JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not

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

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index e665982..1d8b944 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -21,12 +21,14 @@
 package jalview.ext.rbvi.chimera;
 
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
@@ -59,16 +61,16 @@ public class ChimeraCommands
    * @param sequence
    * @param sr
    * @param fr
-   * @param viewport
+   * @param viewPanel
    * @return
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
     Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
-            sequence, sr, fr, viewport);
+            sequence, sr, viewPanel);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -186,9 +188,12 @@ public class ChimeraCommands
    */
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
     ColumnSelection cs = viewport.getColumnSelection();
     AlignmentI al = viewport.getAlignment();
     Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
@@ -228,7 +233,7 @@ public class ChimeraCommands
                 continue;
               }
 
-              Color colour = sr.getResidueColour(seq, r, fr);
+              Color colour = sr.getResidueColour(seq, r, finder);
 
               /*
                * darker colour for hidden regions
@@ -310,16 +315,15 @@ public class ChimeraCommands
    * @param ssm
    * @param files
    * @param seqs
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+          SequenceI[][] seqs, AlignmentViewPanel viewPanel)
   {
     Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
-            ssm, files, seqs, fr, alignment);
+            ssm, files, seqs, viewPanel);
 
     List<String> commands = buildSetAttributeCommands(featureMap);
 
@@ -339,22 +343,28 @@ public class ChimeraCommands
    * @param ssm
    * @param files
    * @param seqs
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+          SequenceI[][] seqs, AlignmentViewPanel viewPanel)
   {
     Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
 
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    if (fr == null)
+    {
+      return theMap;
+    }
+
     List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
     if (visibleFeatures.isEmpty())
     {
       return theMap;
     }
 
+    AlignmentI alignment = viewPanel.getAlignment();
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);