X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;fp=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=d92c78a841182343b77f7d201ef6833f520a2adc;hb=d87b55e45cc1e6a5b7df3865ded1b87a0e3dc7ff;hp=f69a423b5c9ec962a5ee35d68247476173dab8a1;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index f69a423..d92c78a 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -47,6 +47,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -56,6 +57,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
 import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureListener;
@@ -83,20 +85,20 @@ public abstract class AAStructureBindingModel
   public static class SuperposeData
   {
     public String filename;
-  
+
     public String pdbId;
-  
+
     public String chain = "";
-  
+
     public boolean isRna;
-  
+
     /*
      * The pdb residue number (if any) mapped to columns of the alignment
      */
     public int[] pdbResNo; // or use SparseIntArray?
-  
+
     public String modelId;
-  
+
     /**
      * Constructor
      * 
@@ -262,6 +264,7 @@ public abstract class AAStructureBindingModel
     chains = newchains;
     return chainmaps > 0;
   }
+
   public StructureSelectionManager getSsm()
   {
     return ssm;
@@ -659,7 +662,8 @@ public abstract class AAStructureBindingModel
    * @return
    */
   protected int findSuperposableResidues(AlignmentI alignment,
-          BitSet matched, AAStructureBindingModel.SuperposeData[] structures)
+          BitSet matched,
+          AAStructureBindingModel.SuperposeData[] structures)
   {
     int refStructure = -1;
     String[] files = getStructureFiles();
@@ -885,8 +889,8 @@ public abstract class AAStructureBindingModel
        * Calculate the superposable alignment columns ('matched'), and the
        * corresponding structure residue positions (structures.pdbResNo)
        */
-      int refStructure = findSuperposableResidues(alignment,
-              matched, structures);
+      int refStructure = findSuperposableResidues(alignment, matched,
+              structures);
 
       /*
        * require at least 4 positions to be able to execute superposition
@@ -894,8 +898,8 @@ public abstract class AAStructureBindingModel
       int nmatched = matched.cardinality();
       if (nmatched < MIN_POS_TO_SUPERPOSE)
       {
-        String msg = MessageManager.formatMessage("label.insufficient_residues",
-                nmatched);
+        String msg = MessageManager
+                .formatMessage("label.insufficient_residues", nmatched);
         error += view.getViewName() + ": " + msg + "; ";
         continue;
       }
@@ -939,7 +943,8 @@ public abstract class AAStructureBindingModel
     return error;
   }
 
-  private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
+  private AtomSpecModel getAtomSpec(
+          AAStructureBindingModel.SuperposeData superposeData,
           BitSet matched)
   {
     AtomSpecModel model = new AtomSpecModel();
@@ -1008,7 +1013,7 @@ public abstract class AAStructureBindingModel
     {
       return;
     }
-    
+
     /*
      * build a map of {Residue3LetterCode, Color}
      */
@@ -1078,7 +1083,7 @@ public abstract class AAStructureBindingModel
        */
       final JalviewStructureDisplayI theViewer = getViewer();
       final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-      
+
       SwingUtilities.invokeLater(new Runnable()
       {
         @Override
@@ -1126,7 +1131,7 @@ public abstract class AAStructureBindingModel
      */
     final JalviewStructureDisplayI theViewer = getViewer();
     final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-    
+
     List<String> response = getReply ? new ArrayList<>() : null;
     try
     {
@@ -1356,17 +1361,17 @@ public abstract class AAStructureBindingModel
     AlignmentI al = viewport.getAlignment();
     Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
     Color lastColour = null;
-  
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       final String modelId = getModelIdForFile(files[pdbfnum]);
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-  
+
       if (mapping == null || mapping.length < 1)
       {
         continue;
       }
-  
+
       int startPos = -1, lastPos = -1;
       String lastChain = "";
       for (int s = 0; s < sequence[pdbfnum].length; s++)
@@ -1386,14 +1391,14 @@ public abstract class AAStructureBindingModel
                 continue;
               }
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-  
+
               if (pos < 1 || pos == lastPos)
               {
                 continue;
               }
-  
+
               Color colour = sr.getResidueColour(seq, r, finder);
-  
+
               /*
                * darker colour for hidden regions
                */
@@ -1401,9 +1406,9 @@ public abstract class AAStructureBindingModel
               {
                 colour = Color.GRAY;
               }
-  
+
               final String chain = mapping[m].getChain();
-  
+
               /*
                * Just keep incrementing the end position for this colour range
                * _unless_ colour, PDB model or chain has changed, or there is a
@@ -1416,8 +1421,8 @@ public abstract class AAStructureBindingModel
               {
                 if (startPos != -1)
                 {
-                  addAtomSpecRange(colourMap, lastColour, modelId,
-                          startPos, lastPos, lastChain);
+                  addAtomSpecRange(colourMap, lastColour, modelId, startPos,
+                          lastPos, lastChain);
                 }
                 startPos = pos;
               }
@@ -1469,8 +1474,9 @@ public abstract class AAStructureBindingModel
   }
 
