JAL-2295 (unoptimised) write Jalview features as Chimera attributes

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 7ba9186..2534421 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -27,14 +27,17 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.httpserver.AbstractRequestHandler;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -1125,4 +1128,87 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       sm.highlightStructure(this, seq, positions);
     }
   }
+
+  /**
+   * Constructs and send commands to Chimera to set attributes on residues for
+   * features visible in Jalview
+   * 
+   * @param avp
+   */
+  public void sendFeaturesToChimera(AlignmentViewPanel avp)
+  {
+    // TODO send a command per feature with the range of residues it applies to
+    AlignmentI alignment = avp.getAlignment();
+    FeatureRenderer fr = getFeatureRenderer(avp);
+
+    /*
+     * fr is null if feature display is turned off
+     */
+    if (fr == null)
+    {
+      return;
+    }
+
+    String[] files = getPdbFile();
+    if (files == null)
+    {
+      return;
+    }
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
+
+      if (mapping == null || mapping.length < 1)
+      {
+        continue;
+      }
+
+      int lastPos = -1;
+      for (int seqNo = 0; seqNo < getSequence()[pdbfnum].length; seqNo++)
+      {
+        for (int m = 0; m < mapping.length; m++)
+        {
+          final SequenceI seq = getSequence()[pdbfnum][seqNo];
+          int sp = alignment.findIndex(seq);
+          if (mapping[m].getSequence() == seq && sp > -1)
+          {
+            SequenceI asp = alignment.getSequenceAt(sp);
+            for (int r = 0; r < asp.getLength(); r++)
+            {
+              // no mapping to gaps in sequence
+              if (Comparison.isGap(asp.getCharAt(r)))
+              {
+                continue;
+              }
+              int residuePos = asp.findPosition(r);
+              int pos = mapping[m].getPDBResNum(residuePos);
+
+              if (pos < 1 || pos == lastPos)
+              {
+                continue;
+              }
+              final String chain = mapping[m].getChain();
+              List<SequenceFeature> features = fr.findFeaturesAtRes(asp,
+                      residuePos);
+              for (SequenceFeature feature : features)
+              {
+                String desc = feature.getDescription();
+                float score = feature.getScore();
+                if (score != 0 && score != Float.NaN)
+                {
+                  desc = Float.toString(score);
+                }
+                String attName = "jv:"
+                        + feature.getType().replace(" ", "_");
+                String cmd = "setattr r " + attName + " \""
+                        + desc + "\" #" + pdbfnum + ":" + pos + "." + chain;
+                System.out.println(cmd);
+                sendAsynchronousCommand(cmd, null);
+              }
+            }
+          }
+        }
+      }
+    }
+  }
 }