X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=3bac3bc1f9bb67c082b371fca52f54c9697f41f3;hb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;hp=80cc8af16df0f3009d9ff28d6f4ba41c7bdd617c;hpb=b3d9ad42a4cc73a11a1478d8735dfe66a88a2953;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 80cc8af..3bac3bc 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -24,6 +24,8 @@ import java.applet.Applet;
 import java.awt.*;
 import java.awt.event.*;
 
+import javax.swing.JPanel;
+
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;
@@ -36,11 +38,13 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter;
 
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
+import org.jmol.viewer.Viewer;
 
 import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
+        JmolStatusListener, SequenceStructureBinding,
+        JmolSelectionListener, ComponentListener
 
 {
   /**
@@ -77,6 +81,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public Vector chainNames;
 
+  Hashtable chainFile;
+
   /**
    * array of target chains for seuqences - tied to pdbentry and sequence[]
    */
@@ -161,10 +167,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public String getViewerTitle()
   {
     if (sequence == null || pdbentry == null || sequence.length < 1
-            || pdbentry.length < 1)
+            || pdbentry.length < 1 || sequence[0].length < 1)
     {
       return ("Jalview Jmol Window");
     }
+    // TODO: give a more informative title when multiple structures are
+    // displayed.
     StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
             + pdbentry[0].getId());
 
@@ -205,8 +213,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
         p = mlength;
         mlength = lbl.indexOf(":", p);
       } 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) + " /"
-              + getModelNum(lbl.substring(0, mlength)) + " or ");
+              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
@@ -224,12 +233,20 @@ public abstract class JalviewJmolBinding implements StructureListener,
     viewer.setJmolStatusListener(null);
     lastCommand = null;
     viewer = null;
+    releaseUIResources();
   }
 
+  /**
+   * called by JalviewJmolbinding after closeViewer is called - release any
+   * resources and references so they can be garbage collected.
+   */
+  protected abstract void releaseUIResources();
+
   public void colourByChain()
   {
     colourBySequence = false;
-    // TODO: colour by chain should colour each chain distinctly across all visible models 
+    // TODO: colour by chain should colour each chain distinctly across all
+    // visible models
     // TODO: http://issues.jalview.org/browse/JAL-628
     evalStateCommand("select *;color chain");
   }
@@ -266,32 +283,36 @@ public abstract class JalviewJmolBinding implements StructureListener,
   /**
    * superpose the structures associated with sequences in the alignment
    * according to their corresponding positions. ded)
+   * 
    * @param refStructure
    *          - select which pdb file to use as reference (default is -1 - the
    *          first structure in the alignment)
-   * @param hiddenCols TODO
+   * @param hiddenCols
+   *          TODO
    */
-  public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+  public void superposeStructures(AlignmentI alignment, int refStructure,
+          ColumnSelection hiddenCols)
   {
     String[] files = getPdbFile();
-    if (refStructure>=files.length)
+    if (refStructure >= files.length)
     {
-      System.err.println("Invalid reference structure value "+refStructure);
-      refStructure= -1;
+      System.err.println("Invalid reference structure value "
+              + refStructure);
+      refStructure = -1;
     }
-    if (refStructure<-1)
+    if (refStructure < -1)
     {
-      refStructure=-1;
+      refStructure = -1;
     }
     StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-    
+
     boolean matched[] = new boolean[alignment.getWidth()];
     for (int m = 0; m < matched.length; m++)
     {
-      
-      matched[m] = (hiddenCols!=null) ? hiddenCols.isVisible(m) : true;
+
+      matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
     }
-    
+
     int commonrpositions[][] = new int[files.length][alignment.getWidth()];
     String isel[] = new String[files.length];
     // reference structure - all others are superposed in it
@@ -366,6 +387,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
       }
     }
     String[] selcom = new String[files.length];
+    int nmatched = 0;
     // generate select statements to select regions to superimpose structures
     {
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
@@ -379,7 +401,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
         {
           if (matched[r])
           {
-
+            if (pdbfnum == 0)
+            {
+              nmatched++;
+            }
             if (lpos != commonrpositions[pdbfnum][r] - 1)
             {
               // discontinuity
@@ -413,19 +438,23 @@ public abstract class JalviewJmolBinding implements StructureListener,
           molsel.append(chainCd);
           molsel.append("}");
         }
-        selcom[pdbfnum] = molsel.toString(); 
+        selcom[pdbfnum] = molsel.toString();
         selectioncom.append("((");
-        selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1));
+        selectioncom.append(selcom[pdbfnum].substring(1,
+                selcom[pdbfnum].length() - 1));
         selectioncom.append(" )& ");
-        selectioncom.append(pdbfnum+1);
+        selectioncom.append(pdbfnum + 1);
         selectioncom.append(".1)");
-        if (pdbfnum<files.length-1)
+        if (pdbfnum < files.length - 1)
         {
           selectioncom.append("|");
         }
       }
     }
-
+    // TODO: consider bailing if nmatched less than 4 because superposition not
+    // well defined.
+    // TODO: refactor superposable position search (above) from jmol selection
+    // construction (below)
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       if (pdbfnum == refStructure)
@@ -448,12 +477,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
       command.append(" ROTATE TRANSLATE;\n");
     }
     System.out.println("Select regions:\n" + selectioncom.toString());
-    evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; ");
+    evalStateCommand("select *; cartoons off; backbone; select ("
+            + selectioncom.toString() + "); cartoons; ");
     // selcom.append("; ribbons; ");
     System.out.println("Superimpose command(s):\n" + command.toString());
 
