X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=c6871a9d0c6a403f08a70ac75c4c38e54976681e;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=af83e484f0fa72aa795200da0f9b61f24d6809c9;hpb=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index af83e48..c6871a9 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -20,9 +20,12 @@ package jalview.ext.jmol;
 import java.io.File;
 import java.net.URL;
 import java.util.*;
+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;
@@ -35,11 +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
+        JmolStatusListener, SequenceStructureBinding,
+        JmolSelectionListener, ComponentListener
 
 {
   /**
@@ -48,11 +53,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * time.
    */
   private boolean loadingFromArchive = false;
+
   /**
    * state flag used to check if the Jmol viewer's paint method can be called
    */
-  private boolean finishedInit=false;
-  
+  private boolean finishedInit = false;
+
   public boolean isFinishedInit()
   {
     return finishedInit;
@@ -75,7 +81,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public Vector chainNames;
 
-  String[] chains;
+  Hashtable chainFile;
+
+  /**
+   * array of target chains for seuqences - tied to pdbentry and sequence[]
+   */
+  protected String[][] chains;
 
   boolean colourBySequence = true;
 
@@ -111,20 +122,26 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   StringBuffer resetLastRes = new StringBuffer();
 
-  public SequenceI[] sequence;
+  /**
+   * sequences mapped to each pdbentry
+   */
+  public SequenceI[][] sequence;
 
   StructureSelectionManager ssm;
 
   public JmolViewer viewer;
 
-  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
-          String[] chains, String protocol)
+  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          String[][] chains, String protocol)
   {
-    this.sequence = seq;
+    this.sequence = sequenceIs;
     this.chains = chains;
     this.pdbentry = pdbentry;
     this.protocol = protocol;
-
+    if (chains == null)
+    {
+      this.chains = new String[pdbentry.length][];
+    }
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -134,16 +151,29 @@ public abstract class JalviewJmolBinding implements StructureListener,
      */
   }
 
+  public JalviewJmolBinding(JmolViewer viewer2)
+  {
+    viewer = viewer2;
+    viewer.setJmolStatusListener(this);
+    viewer.addSelectionListener(this);
+  }
+
   /**
-   * construct a title string for the viewer window based on the data jalview knows about
-   * @return 
+   * construct a title string for the viewer window based on the data jalview
+   * knows about
+   * 
+   * @return
    */
-  public String getViewerTitle() {
-    if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
+  public String getViewerTitle()
+  {
+    if (sequence == null || pdbentry == null || sequence.length < 1
+            || pdbentry.length < 1 || sequence[0].length < 1)
     {
-      return("Jalview Jmol Window");
+      return ("Jalview Jmol Window");
     }
-    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+    // TODO: give a more informative title when multiple structures are
+    // displayed.
+    StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
             + pdbentry[0].getId());
 
     if (pdbentry[0].getProperty() != null)
@@ -183,13 +213,13 @@ 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);
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
-                    + cmd);
+    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
   }
 
   public void closeViewer()
@@ -201,13 +231,23 @@ public abstract class JalviewJmolBinding implements StructureListener,
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
-    lastCommand=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: http://issues.jalview.org/browse/JAL-628
     evalStateCommand("select *;color chain");
   }
 
@@ -224,12 +264,59 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public void superposeStructures(AlignmentI alignment)
   {
+    superposeStructures(alignment, -1, null);
+  }
+
+  /**
+   * 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)
+   */
+  public void superposeStructures(AlignmentI alignment, int refStructure)
+  {
+    superposeStructures(alignment, refStructure, null);
+  }
+
+  /**
+   * 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
+   */
+  public void superposeStructures(AlignmentI alignment, int refStructure,
+          ColumnSelection hiddenCols)
+  {
     String[] files = getPdbFile();
+    if (refStructure >= files.length)
+    {
+      System.err.println("Invalid reference structure value "
+              + refStructure);
+      refStructure = -1;
+    }
+    if (refStructure < -1)
+    {
+      refStructure = -1;
+    }
+    StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
 
-    StringBuffer command = new StringBuffer();
     boolean matched[] = new boolean[alignment.getWidth()];
-    String commonpositions[][] = new String[files.length][alignment
-            .getWidth()];
+    for (int m = 0; m < matched.length; m++)
+    {
+
+      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
+    String[] targetC = new String[files.length];
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -238,71 +325,179 @@ public abstract class JalviewJmolBinding implements StructureListener,
         continue;
 
       int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
+      for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
         for (int sp, m = 0; m < mapping.length; m++)
         {
-          if (mapping[m].getSequence() == sequence[s]
-                  && (sp = alignment.findIndex(sequence[s])) > -1)
+          if (mapping[m].getSequence() == sequence[pdbfnum][s]
+                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
           {
+            if (refStructure == -1)
+            {
+              refStructure = pdbfnum;
+            }
             SequenceI asp = alignment.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
+            for (int r = 0; r < matched.length; r++)
             {
-              // no mapping to gaps in sequence
+              if (!matched[r])
+              {
+                continue;
+              }
+              matched[r] = false; // assume this is not a good site
+              if (r >= asp.getLength())
+              {
+                continue;
+              }
+
               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
               {
-                matched[r] = false; // exclude from common set
+                // no mapping to gaps in sequence
                 continue;
               }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+              int t = asp.findPosition(r); // sequence position
+              int apos = mapping[m].getAtomNum(t);
+              int pos = mapping[m].getPDBResNum(t);
 
