Merge branch 'develop' into bug/JAL-2346annotationChoice

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index bf80831..94df99a 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -34,6 +35,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -43,6 +45,7 @@ import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -227,21 +230,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * Construct and send a command to align structures against a reference
-   * structure, based on one or more sequence alignments
-   * 
-   * @param _alignment
-   *          an array of alignments to process
-   * @param _refStructure
-   *          an array of corresponding reference structures (index into pdb
-   *          file array); if a negative value is passed, the first PDB file
-   *          mapped to an alignment sequence is used as the reference for
-   *          superposition
-   * @param _hiddenCols
-   *          an array of corresponding hidden columns for each alignment
+   * {@inheritDoc}
    */
   @Override
-  public void superposeStructures(AlignmentI[] _alignment,
+  public String superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
     while (viewer.isScriptExecuting())
@@ -261,7 +253,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     String[] files = getPdbFile();
     if (!waitForFileLoad(files))
     {
-      return;
+      return null;
     }
 
     StringBuilder selectioncom = new StringBuilder(256);
@@ -277,6 +269,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       nSeconds = " " + (2.0 / files.length) + " ";
       // if (nSeconds).substring(0,5)+" ";
     }
+
     // see JAL-1345 - should really automatically turn off the animation for
     // large numbers of structures, but Jmol doesn't seem to allow that.
     // nSeconds = " ";
@@ -302,14 +295,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
 
       /*
-       * 'matched' array will hold 'true' for visible alignment columns where
+       * 'matched' bit j will be set for visible alignment columns j where
        * all sequences have a residue with a mapping to the PDB structure
        */
-      // TODO could use a BitSet for matched
-      boolean matched[] = new boolean[alignment.getWidth()];
-      for (int m = 0; m < matched.length; m++)
+      BitSet matched = new BitSet();
+      for (int m = 0; m < alignment.getWidth(); m++)
       {
-        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+        if (hiddenCols == null || hiddenCols.isVisible(m))
+        {
+          matched.set(m);
+        }
       }
 
       SuperposeData[] structures = new SuperposeData[files.length];
@@ -334,17 +329,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
 
       String[] selcom = new String[files.length];
-      int nmatched = 0;
-      for (boolean b : matched)
-      {
-        if (b)
-        {
-          nmatched++;
-        }
-      }
+      int nmatched = matched.cardinality();
       if (nmatched < 4)
       {
-        // TODO: bail out here because superposition illdefined?
+        return (MessageManager.formatMessage(
+"label.insufficient_residues",
+                nmatched));
       }
 
       /*
@@ -359,35 +349,35 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           boolean run = false;
           StringBuilder molsel = new StringBuilder();
           molsel.append("{");
-          for (int r = 0; r < matched.length; r++)
+
+          int nextColumnMatch = matched.nextSetBit(0);
+          while (nextColumnMatch != -1)
           {
-            if (matched[r])
+            int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
+            if (lpos != pdbResNo - 1)
             {
-              int pdbResNo = structures[pdbfnum].pdbResNo[r];
-              if (lpos != pdbResNo - 1)
+              // discontinuity
+              if (lpos != -1)
               {
-                // discontinuity
-                if (lpos != -1)
-                {
-                  molsel.append(lpos);
-                  molsel.append(chainCd);
-                  molsel.append("|");
-                }
-                run = false;
+                molsel.append(lpos);
+                molsel.append(chainCd);
+                molsel.append("|");
               }
-              else
+              run = false;
+            }
+            else
+            {
+              // continuous run - and lpos >-1
+              if (!run)
               {
-                // continuous run - and lpos >-1
-                if (!run)
-                {
-                  // at the beginning, so add dash
-                  molsel.append(lpos);
-                  molsel.append("-");
-                }
-                run = true;
+                // at the beginning, so add dash
+                molsel.append(lpos);
+                molsel.append("-");
               }
-              lpos = pdbResNo;
+              run = true;
             }
+            lpos = pdbResNo;
+            nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
           }
           /*
            * add final selection phrase
@@ -473,6 +463,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
               + selectioncom.toString() + "); cartoons; ");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
     }
+
+    return null;
   }
 
   public void evalStateCommand(String command)
@@ -507,17 +499,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, alignment);
+            getSequence(), sr, viewPanel);
   }
 
   /**