     evalStateCommand(command.toString());
-    
+
     // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
   }
 
@@ -524,7 +554,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 
-              if (showFeatures)
+              if (showFeatures && fr != null)
                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
@@ -662,19 +692,35 @@ public abstract class JalviewJmolBinding implements StructureListener,
     return -1;
   }
 
+  /**
+   * map between index of model filename returned from getPdbFile and the first
+   * index of models from this file in the viewer. Note - this is not trimmed -
+   * use getPdbFile to get number of unique models.
+   */
+  private int _modelFileNameMap[];
+
   // ////////////////////////////////
   // /StructureListener
   public synchronized String[] getPdbFile()
   {
+    if (viewer == null)
+    {
+      return new String[0];
+    }
     if (modelFileNames == null)
     {
+
       String mset[] = new String[viewer.getModelCount()];
-      int j=1;
+      _modelFileNameMap = new int[mset.length];
+      int j = 1;
       mset[0] = viewer.getModelFileName(0);
       for (int i = 1; i < mset.length; i++)
       {
-        // skip any additional models in the same file (NMR structures) 
-        if (!(mset[j] = viewer.getModelFileName(i)).equals(mset[j-1]))
+        mset[j] = viewer.getModelFileName(i);
+        _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]))))
         {
           j++;
         }
@@ -781,6 +827,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void loadInline(String string)
   {
     loadedInline = true;
+    // TODO: re JAL-623
+    // viewer.loadInline(strModel, isAppend);
+    // could do this:
+    // construct fake fullPathName and fileName so we can identify the file
+    // later.
+    // Then, construct pass a reader for the string to Jmol.
+    // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+    // fileName, null, reader, false, null, null, 0);
     viewer.openStringInline(string);
   }
 
@@ -945,7 +999,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
       case JmolConstants.CALLBACK_MEASURE:
 
       case JmolConstants.CALLBACK_CLICK:
-
       default:
         System.err.println("Unhandled callback " + type + " "
                 + data[1].toString());
@@ -980,6 +1033,16 @@ public abstract class JalviewJmolBinding implements StructureListener,
     return false;
   }
 
