add partial button fix to annotation and statistics output

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index dfd120b..61b0b00 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -699,7 +699,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation[] groupConservation;
 
-  protected AlignmentAnnotation hmmConsensus;
+  protected AlignmentAnnotation informationContent;
 
   /**
    * results of alignment consensus analysis for visible portion of view
@@ -793,6 +793,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public AlignmentAnnotation getAlignmentInformationAnnotation()
+  {
+    return informationContent;
+  }
+
+  @Override
   public AlignmentAnnotation getAlignmentGapAnnotation()
   {
     return gapcounts;
@@ -996,6 +1002,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected boolean showConsensusHistogram = true;
 
   /**
+   * should hmm profile be rendered by default
+   */
+  protected boolean showHMMSequenceLogo = false;
+
+  /**
+   * should hmm profile be rendered normalised to row height
+   */
+  protected boolean normaliseHMMSequenceLogo = false;
+
+  /**
+   * should information histograms be rendered by default
+   */
+  protected boolean showInformationHistogram = true;
+
+  /**
    * @return the showConsensusProfile
    */
   @Override
@@ -1005,6 +1026,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
+   * @return the showInformationProfile
+   */
+  @Override
+  public boolean isShowHMMSequenceLogo()
+  {
+    return showHMMSequenceLogo;
+  }
+
+  /**
    * @param showSequenceLogo
    *          the new value
    */
@@ -1022,6 +1052,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
     this.showSequenceLogo = showSequenceLogo;
   }
 
+  public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+  {
+    if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+    {
+      this.showHMMSequenceLogo = showHMMSequenceLogo;
+    }
+    this.showHMMSequenceLogo = showHMMSequenceLogo;
+  }
+
   /**
    * @param showConsensusHistogram
    *          the showConsensusHistogram to set
@@ -1032,6 +1071,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
+   * @param showInformationHistogram
+   *          the showInformationHistogram to set
+   */
+  public void setShowInformationHistogram(boolean showInformationHistogram)
+  {
+    this.showInformationHistogram = showInformationHistogram;
+  }
+
+  /**
    * @return the showGroupConservation
    */
   public boolean isShowGroupConservation()
@@ -1077,6 +1125,17 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
+   * 
+   * @return flag to indicate if the information content histogram should be
+   *         rendered by default
+   */
+  @Override
+  public boolean isShowInformationHistogram()
+  {
+    return this.showInformationHistogram;
+  }
+
+  /**
    * when set, updateAlignment will always ensure sequences are of equal length
    */
   private boolean padGaps = false;
@@ -1304,6 +1363,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
+  @Override
   public boolean isIgnoreBelowBackground()
   {
     return ignoreBelowBackGroundFrequencyCalculation;