JAL-3390 first draft of showing only visible alignment in Chimera

[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 00446f2..6fa06d2 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
@@ -31,11 +32,13 @@ import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.httpserver.AbstractRequestHandler;
 import jalview.io.DataSourceType;
 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;
@@ -76,9 +79,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
-  private List<String> chainNames = new ArrayList<String>();
+  private List<String> chainNames = new ArrayList<>();
 
-  private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+  private Hashtable<String, String> chainFile = new Hashtable<>();
 
   /*
    * Object through which we talk to Chimera
@@ -106,7 +109,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /*
    * Map of ChimeraModel objects keyed by PDB full local file name
    */
-  private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
+  private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
 
   String lastHighlightCommand;
 
@@ -133,7 +136,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     String file = pe.getFile();
     try
     {
-      List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
+      List<ChimeraModel> modelsToMap = new ArrayList<>();
       List<ChimeraModel> oldList = viewer.getModelList();
       boolean alreadyOpen = false;
 
@@ -519,8 +522,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           System.out.println(
                   "Superimpose command(s):\n" + command.toString());
         }
-        allComs.append("~display all; chain @CA|P; ribbon ")
-                .append(selectioncom.toString())
+        allComs/*.append("~display all; chain @CA|P; ribbon ")
+                .append(selectioncom.toString())*/
                 .append(";" + command.toString());
       }
     }
@@ -537,13 +540,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       {
         System.out.println("Select regions:\n" + selectioncom.toString());
       }
-      allComs.append("; ~display all; chain @CA|P; ribbon ")
-              .append(selectioncom.toString()).append("; focus");
+      allComs.append("; ~display "); // all");
+      if (!isShowAlignmentOnly())
+      {
+        allComs.append("; ribbon; chain @CA|P");
+      }
+      else
+      {
+        allComs.append("; ~ribbon");
+      }
+      allComs.append("; ribbon ").append(selectioncom.toString())
+              .append("; focus");
       List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
               true);
       for (String reply : chimeraReplies)
       {
-        if (reply.toLowerCase().contains("unequal numbers of atoms"))
+        String lowerCase = reply.toLowerCase();
+        if (lowerCase.contains("unequal numbers of atoms")
+                || lowerCase.contains("at least"))
         {
           error = reply;
         }
@@ -857,7 +871,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   protected List<AtomSpec> convertStructureResiduesToAlignment(
           List<String> structureSelection)
   {
-    List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
+    List<AtomSpec> atomSpecs = new ArrayList<>();
     for (String atomSpec : structureSelection)
     {
       try
@@ -1308,4 +1322,102 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     return -1;
   }
+
+  @Override
+  public void showStructures(AlignViewportI av)
+  {
+    StringBuilder cmd = new StringBuilder(128);
+    cmd.append("~display; ~ribbon;");
+    if (isShowAlignmentOnly())
+    {
+      String atomSpec = getMappedResidues(av);
+      cmd.append("ribbon ").append(atomSpec);
+    }
+    else
+    {
+      cmd.append("chain @CA|P; ribbon");
+    }
+    cmd.append("; focus");
+    sendChimeraCommand(cmd.toString(), false);
+  }
+
+  /**
+   * Builds a Chimera atomSpec of residues mapped from sequences, of the format
+   * (#model:residues.chain)
+   * 
+   * <pre>
+   * #0:2-94.A | #1:1-93.C | #2:1-93.A
+   * </pre>
+   * 
+   * Only residues visible in the alignment are included, that is, hidden columns
+   * and sequences are excluded.
+   * 
+   * @param av
+   * @return
+   */
+  private String getMappedResidues(AlignViewportI av)
+  {
+    AlignmentI alignment = av.getAlignment();
+    final int width = alignment.getWidth();
+  
+    String[] files = getStructureFiles();
+
+    StringBuilder atomSpec = new StringBuilder(256);
+
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+
+      /*
+       * Find the first mapped sequence (if any) for this PDB entry which is in
+       * the alignment
+       */
+      final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+      for (int s = 0; s < seqCountForPdbFile; s++)
+      {
+        for (StructureMapping mapping : mappings)
+        {
+          final SequenceI theSequence = getSequence()[pdbfnum][s];
+          if (mapping.getSequence() == theSequence
+                  && alignment.findIndex(theSequence) > -1)
+          {
+            String chainCd = mapping.getChain();
+
+            // TODO only process sequence ranges within visible columns
+            VisibleContigsIterator visible = alignment.getHiddenColumns()
+                    .getVisContigsIterator(0, width, true);
+            while (visible.hasNext())
+            {
+              int[] visibleRegion = visible.next();
+              int seqStartPos = theSequence.findPosition(visibleRegion[0]);
+              int seqEndPos = theSequence.findPosition(visibleRegion[1]);
+              List<int[]> residueRanges = mapping
+                      .getPDBResNumRanges(seqStartPos, seqEndPos);
+              if (!residueRanges.isEmpty())
+              {
+                if (atomSpec.length() > 0)
+                {
+                  atomSpec.append("| ");
+                }
+                atomSpec.append(getModelSpec(pdbfnum)).append(":");
+                boolean first = true;
+                for (int[] range : residueRanges)
+                {
+                  if (!first)
+                  {
+                    atomSpec.append(",");
+                  }
+                  first = false;
+                  atomSpec.append(range[0]).append("-").append(range[1]);
+                  atomSpec.append(".").append(chainCd);
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+
+    return atomSpec.toString();
+  }
 }