JAL-2430 colour columns hidden in alignment gray on structure

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index fda08fd..7d57886 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,6 +20,7 @@
  */
 package jalview.structures.models;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -42,6 +43,7 @@ import jalview.util.MessageManager;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 /**
@@ -521,15 +523,15 @@ public abstract class AAStructureBindingModel extends
    *          the sequence alignment which is the basis of structure
    *          superposition
    * @param matched
-   *          an array of booleans, indexed by alignment column, where true
-   *          indicates that every structure has a mapped residue present in the
-   *          column (so the column can participate in structure alignment)
+   *          a BitSet, where bit j is set to indicate that every structure has
+   *          a mapped residue present in column j (so the column can
+   *          participate in structure alignment)
    * @param structures
    *          an array of data beans corresponding to pdb file index
    * @return
    */
   protected int findSuperposableResidues(AlignmentI alignment,
-          boolean[] matched, SuperposeData[] structures)
+          BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
     String[] files = getPdbFile();
@@ -559,16 +561,16 @@ public abstract class AAStructureBindingModel extends
             {
               refStructure = pdbfnum;
             }
-            for (int r = 0; r < matched.length; r++)
+            for (int r = 0; r < alignment.getWidth(); r++)
             {
-              if (!matched[r])
+              if (!matched.get(r))
               {
                 continue;
               }
               int pos = getMappedPosition(theSequence, r, mapping);
               if (pos < 1 || pos == lastPos)
               {
-                matched[r] = false;
+                matched.clear(r);
                 continue;
               }
               lastPos = pos;
@@ -700,14 +702,30 @@ public abstract class AAStructureBindingModel extends
 
   public abstract void setJalviewColourScheme(ColourSchemeI cs);
 
-  public abstract void superposeStructures(AlignmentI[] als, int[] alm,
-          ColumnSelection[] alc);
+  /**
+   * Constructs and sends a command to align structures against a reference
+   * structure, based on one or more sequence alignments. May optionally return
+   * an error or warning message for the alignment command.
+   * 
+   * @param alignments
+   *          an array of alignments to process
+   * @param structureIndices
+   *          an array of corresponding reference structures (index into pdb
+   *          file array); if a negative value is passed, the first PDB file
+   *          mapped to an alignment sequence is used as the reference for
+   *          superposition
+   * @param hiddenCols
+   *          an array of corresponding hidden columns for each alignment
+   * @return
+   */
+  public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
+          ColumnSelection[] hiddenCols);
 
   public abstract void setBackgroundColour(Color col);
 
   protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment);
+          AlignViewportI alignViewportI);
 
   /**
    * returns the current featureRenderer that should be used to colour the
@@ -743,8 +761,6 @@ public abstract class AAStructureBindingModel extends
    */
   public void colourBySequence(AlignmentViewPanel alignmentv)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
     if (!colourBySequence || !isLoadingFinished())
     {
       return;
@@ -758,14 +774,15 @@ public abstract class AAStructureBindingModel extends
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
     FeatureRenderer fr = null;
+    boolean showFeatures = alignmentv.getAlignViewport()
+            .isShowSequenceFeatures();
     if (showFeatures)
     {
       fr = getFeatureRenderer(alignmentv);
     }
-    AlignmentI alignment = alignmentv.getAlignment();
   
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, fr, alignment);
+            files, sr, fr, alignmentv.getAlignViewport());
     colourBySequence(colourBySequenceCommands);
   }