Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ab67202..abca110 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -900,18 +900,14 @@ public abstract class AlignmentViewport
     }
   }
 
-  /**
-   * trigger update of information annotation
-   */
   @Override
-  public void updateInformation(final AlignmentViewPanel ap)
+  public void initInformationWorker(final AlignmentViewPanel ap)
   {
     if (calculator
             .getRegisteredWorkersOfClass(InformationThread.class) == null)
     {
       calculator.registerWorker(new InformationThread(this, ap));
     }
-
   }
 
   // --------START Structure Conservation
@@ -1032,17 +1028,17 @@ public abstract class AlignmentViewport
   /**
    * should hmm profile be rendered by default
    */
-  protected boolean showHMMSequenceLogo = false;
+  protected boolean hmmShowSequenceLogo = false;
 
   /**
    * should hmm profile be rendered normalised to row height
    */
-  protected boolean normaliseHMMSequenceLogo = false;
+  protected boolean hmmNormaliseSequenceLogo = false;
 
   /**
    * should information histograms be rendered by default
    */
-  protected boolean showInformationHistogram = true;
+  protected boolean hmmShowHistogram = true;
 
   /**
    * @return the showConsensusProfile
@@ -1059,7 +1055,7 @@ public abstract class AlignmentViewport
   @Override
   public boolean isShowHMMSequenceLogo()
   {
-    return showHMMSequenceLogo;
+    return hmmShowSequenceLogo;
   }
 
   /**
@@ -1082,12 +1078,14 @@ public abstract class AlignmentViewport
 
   public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
   {
-    if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+    if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
     {
-      this.showHMMSequenceLogo = showHMMSequenceLogo;
-      calculator.updateAnnotationFor(InformationThread.class);
+      this.hmmShowSequenceLogo = showHMMSequenceLogo;
+      // TODO: updateAnnotation if description (tooltip) will show
+      // profile in place of information content?
+      // calculator.updateAnnotationFor(InformationThread.class);
     }
-    this.showHMMSequenceLogo = showHMMSequenceLogo;
+    this.hmmShowSequenceLogo = showHMMSequenceLogo;
   }
 
   /**
@@ -1101,11 +1099,10 @@ public abstract class AlignmentViewport
 
   /**
    * @param showInformationHistogram
-   *          the showInformationHistogram to set
    */
   public void setShowInformationHistogram(boolean showInformationHistogram)
   {
-    this.showInformationHistogram = showInformationHistogram;
+    this.hmmShowHistogram = showInformationHistogram;
   }
 
   /**
@@ -1161,7 +1158,7 @@ public abstract class AlignmentViewport
   @Override
   public boolean isShowInformationHistogram()
   {
-    return this.showInformationHistogram;
+    return this.hmmShowHistogram;
   }
 
   /**
@@ -1313,7 +1310,6 @@ public abstract class AlignmentViewport
     ignoreGapsInConsensusCalculation = b;
     if (ap != null)
     {
-      updateConsensus(ap);
       if (residueShading != null)
       {
         residueShading.setThreshold(residueShading.getThreshold(),
@@ -1324,22 +1320,12 @@ public abstract class AlignmentViewport
 
   public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
   {
-    boolean was = ignoreBelowBackGroundFrequencyCalculation;
     ignoreBelowBackGroundFrequencyCalculation = b;
-    if (ap != null && was != b)
-    {
-      updateInformation(ap);
-    }
   }
 
   public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
   {
-    boolean was = infoLetterHeight;
     infoLetterHeight = b;
-    if (ap != null && was != b)
-    {
-      updateInformation(ap);
-    }
   }
 
   private long sgrouphash = -1, colselhash = -1;
@@ -1773,7 +1759,8 @@ public abstract class AlignmentViewport
     }
     else
     {
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment,
+              true);
     }
 
     return sequences;
@@ -1967,20 +1954,6 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
-    {
-      updateConsensus(ap);
-    }
-    if (consensusProfiles != null && autoCalculateConsensus)
-    {
-      updateConservation(ap);
-    }
-    if (autoCalculateStrucConsensus)
-    {
-      updateStrucConsensus(ap);
-    }
-    // initInformation();
-    updateInformation(ap);
 
     // Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
@@ -2003,7 +1976,6 @@ public abstract class AlignmentViewport
 
     updateAllColourSchemes();
     calculator.restartWorkers();
-    // alignment.adjustSequenceAnnotations();
   }
 
   /**
@@ -2303,7 +2275,7 @@ public abstract class AlignmentViewport
           sg.setshowSequenceLogo(showprf);
           sg.setShowConsensusHistogram(showConsHist);
           sg.setNormaliseSequenceLogo(normLogo);
-          sg.setshowHMMSequenceLogo(showHMMPrf);
+          sg.setShowHMMSequenceLogo(showHMMPrf);
           sg.setShowInformationHistogram(showInfoHist);
           sg.setNormaliseHMMSequenceLogo(normHMMLogo);
         }
@@ -3090,4 +3062,26 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return hmmNormaliseSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    hmmNormaliseSequenceLogo = state;
+  }
 }