X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=95757fd3e1a8904131e96a029bba15ba1e0544e4;hb=207b06de28859536277608ad94897eaa526b1279;hp=d34ac255a8622c5a2fab2cb978725e62e287466e;hpb=8c0955545a1a10062467e2d6dc7feb1e855655c0;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index d34ac25..95757fd 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.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;
@@ -33,6 +37,7 @@ import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -46,20 +51,26 @@ import java.util.Map;
 public class ChimeraCommands
 {
 
+  public static final String NAMESPACE_PREFIX = "jv_";
+
   /**
-   * utility to construct the commands to colour chains by the given alignment
-   * for passing to Chimera
-   * 
-   * @returns Object[] { Object[] { <model being coloured>,
+   * Constructs Chimera commands to colour residues as per the Jalview alignment
    * 
+   * @param ssm
+   * @param files
+   * @param sequence
+   * @param sr
+   * @param fr
+   * @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);
 
@@ -67,7 +78,7 @@ public class ChimeraCommands
             ChimeraCommands.class, null,
             colourCommands.toArray(new String[colourCommands.size()]));
 
-    return cs;
+    return new StructureMappingcommandSet[] { cs };
   }
 
   /**
@@ -106,8 +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());
@@ -167,9 +177,8 @@ 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
@@ -179,11 +188,17 @@ 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)
   {
+    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>();
     Color lastColour = null;
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -201,9 +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
@@ -218,7 +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();
 
               /*
@@ -233,7 +257,7 @@ public class ChimeraCommands
               {
                 if (startPos != -1)
                 {
-                  addRange(colourMap, lastColour, pdbfnum, startPos,
+                  addColourRange(colourMap, lastColour, pdbfnum, startPos,
                           lastPos, lastChain);
                 }
                 startPos = pos;
@@ -245,8 +269,8 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addRange(colourMap, lastColour, pdbfnum, startPos,
-                      lastPos, lastChain);
+              addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
+                      lastChain);
             }
             // break;
           }
@@ -266,7 +290,7 @@ public class ChimeraCommands
    * @param endPos
    * @param chain
    */
-  protected static void addRange(Map<Object, AtomSpecModel> map,
+  protected static void addColourRange(Map<Object, AtomSpecModel> map,
           Object key, int model, int startPos, int endPos, String chain)
   {
     /*
@@ -283,22 +307,22 @@ public class ChimeraCommands
   }
 
   /**
-   * Constructs and returns a set of Chimera commands to set attributes on
-   * residues corresponding to features in Jalview
+   * Constructs and returns Chimera commands to set attributes on residues
+   * corresponding to features in Jalview. Attribute names are the Jalview
+   * feature type, with a "jv_" prefix.
    * 
    * @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, AtomSpecModel> featureMap = buildFeaturesMap(
-            ssm, files, seqs, fr, alignment);
+    Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+            ssm, files, seqs, viewPanel);
 
     List<String> commands = buildSetAttributeCommands(featureMap);
 
@@ -310,27 +334,36 @@ public class ChimeraCommands
   }
 
   /**
-   * Helper method to build a map of { featureType, AtomSpecModel }
+   * <pre>
+   * Helper method to build a map of 
+   *   { featureType, { feature value, AtomSpecModel } }
+   * </pre>
    * 
    * @param ssm
    * @param files
    * @param seqs
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
-  protected static Map<String, AtomSpecModel> buildFeaturesMap(
+  protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+          SequenceI[][] seqs, AlignmentViewPanel viewPanel)
   {
-    Map<String, AtomSpecModel> theMap = new LinkedHashMap<String, AtomSpecModel>();
+    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]);
@@ -376,7 +409,7 @@ public class ChimeraCommands
    */
   protected static void scanSequenceFeatures(List<String> visibleFeatures,
           StructureMapping mapping, SequenceI seq,
-          Map<String, AtomSpecModel> theMap, int modelNumber)
+          Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
   {
     SequenceFeature[] sfs = seq.getSequenceFeatures();
     if (sfs == null)
@@ -387,7 +420,14 @@ public class ChimeraCommands
     for (SequenceFeature sf : sfs)
     {
       String type = sf.getType();
-      if (!visibleFeatures.contains(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 || !visibleFeatures.contains(type))
       {
         continue;
       }
@@ -396,15 +436,25 @@ public class ChimeraCommands
 
       if (!mappedRanges.isEmpty())
       {
-        AtomSpecModel atomSpec = theMap.get(type);
-        if (atomSpec == null)
+        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)
         {
-          atomSpec = new AtomSpecModel();
-          theMap.put(type, atomSpec);
+          featureValues = new HashMap<Object, AtomSpecModel>();
+          theMap.put(type, featureValues);
         }
         for (int[] range : mappedRanges)
         {
-          atomSpec.addRange(modelNumber, range[0], range[1],
+          addColourRange(featureValues, value, modelNumber, range[0], range[1],
                   mapping.getChain());
         }
       }
@@ -412,37 +462,87 @@ public class ChimeraCommands
   }
 
   /**
-   * Traverse the map of features/models/chains/positions to construct a list of
-   * 'setattr' commands (one per feature type). The format of each command is
+   * Traverse the map of features/values/models/chains/positions to construct a
+   * list of 'setattr' commands (one per distinct feature type and value).
+   * <p>
+   * The format of each command is
    * 
    * <pre>
    * <blockquote> setattr r <featureName> " " #modelnumber:range.chain 
-   * e.g. setattr r jv:chain " " #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
    * </blockquote>
    * </pre>
-   * <p>
-   * Note we are not (currently) setting attribute values, only the type
-   * (presence) of each attribute. This is to avoid overloading the Chimera REST
-   * interface by sending too many distinct commands. Analysis by feature values
-   * may still be performed in Jalview, on selections created in Chimera.
    * 
    * @param featureMap
    * @return
    */
   protected static List<String> buildSetAttributeCommands(
-          Map<String, AtomSpecModel> featureMap)
+          Map<String, Map<Object, AtomSpecModel>> featureMap)
   {
     List<String> commands = new ArrayList<String>();
     for (String featureType : featureMap.keySet())
     {
-      StringBuilder sb = new StringBuilder(128);
-      String sanitised = featureType.replace(" ", "_").replace("-", "_");
-      sb.append("setattr r jv_").append(sanitised).append(" \" \" ");
-      sb.append(featureMap.get(featureType).getAtomSpec());
-      commands.add(sb.toString());
+      String attributeName = makeAttributeName(featureType);
+
+      /*
+       * clear down existing attributes for this feature
+       */
+      // 'problem' - sets attribute to None on all residues - overkill?
+      // commands.add("~setattr r " + attributeName + " :*");
+
+      Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+      for (Object value : values.keySet())
+      {
+        /*
+         * 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);
+        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());
+      }
     }
 
     return commands;
   }
 
+  /**
+   * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+   * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+   * to an underscore.
+   * 
+   * @param featureType
+   * @return <pre>
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   * </pre>
+   */
+  protected static String makeAttributeName(String featureType)
+  {
+    StringBuilder sb = new StringBuilder();
+    if (featureType != null)
+    {
+      for (char c : featureType.toCharArray())
+      {
+        sb.append(Character.isLetterOrDigit(c) ? c : '_');
+      }
+    }
+    String attName = NAMESPACE_PREFIX + sb.toString();
+
+    /*
+     * Chimera treats an attribute name ending in 'color' as colour-valued;
+     * Jalview doesn't, so prevent this by appending an underscore
+     */
+    if (attName.toUpperCase().endsWith("COLOR"))
+    {
+      attName += "_";
+    }
+
+    return attName;
+  }
+
 }