JAL-1953 2.11.2 with Archeopteryx!

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ec3f12e..b4e33c8 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeaturesDisplayedI;
@@ -31,6 +32,7 @@ import jalview.api.ViewStyleI;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
@@ -43,6 +45,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeI;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
@@ -662,7 +665,7 @@ 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,
@@ -708,13 +711,13 @@ public abstract class AlignmentViewport
   /**
    * results of cDNA complement consensus visible portion of view
    */
-  protected Hashtable[] hcomplementConsensus = null;
+  protected Hashtable<String, Object>[] hcomplementConsensus = null;
 
   /**
    * results of secondary structure base pair consensus for visible portion of
    * view
    */
-  protected Hashtable[] hStrucConsensus = null;
+  protected Hashtable<String, Object>[] hStrucConsensus = null;
 
   protected Conservation hconservation = null;
 
@@ -743,7 +746,8 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public void setComplementConsensusHash(Hashtable[] hconsensus)
+  public void setComplementConsensusHash(
+          Hashtable<String, Object>[] hconsensus)
   {
     this.hcomplementConsensus = hconsensus;
   }
@@ -755,19 +759,20 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public Hashtable[] getComplementConsensusHash()
+  public Hashtable<String, Object>[] getComplementConsensusHash()
   {
     return hcomplementConsensus;
   }
 
   @Override
-  public Hashtable[] getRnaStructureConsensusHash()
+  public Hashtable<String, Object>[] getRnaStructureConsensusHash()
   {
     return hStrucConsensus;
   }
 
   @Override
-  public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+  public void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus)
   {
     this.hStrucConsensus = hStrucConsensus;
 
@@ -957,7 +962,9 @@ public abstract class AlignmentViewport
     changeSupport = null;
     ranges = null;
     currentTree = null;
+    currentExtTree = null;
     selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -1636,6 +1643,7 @@ public abstract class AlignmentViewport
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -1796,7 +1804,7 @@ public abstract class AlignmentViewport
       }
     } while (end < max);
 
-    int[][] startEnd = new int[regions.size()][2];
+    // int[][] startEnd = new int[regions.size()][2];
 
     return regions;
   }
@@ -1814,9 +1822,8 @@ 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
         {
@@ -2151,7 +2158,7 @@ public abstract class AlignmentViewport
      * TODO reorder the annotation rows according to group/sequence ordering on
      * alignment
      */
-    boolean sortg = true;
+    // boolean sortg = true;
 
     // remove old automatic annotation
     // add any new annotation
@@ -2261,7 +2268,7 @@ public abstract class AlignmentViewport
   public void clearSequenceColours()
   {
     sequenceColours.clear();
-  };
+  }
 
   @Override
   public AlignViewportI getCodingComplement()
@@ -2726,6 +2733,18 @@ public abstract class AlignmentViewport
     return viewStyle.isShowComplementFeatures();
   }
 
+  @Override
+  public void setShowComplementFeaturesOnTop(boolean b)
+  {
+    viewStyle.setShowComplementFeaturesOnTop(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeaturesOnTop()
+  {
+    return viewStyle.isShowComplementFeaturesOnTop();
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -2896,6 +2915,8 @@ public abstract class AlignmentViewport
 
   protected TreeModel currentTree = null;
 
+  protected TreeI currentExtTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2956,7 +2977,7 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public void setCurrentTree(TreeModel tree)
+  public void setCurrentTree(TreeModel tree) // adapt to Aptx
   {
     currentTree = tree;
   }
@@ -2966,4 +2987,127 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  @Override
+  public AlignmentExportData getAlignExportData(
+          AlignExportSettingsI options)
+  {
+    AlignmentI alignmentToExport = null;
+    String[] omitHidden = null;
+    alignmentToExport = null;
+
+    if (hasHiddenColumns() && !options.isExportHiddenColumns())
+    {
+      omitHidden = getViewAsString(false,
+              options.isExportHiddenSequences());
+    }
+
+    int[] alignmentStartEnd = new int[2];
+    if (hasHiddenRows() && options.isExportHiddenSequences())
+    {
+      alignmentToExport = getAlignment().getHiddenSequences()
+              .getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = getAlignment();
+    }
+    alignmentStartEnd = getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd);
+    return ed;
+  }
+
+  /**
+   * 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);
+    }
+  }
+
+  @Override
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int start = 0;
+    int end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      end = alignment.getWidth();
+    }
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
+  }
+  public TreeI getCurrentExtTree()
+  {
+    return currentExtTree;
+  }
+
+  public void setCurrentExtTree(TreeI externalTree)
+  {
+    currentExtTree = externalTree;
+  }
+
 }