   /**
-   * 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
+   * 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'
@@ -1485,8 +1491,8 @@ public abstract class AAStructureBindingModel
    * @param chain
    */
   public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
-          Object value,
-          String model, int startPos, int endPos, String chain)
+          Object value, String model, int startPos, int endPos,
+          String chain)
   {
     /*
      * Get/initialize map of data for the colour
@@ -1497,7 +1503,7 @@ public abstract class AAStructureBindingModel
       atomSpec = new AtomSpecModel();
       map.put(value, atomSpec);
     }
-  
+
     atomSpec.addRange(model, startPos, endPos, chain);
   }
 
@@ -1530,8 +1536,8 @@ public abstract class AAStructureBindingModel
       saveSession(f);
     } catch (IOException e)
     {
-      Cache.log.error(String.format("Error saving %s session: %s",
-              prefix, e.toString()));
+      Cache.log.error(String.format("Error saving %s session: %s", prefix,
+              e.toString()));
     }
 
     return f;
@@ -1544,8 +1550,7 @@ public abstract class AAStructureBindingModel
    */
   protected void saveSession(File f)
   {
-    StructureCommandI cmd = commandGenerator
-            .saveSession(f.getPath());
+    StructureCommandI cmd = commandGenerator.saveSession(f.getPath());
     if (cmd != null)
     {
       executeCommand(cmd, false);
@@ -1586,7 +1591,7 @@ public abstract class AAStructureBindingModel
     }
 
     stopListening();
-    
+
     if (forceClose)
     {
       StructureCommandI cmd = getCommandGenerator().closeViewer();
@@ -1632,10 +1637,10 @@ public abstract class AAStructureBindingModel
     {
       return theMap;
     }
-  
+
     AlignViewportI viewport = viewPanel.getAlignViewport();
     List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
-  
+
     /*
      * if alignment is showing features from complement, we also transfer
      * these features to the corresponding mapped structure residues
@@ -1657,7 +1662,7 @@ public abstract class AAStructureBindingModel
     {
       return theMap;
     }
-  
+
     AlignmentI alignment = viewPanel.getAlignment();
     SequenceI[][] seqs = getSequence();
 
@@ -1665,12 +1670,12 @@ public abstract class AAStructureBindingModel
     {
       String modelId = getModelIdForFile(files[pdbfnum]);
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-  
+
       if (mapping == null || mapping.length < 1)
       {
         continue;
       }
-  
+
       for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
       {
         for (int m = 0; m < mapping.length; m++)
@@ -1721,8 +1726,8 @@ public abstract class AAStructureBindingModel
   }
 
   /**
-   * Scans visible features in mapped positions of the CDS/peptide complement, and
-   * adds any found to the map of attribute values/structure positions
+   * 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
@@ -1751,7 +1756,7 @@ public abstract class AAStructureBindingModel
         for (SequenceFeature sf : mf.features)
         {
           String type = sf.getType();
-  
+
           /*
            * Don't copy features which originated from Chimera
            */
@@ -1760,14 +1765,14 @@ public abstract class AAStructureBindingModel
           {
             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();
@@ -1817,7 +1822,7 @@ public abstract class AAStructureBindingModel
     for (SequenceFeature sf : sfs)
     {
       String type = sf.getType();
-  
+
       /*
        * Don't copy features which originated from Chimera
        */
@@ -1826,10 +1831,10 @@ public abstract class AAStructureBindingModel
       {
         continue;
       }
-  
+
       List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
               sf.getEnd());
-  
+
       if (!mappedRanges.isEmpty())
       {
         String value = sf.getDescription();
@@ -1882,7 +1887,7 @@ public abstract class AAStructureBindingModel
   {
     externalViewerMonitor = new Thread(new Runnable()
     {
-  
+
       @Override
       public void run()
       {
@@ -1933,4 +1938,51 @@ public abstract class AAStructureBindingModel
       executeCommands(commands, false, null);
     }
   }
+
+  /**
+   * If supported by the structure viewer, queries it for all residue attributes
+   * with the given attribute name, and creates features on corresponding
+   * residues of the alignment. Returns the number of features added.
+   * 
+   * @param attName
+   * @param alignmentPanel
+   * @return
+   */
+  public int copyStructureAttributesToFeatures(String attName,
+          AlignmentPanel alignmentPanel)
+  {
+    StructureCommandI cmd = getCommandGenerator()
+            .getResidueAttributes(attName);
+    if (cmd == null)
+    {
+      return 0;
+    }
+    List<String> residueAttributes = executeCommand(cmd, true);
+
+    int featuresAdded = createFeaturesForAttributes(attName,
+            residueAttributes);
+    if (featuresAdded > 0)
+    {
+      alignmentPanel.getFeatureRenderer().featuresAdded();
+    }
+    return featuresAdded;
+  }
+
+  /**
+   * Parses {@code residueAttributes} and creates sequence features on any
+   * mapped alignment residues. Returns the number of features created.
+   * <p>
+   * {@code residueAttributes} is the reply from the structure viewer to a
+   * command to list any residue attributes for the given attribute name. Syntax
+   * and parsing of this is viewer-specific.
+   * 
+   * @param attName
+   * @param residueAttributes
+   * @return
+   */
+  protected int createFeaturesForAttributes(String attName,
+          List<String> residueAttributes)
+  {
+    return 0;
+  }
 }