group autoannotation and consensus display settings

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 289fab7..159acb1 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -349,7 +349,15 @@ public class AlignViewport implements SelectionSource
 
           alignment.addAnnotation(quality);
         }
+        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false);
+        
+        {
+          
+        }
       }
+      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true);
+      showConsensusProfile = Cache.getDefault("SHOW_CONSENSUS_PROFILE", false);
+      showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
@@ -2086,6 +2094,35 @@ public class AlignViewport implements SelectionSource
    * should consensus rows be shown for groups
    */
   boolean showGroupConsensus = false;
+  /**
+   * should consensus profile be rendered by default
+   */
+  public boolean showConsensusProfile = false;
+  /**
+   * should consensus histograms be rendered by default
+   */
+  public boolean showConsensusHistogram = true;
+  /**
+   * @return the showConsensusProfile
+   */
+  public boolean isShowConsensusProfile()
+  {
+    return showConsensusProfile;
+  }
+  /**
+   * @param showConsensusProfile the showConsensusProfile to set
+   */
+  public void setShowConsensusProfile(boolean showConsensusProfile)
+  {
+    this.showConsensusProfile = showConsensusProfile;
+  }
+  /**
+   * @param showConsensusHistogram the showConsensusHistogram to set
+   */
+  public void setShowConsensusHistogram(boolean showConsensusHistogram)
+  {
+    this.showConsensusHistogram = showConsensusHistogram;
+  }
   
   /**
    * @return the showGroupConservation
@@ -2130,4 +2167,13 @@ public class AlignViewport implements SelectionSource
     this.includeAllConsensusSymbols = includeAllConsensusSymbols;
   }
   
+  /**
+   * 
+   * @return flag to indicate if the consensus histogram should be rendered by default
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return this.showConsensusHistogram;
+  }
+  
 }