X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=3caaac3532367e30f3f2d11003cbdb23c9560437;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=9ef89fd8d538c4a4ebefbe27454121d5496aa091;hpb=fb315d08a73717eebc3d3a8832a9456fcef52484;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 9ef89fd..3caaac3 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,11 +20,17 @@
  */
 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.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
@@ -38,8 +44,6 @@ 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 +53,7 @@ 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 +63,16 @@ 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<Object, AtomSpecModel> colourMap = buildColoursMap(
-            ssm, files, sequence, sr, fr, alignment);
+    Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+            sequence, sr, viewPanel);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -76,7 +80,7 @@ public class ChimeraCommands
             ChimeraCommands.class, null,
             colourCommands.toArray(new String[colourCommands.size()]));
 
-    return cs;
+    return new StructureMappingcommandSet[] { cs };
   }
 
   /**
@@ -102,7 +106,7 @@ public class ChimeraCommands
      * delimited). If length limit issues arise, refactor to return one color
      * command per colour.
      */
-    List<String> commands = new ArrayList<String>();
+    List<String> commands = new ArrayList<>();
     StringBuilder sb = new StringBuilder(256);
     boolean firstColour = true;
     for (Object key : colourMap.keySet())
@@ -115,8 +119,7 @@ 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 +179,8 @@ public class ChimeraCommands
 
   /**
    * <pre>
-   * 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 +190,17 @@ public class ChimeraCommands
    */
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-    Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
+    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<>();
     Color lastColour = null;
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -210,9 +218,9 @@ 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 +235,16 @@ 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 +259,7 @@ public class ChimeraCommands
               {
                 if (startPos != -1)
                 {
-                  addRange(colourMap, lastColour, pdbfnum, startPos,
+                  addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos,
                           lastPos, lastChain);
                 }
                 startPos = pos;
@@ -254,7 +271,7 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addRange(colourMap, lastColour, pdbfnum, startPos,
+              addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
             // break;
@@ -266,26 +283,32 @@ public class ChimeraCommands
   }
 
   /**
-   * Helper method to add one contiguous colour range to the colour map.
+   * Helper method to add one contiguous range to the AtomSpec model for the given
+   * value (creating the model if necessary). As used by Jalview, {@code value} is
+   * <ul>
+   * <li>a colour, when building a 'colour structure by sequence' command</li>
+   * <li>a feature value, when building a 'set Chimera attributes from features'
+   * command</li>
+   * </ul>
    * 
    * @param map
-   * @param key
+   * @param value
    * @param model
    * @param startPos
    * @param endPos
    * @param chain
    */
-  protected static void addRange(Map<Object, AtomSpecModel> map,
-          Object key, int model, int startPos, int endPos, String chain)
+  protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
+          Object value, int model, int startPos, int endPos, String chain)
   {
     /*
      * Get/initialize map of data for the colour
      */
-    AtomSpecModel atomSpec = map.get(key);
+    AtomSpecModel atomSpec = map.get(value);
     if (atomSpec == null)
     {
       atomSpec = new AtomSpecModel();
-      map.put(key, atomSpec);
+      map.put(value, atomSpec);
     }
 
     atomSpec.addRange(model, startPos, endPos, chain);
@@ -299,16 +322,15 @@ 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);
 
@@ -328,22 +350,47 @@ 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>>();
+    Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
+
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    if (fr == null)
+    {
+      return theMap;
+    }
 
+    AlignViewportI viewport = viewPanel.getAlignViewport();
     List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
-    if (visibleFeatures.isEmpty())
+
+    /*
+     * if alignment is showing features from complement, we also transfer
+     * these features to the corresponding mapped structure residues
+     */
+    boolean showLinkedFeatures = viewport.isShowComplementFeatures();
+    List<String> complementFeatures = new ArrayList<>();
+    FeatureRenderer complementRenderer = null;
+    if (showLinkedFeatures)
+    {
+      AlignViewportI comp = fr.getViewport().getCodingComplement();
+      if (comp != null)
+      {
+        complementRenderer = Desktop.getAlignFrameFor(comp)
+                .getFeatureRenderer();
+        complementFeatures = complementRenderer.getDisplayedFeatureTypes();
+      }
+    }
+    if (visibleFeatures.isEmpty() && complementFeatures.isEmpty())
     {
       return theMap;
     }
-    
+
+    AlignmentI alignment = viewPanel.getAlignment();
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -359,16 +406,23 @@ public class ChimeraCommands
         {
           final SequenceI seq = seqs[pdbfnum][seqNo];
           int sp = alignment.findIndex(seq);
-          if (mapping[m].getSequence() == seq && sp > -1)
+          StructureMapping structureMapping = mapping[m];
+          if (structureMapping.getSequence() == seq && sp > -1)
           {
             /*
              * found a sequence with a mapping to a structure;
              * now scan its features
              */
-            SequenceI asp = alignment.getSequenceAt(sp);
-
-            scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
-                    pdbfnum);
+            if (!visibleFeatures.isEmpty())
+            {
+              scanSequenceFeatures(visibleFeatures, structureMapping, seq,
+                      theMap, pdbfnum);
+            }
+            if (showLinkedFeatures)
+            {
+              scanComplementFeatures(complementRenderer, structureMapping,
+                      seq, theMap, pdbfnum);
+            }
           }
         }
       }
@@ -377,9 +431,85 @@ public class ChimeraCommands
   }
 