+  // incremented every time a load notification is successfully handled -
+  // lightweight mechanism for other threads to detect when they can start
+  // referrring to new structures.
+  private long loadNotifiesHandled = 0;
+
+  public long getLoadNotifiesHandled()
+  {
+    return loadNotifiesHandled;
+  }
+
   public void notifyFileLoaded(String fullPathName, String fileName2,
           String modelName, String errorMsg, int modelParts)
   {
@@ -989,6 +1052,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
       refreshGUI();
       return;
     }
+    // TODO: deal sensibly with models loaded inLine:
+    // modelName will be null, as will fullPathName.
+
     // the rest of this routine ignores the arguments, and simply interrogates
     // the Jmol view to find out what structures it contains, and adds them to
     // the structure selection manager.
@@ -996,6 +1062,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
+    chainFile = new Hashtable();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
@@ -1038,84 +1105,103 @@ public abstract class JalviewJmolBinding implements StructureListener,
     for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
     {
       String fileName = modelfilenames[modelnum];
-      if (fileName != null)
+      boolean foundEntry = false;
+      MCview.PDBfile pdb = null;
+      String pdbfile = null, pdbfhash = null;
+      // model was probably loaded inline - so check the pdb file hashcode
+      if (loadedInline)
       {
-        boolean foundEntry = false;
-        // search pdbentries and sequences to find correct pdbentry and
-        // sequence[] pair for this filename
-        if (pdbentry != null)
+        // calculate essential attributes for the pdb data imported inline.
+        // prolly need to resolve modelnumber properly - for now just use our
+        // 'best guess'
+        pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+                + ".0", "PDB");
+        pdbfhash = "" + pdbfile.hashCode();
+      }
+      if (pdbentry != null)
+      {
+        // search pdbentries and sequences to find correct pdbentry for this
+        // model
+        for (int pe = 0; pe < pdbentry.length; pe++)
         {
-          for (int pe = 0; pe < pdbentry.length; pe++)
+          boolean matches = false;
+          if (fileName == null)
           {
-            if (pdbentry[pe].getFile().equals(fileName))
+            if (false)
+            // see JAL-623 - need method of matching pasted data up
             {
+              pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+                      AppletFormatAdapter.PASTE);
+              pdbentry[modelnum].setFile("INLINE" + pdb.id);
+              matches = true;
               foundEntry = true;
-              MCview.PDBfile pdb;
-              if (loadedInline)
-              {
-                // TODO: replace with getData ?
-                pdb = ssm.setMapping(sequence[pe], chains[pe],
-                        pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
-                pdbentry[pe].setFile("INLINE" + pdb.id);
-              }
-              else
+            }
+          }
+          else
+          {
+            if (matches = pdbentry[pe].getFile().equals(fileName))
+            {
+              foundEntry = true;
+              // TODO: Jmol can in principle retrieve from CLASSLOADER but
+              // this
+              // needs
+              // to be tested. See mantis bug
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+              String protocol = AppletFormatAdapter.URL;
+              try
               {
-                // TODO: Jmol can in principle retrieve from CLASSLOADER but
-                // this
-                // needs
-                // to be tested. See mantis bug
-                // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-                String protocol = AppletFormatAdapter.URL;
-                try
-                {
-                  File fl = new java.io.File(pdbentry[pe].getFile());
-                  if (fl.exists())
-                  {
-                    protocol = AppletFormatAdapter.FILE;
-                  }
-                } catch (Exception e)
-                {
-                } catch (Error e)
+                File fl = new java.io.File(pdbentry[pe].getFile());
+                if (fl.exists())
                 {
+                  protocol = AppletFormatAdapter.FILE;
                 }
-                ;
-                pdb = ssm.setMapping(sequence[pe], chains[pe],
-                        pdbentry[pe].getFile(), protocol);
-
-              }
-
-              pdbentry[pe].setId(pdb.id);
-
-              for (int i = 0; i < pdb.chains.size(); i++)
+              } catch (Exception e)
+              {
+              } catch (Error e)
               {
-                chainNames.addElement(new String(pdb.id + ":"
-                        + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
               }
-              notifyLoaded = true;
+              ;
+              pdb = ssm.setMapping(sequence[pe], chains[pe],
+                      pdbentry[pe].getFile(), protocol);
+
+            }
+          }
+          if (matches)
+          {
+            pdbentry[pe].setId(pdb.id);
+            // add an entry for every chain in the model
+            for (int i = 0; i < pdb.chains.size(); i++)
+            {
+              String chid = new String(pdb.id + ":"
+                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+              chainFile.put(chid, pdbentry[pe].getFile());
+              chainNames.addElement(chid);
             }
+            notifyLoaded = true;
           }
         }
-        if (!foundEntry && associateNewStructs)
-        {
-          // this is a foreign pdb file that jalview doesn't know about - add
-          // it to the dataset and try to find a home - either on a matching
-          // sequence or as a new sequence.
-          String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                  "PDB");
-          // parse pdb file into a chain, etc.
-          // locate best match for pdb in associated views and add mapping to
-          // ssm
-          // if properly registered then
-          notifyLoaded = true;
+      }
+      if (!foundEntry && associateNewStructs)
+      {
+        // this is a foreign pdb file that jalview doesn't know about - add
+        // it to the dataset and try to find a home - either on a matching
+        // sequence or as a new sequence.
+        String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+                "PDB");
+        // parse pdb file into a chain, etc.
+        // locate best match for pdb in associated views and add mapping to
+        // ssm
+        // if properly registered then
+        notifyLoaded = true;
 
