JAL-1553 implementation of column selection by annotation and threshold queries

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 632d2b2..10e14d1 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -97,7 +97,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean showSequenceFeatures = false;
 
-  boolean showAnnotation = true;
+  private boolean showAnnotation = true;
 
   SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -149,8 +149,9 @@ public class AlignViewport extends AlignmentViewport implements
 
   Color textColour2 = Color.white;
 
-  boolean rightAlignIds = false;
+  private boolean rightAlignIds = false;
 
+  private AnnotationColumnSelection currentAnnotationColumnSelectionState;
   /**
    * Creates a new AlignViewport object.
    * 
@@ -286,9 +287,9 @@ public class AlignViewport extends AlignmentViewport implements
     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
     showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -839,7 +840,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public boolean getShowAnnotation()
   {
-    return showAnnotation;
+    return isShowAnnotation();
   }
 
   /**
@@ -1303,4 +1304,30 @@ public class AlignViewport extends AlignmentViewport implements
   {
     this.showAutocalculatedAbove = showAutocalculatedAbove;
   }
+
+  public boolean isShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
+
+  public AnnotationColumnSelection getCurrentAnnotationColumnSelectionState()
+  {
+    return currentAnnotationColumnSelectionState;
+  }
+
+  public void setCurrentAnnotationColumnSelectionState(
+          AnnotationColumnSelection currentAnnotationColumnSelectionState)
+  {
+    this.currentAnnotationColumnSelectionState = currentAnnotationColumnSelectionState;
+  }
 }