Merge branch 'develop' into developtomchmmer

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 7c0c045..39a1c18 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -702,7 +702,8 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs);
+        sg.setColourScheme(
+                cs == null ? null : cs.getInstance(this, sg));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
@@ -1028,17 +1029,17 @@ public abstract class AlignmentViewport
   /**
    * should hmm profile be rendered by default
    */
-  protected boolean showHMMSequenceLogo = false;
+  protected boolean hmmShowSequenceLogo = false;
 
   /**
    * should hmm profile be rendered normalised to row height
    */
-  protected boolean normaliseHMMSequenceLogo = false;
+  protected boolean hmmNormaliseSequenceLogo = false;
 
   /**
    * should information histograms be rendered by default
    */
-  protected boolean showInformationHistogram = true;
+  protected boolean hmmShowHistogram = true;
 
   /**
    * @return the showConsensusProfile
@@ -1055,7 +1056,7 @@ public abstract class AlignmentViewport
   @Override
   public boolean isShowHMMSequenceLogo()
   {
-    return showHMMSequenceLogo;
+    return hmmShowSequenceLogo;
   }
 
   /**
@@ -1078,14 +1079,14 @@ public abstract class AlignmentViewport
 
   public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
   {
-    if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+    if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
     {
-      this.showHMMSequenceLogo = showHMMSequenceLogo;
+      this.hmmShowSequenceLogo = showHMMSequenceLogo;
       // TODO: updateAnnotation if description (tooltip) will show
       // profile in place of information content?
       // calculator.updateAnnotationFor(InformationThread.class);
     }
-    this.showHMMSequenceLogo = showHMMSequenceLogo;
+    this.hmmShowSequenceLogo = showHMMSequenceLogo;
   }
 
   /**
@@ -1099,11 +1100,10 @@ public abstract class AlignmentViewport
 
   /**
    * @param showInformationHistogram
-   *          the showInformationHistogram to set
    */
   public void setShowInformationHistogram(boolean showInformationHistogram)
   {
-    this.showInformationHistogram = showInformationHistogram;
+    this.hmmShowHistogram = showInformationHistogram;
   }
 
   /**
@@ -1159,7 +1159,7 @@ public abstract class AlignmentViewport
   @Override
   public boolean isShowInformationHistogram()
   {
-    return this.showInformationHistogram;
+    return this.hmmShowHistogram;
   }
 
   /**
@@ -1737,6 +1737,7 @@ public abstract class AlignmentViewport
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -1760,7 +1761,8 @@ public abstract class AlignmentViewport
     }
     else
     {
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment,
+              true);
     }
 
     return sequences;
@@ -2275,7 +2277,7 @@ public abstract class AlignmentViewport
           sg.setshowSequenceLogo(showprf);
           sg.setShowConsensusHistogram(showConsHist);
           sg.setNormaliseSequenceLogo(normLogo);
-          sg.setshowHMMSequenceLogo(showHMMPrf);
+          sg.setShowHMMSequenceLogo(showHMMPrf);
           sg.setShowInformationHistogram(showInfoHist);
           sg.setNormaliseHMMSequenceLogo(normHMMLogo);
         }
@@ -3077,11 +3079,75 @@ public abstract class AlignmentViewport
   @Override
   public boolean isNormaliseHMMSequenceLogo()
   {
-    return normaliseHMMSequenceLogo;
+    return hmmNormaliseSequenceLogo;
   }
 
   public void setNormaliseHMMSequenceLogo(boolean state)
   {
-    normaliseHMMSequenceLogo = state;
+    hmmNormaliseSequenceLogo = state;
+  }
+
+  /**
+   * flag set to indicate if structure views might be out of sync with sequences
+   * in the alignment
+   */
+
+  private boolean needToUpdateStructureViews = false;
+
+  @Override
+  public boolean isUpdateStructures()
+  {
+    return needToUpdateStructureViews;
+  }
+
+  @Override
+  public void setUpdateStructures(boolean update)
+  {
+    needToUpdateStructureViews = update;
+  }
+
+  @Override
+  public boolean needToUpdateStructureViews()
+  {
+    boolean update = needToUpdateStructureViews;
+    needToUpdateStructureViews = false;
+    return update;
+  }
+
+  @Override
+  public void addSequenceGroup(SequenceGroup sequenceGroup)
+  {
+    alignment.addGroup(sequenceGroup);
+
+    Color col = sequenceGroup.idColour;
+    if (col != null)
+    {
+      col = col.brighter();
+
+      for (SequenceI sq : sequenceGroup.getSequences())
+      {
+        setSequenceColour(sq, col);
+      }
+    }
+
+    if (codingComplement != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils
+              .mapSequenceGroup(sequenceGroup, this, codingComplement);
+      if (mappedGroup.getSequences().size() > 0)
+      {
+        codingComplement.getAlignment().addGroup(mappedGroup);
+
+        if (col != null)
+        {
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+      // propagate the structure view update flag according to our own setting
+      codingComplement.setUpdateStructures(needToUpdateStructureViews);
+    }
   }
 }