   /**
-   * Inspect features on the sequence; for each feature that is visible,
-   * determine its mapped ranges in the structure (if any) according to the
-   * given mapping, and add them to the map
+   * Scans visible features in mapped positions of the CDS/peptide complement, and
+   * adds any found to the map of attribute values/structure positions
+   * 
+   * @param complementRenderer
+   * @param structureMapping
+   * @param seq
+   * @param theMap
+   * @param modelNumber
+   */
+  protected static void scanComplementFeatures(
+          FeatureRenderer complementRenderer,
+          StructureMapping structureMapping, SequenceI seq,
+          Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+  {
+    /*
+     * for each sequence residue mapped to a structure position...
+     */
+    for (int seqPos : structureMapping.getMapping().keySet())
+    {
+      /*
+       * find visible complementary features at mapped position(s)
+       */
+      MappedFeatures mf = complementRenderer
+              .findComplementFeaturesAtResidue(seq, seqPos);
+      if (mf != null)
+      {
+        for (SequenceFeature sf : mf.features)
+        {
+          String type = sf.getType();
+
+          /*
+           * Don't copy features which originated from Chimera
+           */
+          if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+                  .equals(sf.getFeatureGroup()))
+          {
+            continue;
+          }
+
+          /*
+           * record feature 'value' (score/description/type) as at the
+           * corresponding structure position
+           */
+          List<int[]> mappedRanges = structureMapping
+                  .getPDBResNumRanges(seqPos, seqPos);
+
+          if (!mappedRanges.isEmpty())
+          {
+            String value = sf.getDescription();
+            if (value == null || value.length() == 0)
+            {
+              value = type;
+            }
+            float score = sf.getScore();
+            if (score != 0f && !Float.isNaN(score))
+            {
+              value = Float.toString(score);
+            }
+            Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+            if (featureValues == null)
+            {
+              featureValues = new HashMap<>();
+              theMap.put(type, featureValues);
+            }
+            for (int[] range : mappedRanges)
+            {
+              addAtomSpecRange(featureValues, value, modelNumber, range[0],
+                      range[1], structureMapping.getChain());
+            }
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Inspect features on the sequence; for each feature that is visible, determine
+   * its mapped ranges in the structure (if any) according to the given mapping,
+   * and add them to the map.
    * 
    * @param visibleFeatures
    * @param mapping
@@ -391,19 +521,21 @@ 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();
-      if (!visibleFeatures.contains(type) || suppressFeature(type))
+
+      /*
+       * Don't copy features which originated from Chimera
+       */
+      if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+              .equals(sf.getFeatureGroup()))
       {
         continue;
       }
+
       List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
               sf.getEnd());
 
@@ -415,38 +547,26 @@ public class ChimeraCommands
           value = type;
         }
         float score = sf.getScore();
-        if (score != 0f && score != Float.NaN)
+        if (score != 0f && !Float.isNaN(score))
         {
           value = Float.toString(score);
         }
         Map<Object, AtomSpecModel> featureValues = theMap.get(type);
         if (featureValues == null)
         {
-          featureValues = new HashMap<Object, AtomSpecModel>();
+          featureValues = new HashMap<>();
           theMap.put(type, featureValues);
         }
         for (int[] range : mappedRanges)
         {
-          addRange(featureValues, value, modelNumber, range[0], range[1],
-                  mapping.getChain());
+          addAtomSpecRange(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).
    * <p>
@@ -464,7 +584,7 @@ public class ChimeraCommands
   protected static List<String> buildSetAttributeCommands(
           Map<String, Map<Object, AtomSpecModel>> featureMap)
   {
-    List<String> commands = new ArrayList<String>();
+    List<String> commands = new ArrayList<>();
     for (String featureType : featureMap.keySet())
     {
       String attributeName = makeAttributeName(featureType);
@@ -481,10 +601,13 @@ 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("\\'", "&#39;");
+        sb.append("setattr r ").append(attributeName).append(" '")
+                .append(featureValue).append("' ");
         sb.append(values.get(value).getAtomSpec());
         commands.add(sb.toString());
       }
@@ -499,9 +622,11 @@ 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)
   {