Merge branch 'JAL-1372_referenceseq' into feature_29/JAL-1372_referenceseq

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1b42faf..72cd316 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -24,6 +24,7 @@ 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;
@@ -696,6 +697,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     sequenceSetID = new String(newid);
   }
 
+  @Override
   public String getSequenceSetId()
   {
     if (sequenceSetID == null)
@@ -1029,8 +1031,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return hiddenRepSequences != null
-            && hiddenRepSequences.containsKey(seq);
+    return alignment.getSeqrep()==seq || (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   public SequenceGroup getRepresentedSequences(SequenceI seq)
@@ -1601,6 +1603,34 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
     oldrfs.clear();
   }
+  /**
+   * show the reference sequence in the alignment view
+   */
+  private boolean displayReferenceSeq=false;
+  /**
+   * colour according to the reference sequence defined on the alignment
+   */
+  private boolean colourByReferenceSeq=false;
+
+  public boolean isDisplayReferenceSeq()
+  {
+    return alignment.hasSeqrep() && displayReferenceSeq;
+  }
+
+  public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+  {
+    this.displayReferenceSeq = displayReferenceSeq;
+  }
+
+  public boolean isColourByReferenceSeq()
+  {
+    return alignment.hasSeqrep() && colourByReferenceSeq;
+  }
+
+  public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+  {
+    this.colourByReferenceSeq = colourByReferenceSeq;
+  }
 
   @Override
   public Color getSequenceColour(SequenceI seq)
@@ -1659,4 +1689,97 @@ 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;
+  }
+
+  private boolean showAnnotation = true;
+
+  private boolean rightAlignIds = false;
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowAnnotation()
+  {
+    return isShowAnnotation();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
+
+  public boolean isShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
+
 }