X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=ed0b9503e675c34ab3be117c1392c91385218238;hb=c5a7bc3f03aef928f1b06e5e9ab53d06970aeb12;hp=fc86e1c1669a9898f71c9ca8c4f8730ce88b6383;hpb=578c59366e6a562567a37ad03f66f3cd38272306;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fc86e1c..ed0b950 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -55,7 +55,6 @@ import org.jmol.api.JmolSelectionListener;
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
-import org.jmol.popup.JmolGenericPopup;
 import org.jmol.script.T;
 import org.jmol.viewer.JC;
 import org.jmol.viewer.Viewer;
@@ -77,13 +76,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private boolean associateNewStructs = false;
 
-  Vector atomsPicked = new Vector();
+  Vector<String> atomsPicked = new Vector<String>();
 
-  public Vector chainNames;
+  public Vector<String> chainNames;
 
-  Hashtable chainFile;
-
-  StringBuffer eval = new StringBuffer();
+  Hashtable<String, String> chainFile;
 
   public String fileLoadingError;
 
@@ -93,7 +90,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   int frameNo = 0;
 
-  protected JmolGenericPopup jmolpopup;
+  // protected JmolGenericPopup jmolpopup; // not used - remove?
 
   String lastCommand;
 
@@ -152,15 +149,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param chainList
    *          list of chains to make visible
    */
-  public void centerViewer(Vector chainList)
+  public void centerViewer(Vector<String> chainList)
   {
-    StringBuffer cmd = new StringBuffer();
-    String lbl;
+    StringBuilder cmd = new StringBuilder(128);
     int mlength, p;
-    for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+    for (String lbl : chainList)
     {
       mlength = 0;
-      lbl = (String) chainList.elementAt(i);
       do
       {
         p = mlength;
@@ -168,7 +163,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       } while (p < mlength && mlength < (lbl.length() - 2));
       // TODO: lookup each pdb id and recover proper model number for it.
       cmd.append(":" + lbl.substring(mlength + 1) + " /"
-              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
+              + (1 + getModelNum(chainFile.get(lbl))) + " or ");
     }
     if (cmd.length() > 0)
     {
@@ -483,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
+      System.out.println(command);
       viewer.evalStringQuiet(command + "\n");
     }
     jmolHistory(true);
@@ -494,9 +490,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
    * if colourBySequence is enabled.
    */
-  public void colourBySequence(boolean showFeatures,
-          jalview.api.AlignmentViewPanel alignmentv)
+  public void colourBySequence(AlignmentViewPanel alignmentv)
   {
+    boolean showFeatures = alignmentv.getAlignViewport()
+            .isShowSequenceFeatures();
     if (!colourBySequence || !isLoadingFinished())
     {
       return;
@@ -729,7 +726,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void handlePopupMenu(int x, int y)
   {
     // jmolpopup.show(x, y);
-    jmolpopup.jpiShow(x, y);
+    // jmolpopup.jpiShow(x, y);
   }
 
   /**
@@ -759,12 +756,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     // look up file model number for this pdbfile
     int mdlNum = 0;
-    String fn;
     // may need to adjust for URLencoding here - we don't worry about that yet.
     while (mdlNum < modelFileNames.length
             && !pdbfile.equals(modelFileNames[mdlNum]))
     {
-      // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
       mdlNum++;
     }
     if (mdlNum == modelFileNames.length)
@@ -780,31 +775,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       viewer.evalStringQuiet(resetLastRes.toString());
     }
 
-    eval.setLength(0);
-    eval.append("select " + pdbResNum); // +modelNum
+    StringBuilder cmd = new StringBuilder(64);
+    cmd.append("select " + pdbResNum); // +modelNum
 
     resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum); // +modelNum
 
-    eval.append(":");
+    cmd.append(":");
     resetLastRes.append(":");
     if (!chain.equals(" "))
     {
-      eval.append(chain);
+      cmd.append(chain);
       resetLastRes.append(chain);
     }
     {
-      eval.append(" /" + (mdlNum + 1));
+      cmd.append(" /" + (mdlNum + 1));
       resetLastRes.append("/" + (mdlNum + 1));
     }
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+    cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
 
     resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
             + " and not hetero; spacefill 0;");
 
-    eval.append("spacefill 200;select none");
+    cmd.append("spacefill 200;select none");
 
-    viewer.evalStringQuiet(eval.toString());
+    viewer.evalStringQuiet(cmd.toString());
     jmolHistory(true);
 
   }
@@ -1081,8 +1076,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new Vector();
-    chainFile = new Hashtable();
+    chainNames = new Vector<String>();
+    chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     // first check if we've lost any structures
@@ -1126,7 +1121,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       String fileName = modelfilenames[modelnum];
       boolean foundEntry = false;
       MCview.PDBfile pdb = null;
-      String pdbfile = null, pdbfhash = null;
+      String pdbfile = null;
       // model was probably loaded inline - so check the pdb file hashcode
       if (loadedInline)
       {
@@ -1135,7 +1130,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         // 'best guess'
         pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
                 + ".0", "PDB");
-        pdbfhash = "" + pdbfile.hashCode();
       }
         // search pdbentries and sequences to find correct pdbentry for this
         // model
@@ -1216,11 +1210,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
-    if (jmolpopup != null)
-    {
-      // potential for deadlock here:
-      // jmolpopup.updateComputedMenus();
-    }
+    // if (jmolpopup != null)
+    // {
+    // // potential for deadlock here:
+    // // jmolpopup.updateComputedMenus();
+    // }
     if (!isLoadingFromArchive())
     {
       viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");