Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3691a69..48aadf1 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,18 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
@@ -61,18 +73,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -571,6 +571,28 @@ public abstract class AlignmentViewport
     viewStyle.setSeqNameItalics(default1);
   }
 
+  /**
+   * Set the flag indicating that feature count annotation tracks are to be
+   * displayed
+   * 
+   * @see jalview.api.ViewStyleI#setShowSequenceFeatureCounts(boolean)
+   */
+  @Override
+  public void setShowSequenceFeatureCounts(boolean show)
+  {
+    viewStyle.setShowSequenceFeatureCounts(show);
+  }
+
+  /**
+   * @return true if feature count annotation tracks are to be displayed
+   * @see jalview.api.ViewStyleI#isShowSequenceFeatureCounts()
+   */
+  @Override
+  public boolean isShowSequenceFeatureCounts()
+  {
+    return viewStyle.isShowSequenceFeatureCounts();
+  }
+
   @Override
   public AlignmentI getAlignment()
   {
@@ -664,8 +686,7 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(
-                cs == null ? null : cs.getInstance(this, sg));
+        sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
@@ -1825,9 +1846,8 @@ public abstract class AlignmentViewport
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          clone.makeVisibleAnnotation(
-                  selectionGroup.getStartRes(), selectionGroup.getEndRes(),
-                  alignment.getHiddenColumns());
+          clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+                  selectionGroup.getEndRes(), alignment.getHiddenColumns());
         }
         else
         {
@@ -2991,7 +3011,8 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+  public AlignmentExportData getAlignExportData(
+          AlignExportSettingsI options)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -3019,7 +3040,7 @@ public abstract class AlignmentViewport
             omitHidden, alignmentStartEnd);
     return ed;
   }
-  
+
   /**
    * flag set to indicate if structure views might be out of sync with sequences
    * in the alignment