JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods

[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..fda08fd 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,19 +20,26 @@
  */
 package jalview.structures.models;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 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.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
    */
@@ -688,4 +697,80 @@ public abstract class AAStructureBindingModel extends
   {
     return null;
   }
+
+  public abstract void setJalviewColourScheme(ColourSchemeI cs);
+
+  public abstract void superposeStructures(AlignmentI[] als, int[] alm,
+          ColumnSelection[] alc);
+
+  public abstract void setBackgroundColour(Color col);
+
+  protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+          String[] files, SequenceRenderer sr, FeatureRenderer fr,
+          AlignmentI alignment);
+
+  /**
+   * returns the current featureRenderer that should be used to colour the
+   * structures
+   * 
+   * @param alignment
+   * 
+   * @return
+   */
+  public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+
+  /**
+   * 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)
+  {
+    boolean showFeatures = alignmentv.getAlignViewport()
+            .isShowSequenceFeatures();
+    if (!colourBySequence || !isLoadingFinished())
+    {
+      return;
+    }
+    if (getSsm() == null)
+    {
+      return;
+    }
+    String[] files = getPdbFile();
+  
+    SequenceRenderer sr = getSequenceRenderer(alignmentv);
+  
+    FeatureRenderer fr = null;
+    if (showFeatures)
+    {
+      fr = getFeatureRenderer(alignmentv);
+    }
+    AlignmentI alignment = alignmentv.getAlignment();
+  
+    StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+            files, sr, fr, alignment);
+    colourBySequence(colourBySequenceCommands);
+  }
+
+  public boolean hasFileLoadingError()
+  {
+    return fileLoadingError != null && fileLoadingError.length() > 0;
+  }
 }