JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26

[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 2ccf118..9ee0777 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -43,13 +43,12 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -93,11 +92,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   boolean loadedInline;
 
-  /**
-   * current set of model filenames loaded in the Jmol instance
-   */
-  String[] modelFileNames = null;
-
   StringBuffer resetLastRes = new StringBuffer();
 
   public Viewer viewer;
@@ -171,7 +165,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     // remove listeners for all structures in viewer
     getSsm().removeStructureViewerListener(this, this.getPdbFile());
-     viewer.dispose();
+    viewer.dispose();
     lastCommand = null;
     viewer = null;
     releaseUIResources();
@@ -258,8 +252,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       } catch (InterruptedException i)
       {
       }
-      ;
     }
+
+    /*
+     * get the distinct structure files modelled
+     * (a file with multiple chains may map to multiple sequences)
+     */
     String[] files = getPdbFile();
     if (!waitForFileLoad(files))
     {
@@ -307,6 +305,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * 'matched' array will hold 'true' for visible alignment columns 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++)
       {
@@ -352,6 +351,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * generate select statements to select regions to superimpose structures
        */
       {
+        // TODO extract method to construct selection statements
         for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
         {
           String chainCd = ":" + structures[pdbfnum].chain;
@@ -419,6 +419,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         }
       }
       StringBuilder command = new StringBuilder(256);
+      // command.append("set spinFps 10;\n");
+
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         if (pdbfnum == refStructure || selcom[pdbfnum] == null
@@ -449,12 +451,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
-        System.out.println("Select regions:\n" + selectioncom.toString());
+        // TODO is performing selectioncom redundant here? is done later on
+        // System.out.println("Select regions:\n" + selectioncom.toString());
         evalStateCommand("select *; cartoons off; backbone; select ("
                 + 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);
       }
@@ -465,7 +468,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       {
         selectioncom.setLength(selectioncom.length() - 1);
       }
-      System.out.println("Select regions:\n" + selectioncom.toString());
+      // System.out.println("Select regions:\n" + selectioncom.toString());
       evalStateCommand("select *; cartoons off; backbone; select ("
               + selectioncom.toString() + "); cartoons; ");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
@@ -647,15 +650,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     if (modelFileNames == null)
     {
-      String mset[] = new String[viewer.ms.mc];
-      _modelFileNameMap = new int[mset.length];
+      List<String> mset = new ArrayList<String>();
+      _modelFileNameMap = new int[viewer.ms.mc];
       String m = viewer.ms.getModelFileName(0);
       if (m != null)
       {
-        mset[0] = m;
+        String filePath = m;
         try
         {
-          mset[0] = new File(m).getAbsolutePath();
+          filePath = new File(m).getAbsolutePath();
         } catch (AccessControlException x)
         {
           // usually not allowed to do this in applet
@@ -663,39 +666,43 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                   .println("jmolBinding: Using local file string from Jmol: "
                           + m);
         }
-        if (mset[0].indexOf("/file:") != -1)
+        if (filePath.indexOf("/file:") != -1)
         {
           // applet path with docroot - discard as format won't match pdbfile
-          mset[0] = m;
+          filePath = m;
         }
+        mset.add(filePath);
         _modelFileNameMap[0] = 0; // filename index for first model is always 0.
       }
       int j = 1;
-      for (int i = 1; i < mset.length; i++)
+      for (int i = 1; i < viewer.ms.mc; i++)
       {
         m = viewer.ms.getModelFileName(i);
-        mset[j] = m;
+        String filePath = m;
         if (m != null)
         {
           try
           {
-            mset[j] = new File(m).getAbsolutePath();
+            filePath = new File(m).getAbsolutePath();
           } catch (AccessControlException x)
           {
             // usually not allowed to do this in applet, so keep raw handle
             // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
           }
         }
-        _modelFileNameMap[j] = i; // record the model index for the filename
-        // skip any additional models in the same file (NMR structures)
-        if ((mset[j] == null ? mset[j] != mset[j - 1]
-                : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+
+        /*
+         * add this model unless it is read from a structure file we have
+         * already seen (example: 2MJW is an NMR structure with 10 models)
+         */
+        if (!mset.contains(filePath))
         {
+          mset.add(filePath);
+          _modelFileNameMap[j] = i; // record the model index for the filename
           j++;
         }
       }
-      modelFileNames = new String[j];
-      System.arraycopy(mset, 0, modelFileNames, 0, j);
+      modelFileNames = mset.toArray(new String[mset.size()]);
     }
     return modelFileNames;
   }
@@ -1395,7 +1402,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // Jalview doesn't honour resize panel requests
     return null;