X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=dad85117fb15622f90656836a1bc7fffcc0f31e4;hb=cef8dbc4cf7c8b47864b11aad36596901003639a;hp=e665982a07a962c6b514e46ee7c721201664a929;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index e665982..dad8511 100644
--- 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.HiddenColumns;
 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);
 
@@ -186,10 +188,13 @@ 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)
   {
-    ColumnSelection cs = viewport.getColumnSelection();
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
+    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();
     Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
     Color lastColour = null;
@@ -228,14 +233,13 @@ public class ChimeraCommands
                 continue;
               }
 
-              Color colour = sr.getResidueColour(seq, r, fr);
+              Color colour = sr.getResidueColour(seq, r, finder);
 
               /*
                * darker colour for hidden regions
                */
               if (!cs.isVisible(r))
               {
-                // colour = ColorUtils.darkerThan(colour);
                 colour = Color.GRAY;
               }
 
@@ -265,8 +269,8 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
-                      lastChain);
+              addColourRange(colourMap, lastColour, pdbfnum, startPos,
+                      lastPos, lastChain);
             }
             // break;
           }
@@ -310,16 +314,15 @@ 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)
+          StructureSelectionManager ssm, String[] files, 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 +342,28 @@ 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)
+          StructureSelectionManager ssm, String[] files, 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]);
@@ -402,12 +411,8 @@ public class ChimeraCommands
           StructureMapping mapping, SequenceI seq,
           Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
   {
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    if (sfs == null)
-    {
-      return;
-    }
-
+    List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+            visibleFeatures.toArray(new String[visibleFeatures.size()]));
     for (SequenceFeature sf : sfs)
     {
       String type = sf.getType();
@@ -418,7 +423,7 @@ public class ChimeraCommands
        */
       boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
               .equals(sf.getFeatureGroup());
-      if (isFromViewer || !visibleFeatures.contains(type))
+      if (isFromViewer)
       {
         continue;
       }
@@ -445,8 +450,8 @@ public class ChimeraCommands
         }
         for (int[] range : mappedRanges)
         {
-          addColourRange(featureValues, value, modelNumber, range[0], range[1],
-                  mapping.getChain());
+          addColourRange(featureValues, value, modelNumber, range[0],
+                  range[1], mapping.getChain());
         }
       }
     }
@@ -508,9 +513,11 @@ public class ChimeraCommands
    * to an underscore.
    * 
    * @param featureType
-   * @return <pre>
-   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
-   * </pre>
+   * @return
+   * 
+   *         <pre>
+   * &#64;see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   *         </pre>
    */
   protected static String makeAttributeName(String featureType)
   {