X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=dad85117fb15622f90656836a1bc7fffcc0f31e4;hb=3ac6f45c254aaafa6bdf163bf66bb4031de21fa3;hp=3415815ba3e12e2b74ac4135b75d07d529e0d5d2;hpb=3634aa61b96d7ce541c4abb83502fc67d72e3f27;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 3415815..dad8511 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,11 +20,15 @@ */ 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.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; @@ -38,8 +42,6 @@ import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import MCview.PDBChain; - /** * Routines for generating Chimera commands for Jalview/Chimera binding * @@ -49,7 +51,7 @@ import MCview.PDBChain; public class ChimeraCommands { - private static final String NAMESPACE_PREFIX = "jv_"; + public static final String NAMESPACE_PREFIX = "jv_"; /** * Constructs Chimera commands to colour residues as per the Jalview alignment @@ -59,16 +61,16 @@ public class ChimeraCommands * @param sequence * @param sr * @param fr - * @param alignment + * @param viewPanel * @return */ - public static StructureMappingcommandSet getColourBySequenceCommand( + public static StructureMappingcommandSet[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + SequenceI[][] sequence, SequenceRenderer sr, + AlignmentViewPanel viewPanel) { - Map colourMap = buildColoursMap( - ssm, files, sequence, sr, fr, alignment); + Map colourMap = buildColoursMap(ssm, files, + sequence, sr, viewPanel); List colourCommands = buildColourCommands(colourMap); @@ -76,7 +78,7 @@ public class ChimeraCommands ChimeraCommands.class, null, colourCommands.toArray(new String[colourCommands.size()])); - return cs; + return new StructureMappingcommandSet[] { cs }; } /** @@ -115,8 +117,7 @@ public class ChimeraCommands } sb.append("color ").append(colourCode).append(" "); firstColour = false; - final AtomSpecModel colourData = colourMap - .get(colour); + final AtomSpecModel colourData = colourMap.get(colour); sb.append(colourData.getAtomSpec()); } commands.add(sb.toString()); @@ -176,9 +177,8 @@ public class ChimeraCommands /** * 
-   * Build a data structure which maps contiguous subsequences for each colour. 
-   * This generates a data structure from which we can easily generate the 
-   * Chimera command for colour by sequence.
+   * Build a data structure which records contiguous subsequences for each colour. 
+   * From this we can easily generate the Chimera command for colour by sequence.
    * Color
    *     Model number
    *         Chain
@@ -188,11 +188,17 @@ public class ChimeraCommands
    */
   protected static Map buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
+    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+    AlignmentI al = viewport.getAlignment();
     Map colourMap = new LinkedHashMap();
     Color lastColour = null;
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -210,9 +216,9 @@ public class ChimeraCommands
         {
           final SequenceI seq = sequence[pdbfnum][s];
           if (mapping[m].getSequence() == seq
-                  && (sp = alignment.findIndex(seq)) > -1)
+                  && (sp = al.findIndex(seq)) > -1)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
+            SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
               // no mapping to gaps in sequence
@@ -227,7 +233,16 @@ 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 = Color.GRAY;
+              }
+
               final String chain = mapping[m].getChain();
 
               /*
@@ -242,7 +257,7 @@ public class ChimeraCommands
               {
                 if (startPos != -1)
                 {
-                  addRange(colourMap, lastColour, pdbfnum, startPos,
+                  addColourRange(colourMap, lastColour, pdbfnum, startPos,
                           lastPos, lastChain);
                 }
                 startPos = pos;
@@ -254,7 +269,7 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addRange(colourMap, lastColour, pdbfnum, startPos,
+              addColourRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
             // break;
@@ -275,7 +290,7 @@ public class ChimeraCommands
    * @param endPos
    * @param chain
    */
-  protected static void addRange(Map map,
+  protected static void addColourRange(Map map,
           Object key, int model, int startPos, int endPos, String chain)
   {
     /*
@@ -299,16 +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> featureMap = buildFeaturesMap(
-            ssm, files, seqs, fr, alignment);
+            ssm, files, seqs, viewPanel);
 
     List commands = buildSetAttributeCommands(featureMap);
 
@@ -328,22 +342,28 @@ public class ChimeraCommands
    * @param ssm
    * @param files
    * @param seqs
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   protected static Map> buildFeaturesMap(
-          StructureSelectionManager ssm, String[] files,
-          SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+          StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+          AlignmentViewPanel viewPanel)
   {
     Map> theMap = new LinkedHashMap>();
 
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    if (fr == null)
+    {
+      return theMap;
+    }
+
     List 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]);
@@ -391,16 +411,19 @@ public class ChimeraCommands
           StructureMapping mapping, SequenceI seq,
           Map> theMap, int modelNumber)
   {
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    if (sfs == null)
-    {
-      return;
-    }
-
+    List sfs = seq.getFeatures().getPositionalFeatures(
+            visibleFeatures.toArray(new String[visibleFeatures.size()]));
     for (SequenceFeature sf : sfs)
     {
       String type = sf.getType();
-      if (!visibleFeatures.contains(type) || suppressFeature(type))
+
+      /*
+       * Only copy visible features, don't copy any which originated
+       * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
+       */
+      boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+              .equals(sf.getFeatureGroup());
+      if (isFromViewer)
       {
         continue;
       }
@@ -427,26 +450,14 @@ public class ChimeraCommands
         }
         for (int[] range : mappedRanges)
         {
-          addRange(featureValues, value, modelNumber, range[0], range[1],
-                  mapping.getChain());
+          addColourRange(featureValues, value, modelNumber, range[0],
+                  range[1], mapping.getChain());
         }
       }
     }
   }
 
   /**
-   * Answers true if the feature type is one we don't wish to propagate to
-   * Chimera - for now, RESNUM
-   * 
-   * @param type
-   * @return
-   */
-  static boolean suppressFeature(String type)
-  {
-    return PDBChain.RESNUM_FEATURE.equals(type);
-  }
-
-  /**
    * Traverse the map of features/values/models/chains/positions to construct a
    * list of 'setattr' commands (one per distinct feature type and value).
    * 

@@ -481,10 +492,13 @@ public class ChimeraCommands
         /*
          * for each distinct value recorded for this feature type,
          * add a command to set the attribute on the mapped residues
+         * Put values in single quotes, encoding any embedded single quotes
          */
         StringBuilder sb = new StringBuilder(128);
-        sb.append("setattr r ").append(attributeName).append(" \"")
-                .append(value.toString()).append("\" ");
+        String featureValue = value.toString();
+        featureValue = featureValue.replaceAll("\\'", "'");
+        sb.append("setattr r ").append(attributeName).append(" '")
+                .append(featureValue).append("' ");
         sb.append(values.get(value).getAtomSpec());
         commands.add(sb.toString());
       }
@@ -499,9 +513,11 @@ public class ChimeraCommands
    * to an underscore.
    * 
    * @param featureType
-   * @return 
-   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
-   * 

+   * @return
+   * 
+   *         
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   *         

    */
   protected static String makeAttributeName(String featureType)
   {