-        }
       }
     }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
     if (jmolpopup != null)
     {
-      jmolpopup.updateComputedMenus();
+      // potential for deadlock here:
+      // jmolpopup.updateComputedMenus();
     }
     if (!isLoadingFromArchive())
     {
@@ -1133,6 +1219,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         fr.featuresAdded();
       }
       refreshGUI();
+      loadNotifiesHandled++;
     }
   }
 
@@ -1225,6 +1312,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public abstract void refreshGUI();
 
   /**
+   * called to show or hide the associated console window container.
+   * 
+   * @param show
+   */
+  public abstract void showConsole(boolean show);
+
+  /**
    * @param renderPanel
    * @param jmolfileio
    *          - when true will initialise jmol's file IO system (should be false
@@ -1234,14 +1328,75 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @param codeBase
    * @param commandOptions
    */
-  public void allocateViewer(Component renderPanel, boolean jmolfileio,
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {
+    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+            codeBase, commandOptions, null, null);
+  }
+
+  /**
+   * 
+   * @param renderPanel
+   * @param jmolfileio
+   *          - when true will initialise jmol's file IO system (should be false
+   *          in applet context)
+   * @param htmlName
+   * @param documentBase
+   * @param codeBase
+   * @param commandOptions
+   * @param consolePanel
+   *          - panel to contain Jmol console
+   * @param buttonsToShow
+   *          - buttons to show on the console, in ordr
+   */
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,
+          String htmlName, URL documentBase, URL codeBase,
+          String commandOptions, final Container consolePanel,
+          String buttonsToShow)
+  {
     viewer = JmolViewer.allocateViewer(renderPanel,
             (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
                     + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
+
+    console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+    if (consolePanel != null)
+    {
+      consolePanel.addComponentListener(this);
+
+    }
+
+  }
+
+  protected abstract JmolAppConsoleInterface createJmolConsole(
+          JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+
+  protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+  @Override
+  public void componentResized(ComponentEvent e)
+  {
+
+  }
+
+  @Override
+  public void componentMoved(ComponentEvent e)
+  {
+
+  }
+
+  @Override
+  public void componentShown(ComponentEvent e)
+  {
+    showConsole(true);
+  }
+
+  @Override
+  public void componentHidden(ComponentEvent e)
+  {
+    showConsole(false);
   }
 
   public void setLoadingFromArchive(boolean loadingFromArchive)
@@ -1267,8 +1422,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * 
    * @returns the pdb entries added to the current set.
    */
-  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
-          String[][] chns)
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
   {
     int pe = -1;
     Vector v = new Vector();