Merge branch 'develop' into JAL-1483_featureBasedTreeCalc

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0fa4a3c..3fedb92 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,11 +20,11 @@
  */
 package jalview.viewmodel;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -35,10 +35,10 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
@@ -696,6 +696,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     sequenceSetID = new String(newid);
   }
 
+  @Override
   public String getSequenceSetId()
   {
     if (sequenceSetID == null)
@@ -1638,4 +1639,58 @@ public abstract class AlignmentViewport implements AlignViewportI
   {
     sequenceColours = null;
   };
+
+  FeaturesDisplayedI featuresDisplayed = null;
+
+  @Override
+  public FeaturesDisplayedI getFeaturesDisplayed()
+  {
+    return featuresDisplayed;
+  }
+
+  public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
+  {
+    featuresDisplayed = featuresDisplayedI;
+  }
+
+  public boolean areFeaturesDisplayed()
+  {
+    return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+  }
+
+  /**
+   * display setting for showing/hiding sequence features on alignment view
+   */
+  boolean showSequenceFeatures = false;
+
+  /**
+   * set the flag
+   * 
+   * @param b
+   *          features are displayed if true
+   */
+  @Override
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
+  @Override
+  public boolean isShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
+  boolean showSeqFeaturesHeight;
+
+  public void setShowSequenceFeaturesHeight(boolean selected)
+  {
+    showSeqFeaturesHeight = selected;
+  }
+
+  public boolean isShowSequenceFeaturesHeight()
+  {
+    return showSeqFeaturesHeight;
+  }
+
+
 }