JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 8354410..2171815 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -93,8 +93,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private boolean loadingFinished = true;
 
-  public String fileLoadingError;
-
   /*
    * Map of ChimeraModel objects keyed by PDB full local file name
    */
@@ -254,18 +252,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Construct a title string for the viewer window based on the data Jalview
-   * knows about
-   * 
-   * @param verbose
-   * @return
-   */
-  public String getViewerTitle(boolean verbose)
-  {
-    return getViewerTitle("Chimera", verbose);
-  }
-
-  /**
    * Tells Chimera to display only the specified chains
    * 
    * @param toshow
@@ -328,6 +314,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     releaseUIResources();
   }
 
+  @Override
   public void colourByChain()
   {
     colourBySequence = false;
@@ -343,6 +330,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * <li>all others - white</li>
    * </ul>
    */
+  @Override
   public void colourByCharge()
   {
     colourBySequence = false;
@@ -364,6 +352,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param _hiddenCols
    *          an array of corresponding hidden columns for each alignment
    */
+  @Override
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
@@ -680,34 +669,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String progressMsg);
 
   /**
-   * colour any structures associated with sequences in the given alignment
-   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
-   * if colourBySequence is enabled.
+   * Sends a set of colour commands to the structure viewer
+   * 
+   * @param colourBySequenceCommands
    */
-  public void colourBySequence(boolean showFeatures,
-          jalview.api.AlignmentViewPanel alignmentv)
+  @Override
+  protected void colourBySequence(
+          StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    if (!colourBySequence || !loadingFinished)
-    {
-      return;
-    }
-    if (getSsm() == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
-            files, sr, fr, alignment))
+    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
     {
       for (String command : cpdbbyseq.commands)
       {
@@ -723,6 +693,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param alignment
    * @return
    */
+  @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
@@ -758,40 +729,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // //////////////////////////
 
   /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * instruct the Jalview binding to update the pdbentries vector if necessary
    * prior to matching the viewer's contents to the list of structure files
    * Jalview knows about.
    */
   public abstract void refreshPdbEntries();
 
-  private int getModelNum(String modelFileName)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-
   /**
    * map between index of model filename returned from getPdbFile and the first
    * index of models from this file in the viewer. Note - this is not trimmed -
@@ -814,17 +757,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * returns the current sequenceRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * Construct and send a command to highlight zero, one or more atoms. We do
    * this by sending an "rlabel" command to show the residue label at that
    * position.
@@ -976,6 +908,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     return loadNotifiesHandled;
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI cs)
   {
     colourBySequence = false;
@@ -1050,6 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    *      .html
    * @param col
    */
+  @Override
   public void setBackgroundColour(Color col)
   {
     viewerCommandHistory(false);