
 
@@ -1414,6 +1421,7 @@ public abstract class AlignmentViewport implements AlignViewportI
       }
     }
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -1514,7 +1522,7 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.add(aan[an].groupRef);
-          alignment.deleteAnnotation(aan[an],false);
+          alignment.deleteAnnotation(aan[an], false);
         }
       }
     }
@@ -1554,11 +1562,12 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public Color getSequenceColour(SequenceI seq)
   {
-    Color sqc=Color.white;
+    Color sqc = Color.white;
     if (sequenceColours != null)
     {
       sqc = (Color) sequenceColours.get(seq);
-      if (sqc == null) {
+      if (sqc == null)
+      {
         sqc = Color.white;
       }
     }