X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=a1b69172c865a6435ebd2c632a1daf0400592388;hb=3fd32306db772b6d6756ca20d33519edeb353c2d;hp=0f69aeba48a657a3ab7d123ec7ca5945f41eb41d;hpb=43e35e6940b01e39f046d9005ec3cb1b316a39a9;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 0f69aeb..a1b6917 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -63,11 +63,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
-  /*
-   * state flag used to check if the Jmol viewer's paint method can be called
-   */
-  private boolean finishedInit = false;
-
   boolean allChainsSelected = false;
 
   /*
@@ -236,10 +231,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void superposeStructures(AlignmentI alignment, int refStructure,
           ColumnSelection hiddenCols)
   {
-    superposeStructures(new AlignmentI[]
-    { alignment }, new int[]
-    { refStructure }, new ColumnSelection[]
-    { hiddenCols });
+    superposeStructures(new AlignmentI[] { alignment },
+            new int[] { refStructure },
+            new ColumnSelection[] { hiddenCols });
   }
 
   /**
@@ -463,8 +457,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                 + selectioncom.toString() + "); cartoons; ");
         // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        System.out
-.println("Superimpose command(s):\n" + cmdString);
+        System.out.println("Superimpose command(s):\n" + cmdString);
 
         evalStateCommand(cmdString);
       }
@@ -521,7 +514,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+            files, sr, fr, alignment))
     {
       for (String cbyseq : cpdbbyseq.commands)
       {
@@ -541,10 +535,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    return JmolCommands
-            .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
-                    fr,
-                    alignment);
+    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+            getSequence(), sr, fr, alignment);
   }
 
   /**
@@ -560,6 +552,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     System.out.println("JMOL CREATE IMAGE");
   }
 
+  @Override
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
@@ -567,6 +560,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
+  @Override
   public String eval(String strEval)
   {
     // System.out.println(strEval);
@@ -577,11 +571,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // End StructureListener
   // //////////////////////////
 
+  @Override
   public float[][] functionXY(String functionName, int x, int y)
   {
     return null;
   }
 
+  @Override
   public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
   {
     // TODO Auto-generated method stub
@@ -597,8 +593,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     // TODO: verify atomIndex is selecting correct model.
     // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
-    int colour = viewer.ms.at[atomIndex]
-            .atomPropertyInt(T.color);
+    int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
     return new Color(colour);
   }
 
@@ -676,6 +671,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // applet path with docroot - discard as format won't match pdbfile
           mset[0] = m;
         }
+        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
       }
       int j = 1;
       for (int i = 1; i < mset.length; i++)
@@ -745,6 +741,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      if (resetLastRes.length() > 0)
+      {
+        viewer.evalStringQuiet(resetLastRes.toString());
+        resetLastRes.setLength(0);
+      }
       for (AtomSpec atom : atoms)
       {
         highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
@@ -776,17 +777,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
 
     jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
 
     StringBuilder cmd = new StringBuilder(64);
     cmd.append("select " + pdbResNum); // +modelNum
 
-    resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum); // +modelNum
 
     cmd.append(":");
@@ -895,8 +889,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfilename = modelFileNames[_mp];
         if (pdbfilename == null)
         {
-          pdbfilename = new File(
-                  viewer.ms.getModelFileName(mnumber))
+          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
                   .getAbsolutePath();
         }
 
@@ -951,7 +944,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     String mdlString = "";
     if ((p = strInfo.indexOf(":")) > -1)
     {
-      picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+      picked += strInfo.substring(p, strInfo.indexOf("."));
     }
 
     if ((p = strInfo.indexOf("/")) > -1)
@@ -1139,8 +1132,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
                 + ".0", "PDB");
       }
-        // search pdbentries and sequences to find correct pdbentry for this
-        // model
+      // search pdbentries and sequences to find correct pdbentry for this
+      // model
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
@@ -1273,6 +1266,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   public abstract void sendConsoleMessage(String strStatus);
 
+  @Override
   public void setCallbackFunction(String callbackType,
           String callbackFunction)
   {
@@ -1410,16 +1404,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
-  public boolean isFinishedInit()
-  {
-    return finishedInit;
-  }
-
-  public void setFinishedInit(boolean finishedInit)
-  {
-    this.finishedInit = finishedInit;
-  }
-
   /**
    * 
    */
@@ -1474,4 +1458,3 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     showConsole(false);
   }
 }
-