JAL-2446 merged to spike branch

[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 063eacf..1637631 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,21 +20,28 @@
  */
 package jalview.structures.models;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 /**
@@ -85,6 +92,8 @@ public abstract class AAStructureBindingModel extends
    */
   protected String[] modelFileNames = null;
 
+  public String fileLoadingError;
+
   /**
    * Data bean class to simplify parameterisation in superposeStructures
    */
@@ -512,18 +521,18 @@ 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();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -550,16 +559,16 @@ 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;
@@ -688,4 +697,79 @@ public abstract class AAStructureBindingModel extends
   {
     return null;
   }
+
+  public abstract void setJalviewColourScheme(ColourSchemeI cs);
+
+  /**
+   * 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, HiddenColumns[] hiddenCols);
+
+  public abstract void setBackgroundColour(Color col);
+
+  protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+          String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
+
+  /**
+   * returns the current sequenceRenderer that should be used to colour the
+   * structures
+   * 
+   * @param alignment
+   * 
+   * @return
+   */
+  public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+
+  protected abstract void colourBySequence(
+          StructureMappingcommandSet[] colourBySequenceCommands);
+
+  public abstract void colourByChain();
+
+  public abstract void colourByCharge();
+
+  /**
+   * colour any structures associated with sequences in the given alignment
+   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+   * if colourBySequence is enabled.
+   */
+  public void colourBySequence(AlignmentViewPanel alignmentv)
+  {
+    if (!colourBySequence || !isLoadingFinished())
+    {
+      return;
+    }
+    if (getSsm() == null)
+    {
+      return;
+    }
+    String[] files = getStructureFiles();
+  
+    SequenceRenderer sr = getSequenceRenderer(alignmentv);
+  
+    StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+            files, sr, alignmentv);
+    colourBySequence(colourBySequenceCommands);
+  }
+
+  public boolean hasFileLoadingError()
+  {
+    return fileLoadingError != null && fileLoadingError.length() > 0;
+  }
+
+  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment);
 }