JAL-969 hasHiddenRows is now an interface method

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 3afa1f5..84a62ae 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -6,31 +6,37 @@
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
+import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Font;
+import java.util.Stack;
+
 public class AlignViewport extends AlignmentViewport implements
         AlignViewportI, SelectionSource, VamsasSource
 {
@@ -56,8 +62,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
   boolean showAnnotation = true;
 
   boolean upperCasebold = false;
@@ -84,10 +88,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean scaleRightWrapped = true;
 
-  // The following vector holds the features which are
-  // currently visible, in the correct order or rendering
-  public Hashtable featuresDisplayed;
-
   boolean showHiddenMarkers = true;
 
   public jalview.bin.JalviewLite applet;
@@ -98,6 +98,8 @@ public class AlignViewport extends AlignmentViewport implements
 
   Stack redoList = new Stack();
 
+  private AnnotationColumnChooser annotationColumnSelectionState;
+
   public void finalize()
   {
     applet = null;
@@ -254,16 +256,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -637,12 +629,6 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-  @Override
-  public boolean hasHiddenColumns()
-  {
-    return hasHiddenColumns;
-  }
-
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -662,4 +648,15 @@ public class AlignViewport extends AlignmentViewport implements
     return validCharWidth;
   }
 
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser annotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = annotationColumnSelectionState;
+  }
+
 }