JAL-1553 enhancement of column selection by annotation row to include the query filte...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 40f95e2..b8f575f 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -95,10 +95,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
-  private boolean showAnnotation = true;
-
   SequenceAnnotationOrder sortAnnotationsBy = null;
 
   int charHeight;
@@ -125,12 +121,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean cursorMode = false;
 
-  /**
-   * Keys are the feature types which are currently visible. Note: Values are
-   * not used!
-   */
-  Hashtable featuresDisplayed = null;
-
   boolean antiAlias = false;
 
   Rectangle explodedPosition;
@@ -148,9 +138,9 @@ public class AlignViewport extends AlignmentViewport implements
   Color textColour = Color.black;
 
   Color textColour2 = Color.white;
-
   private boolean rightAlignIds = false;
 
+  private AnnotationColumnChooser annotationColumnSelectionState;
   /**
    * Creates a new AlignViewport object.
    * 
@@ -368,22 +358,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * set the flag
-   * 
-   * @param b
-   *          features are displayed if true
-   */
-  public void setShowSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
-  /**
    * centre columnar annotation labels in displayed alignment annotation TODO:
    * add to jalviewXML and annotation display settings
    */
@@ -837,27 +811,6 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public boolean getShowAnnotation()
-  {
-    return isShowAnnotation();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   public boolean getScaleAboveWrapped()
   {
     return scaleAboveWrapped;
@@ -1101,8 +1054,6 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
-  boolean showSeqFeaturesHeight;
-
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -1111,16 +1062,6 @@ public class AlignViewport extends AlignmentViewport implements
                     new ColumnSelection(getColumnSelection()), this);
   }
 
-  public void setShowSequenceFeaturesHeight(boolean selected)
-  {
-    showSeqFeaturesHeight = selected;
-  }
-
-  public boolean getShowSequenceFeaturesHeight()
-  {
-    return showSeqFeaturesHeight;
-  }
-
   /**
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.
@@ -1294,9 +1235,10 @@ public class AlignViewport extends AlignmentViewport implements
     this.showAutocalculatedAbove = showAutocalculatedAbove;
   }
 
+
   public boolean isShowAnnotation()
   {
-    return showAnnotation;
+    return super.isShowAnnotation();
   }
 
   public boolean isRightAlignIds()
@@ -1308,4 +1250,15 @@ public class AlignViewport extends AlignmentViewport implements
   {
     this.rightAlignIds = rightAlignIds;
   }
+
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser currentAnnotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+  }
 }