               if (pos < 1 || pos == lastPos)
+              {
+                // can't align unmapped sequence
                 continue;
-
+              }
+              matched[r] = true; // this is a good ite
               lastPos = pos;
-
-              commonpositions[m][r] = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/" + (pdbfnum + 1) + ".1";
+              // just record this residue position
+              commonrpositions[pdbfnum][r] = pos;
+            }
+            // create model selection suffix
+            isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+            if (mapping[m].getChain() == null
+                    || mapping[m].getChain().trim().length() == 0)
+            {
+              targetC[pdbfnum] = "";
             }
+            else
+            {
+              targetC[pdbfnum] = ":" + mapping[m].getChain();
+            }
+            // move on to next pdb file
+            s = sequence[pdbfnum].length;
             break;
           }
         }
       }
     }
-    command.append("select ");
-    // form the matched pair selection strings
-    String sep = "";
-    for (int r = 0; r < matched.length; r++)
+    String[] selcom = new String[files.length];
+    int nmatched = 0;
+    // generate select statements to select regions to superimpose structures
     {
-      if (matched[r])
+      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
-        command.append(sep);
-        command.append("(");
-        for (int s = 0; s < commonpositions.length; s++)
+        String chainCd = targetC[pdbfnum];
+        int lpos = -1;
+        boolean run = false;
+        StringBuffer molsel = new StringBuffer();
+        molsel.append("{");
+        for (int r = 0; r < matched.length; r++)
         {
-          if (s > 0)
+          if (matched[r])
           {
-            command.append(" | ");
+            if (pdbfnum == 0)
+            {
+              nmatched++;
+            }
+            if (lpos != commonrpositions[pdbfnum][r] - 1)
+            {
+              // discontinuity
+              if (lpos != -1)
+              {
+                molsel.append(lpos);
+                molsel.append(chainCd);
+                // molsel.append("} {");
+                molsel.append("|");
+              }
+            }
+            else
+            {
+              // continuous run - and lpos >-1
+              if (!run)
+              {
+                // at the beginning, so add dash
+                molsel.append(lpos);
+                molsel.append("-");
+              }
+              run = true;
+            }
+            lpos = commonrpositions[pdbfnum][r];
+            // molsel.append(lpos);
           }
-          command.append(commonpositions[s][r]);
         }
-        command.append(")");
-        sep = " | ";
+        // add final selection phrase
+        if (lpos != -1)
+        {
+          molsel.append(lpos);
+          molsel.append(chainCd);
+          molsel.append("}");
+        }
+        selcom[pdbfnum] = molsel.toString();
+        selectioncom.append("((");
+        selectioncom.append(selcom[pdbfnum].substring(1,
+                selcom[pdbfnum].length() - 1));
+        selectioncom.append(" )& ");
+        selectioncom.append(pdbfnum + 1);
+        selectioncom.append(".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)
+      {
+        continue;
       }
+      command.append("compare ");
+      command.append("{");
+      command.append(1 + pdbfnum);
+      command.append(".1} {");
+      command.append(1 + refStructure);
+      command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+
+      // form the matched pair strings
+      String sep = "";
+      for (int s = 0; s < 2; s++)
+      {
+        command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+      }
+      command.append(" ROTATE TRANSLATE;\n");
     }
+    System.out.println("Select regions:\n" + selectioncom.toString());
+    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());
   }
 
-  public void evalStateCommand(String command) {
+  public void evalStateCommand(String command)
+  {
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
-      viewer.evalStringQuiet(command+"\n");
+      viewer.evalStringQuiet(command + "\n");
     }
     jmolHistory(true);
     lastCommand = command;
   }
+
   /**
    * colour any structures associated with sequences in the given alignment
    * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
@@ -312,7 +507,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (!colourBySequence)
       return;
-    if (ssm==null)
+    if (ssm == null)
     {
       return;
     }
@@ -335,12 +530,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
         continue;
 
       int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
+      for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
         for (int sp, m = 0; m < mapping.length; m++)
         {
-          if (mapping[m].getSequence() == sequence[s]
-                  && (sp = alignment.findIndex(sequence[s])) > -1)
+          if (mapping[m].getSequence() == sequence[pdbfnum][s]
+                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
           {
             SequenceI asp = alignment.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
@@ -357,10 +552,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[s], r);
+              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 
-              if (showFeatures)
-                col = fr.findFeatureColour(col, sequence[s], r);
+              if (showFeatures && fr != null)
+                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"
@@ -404,8 +599,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   StringBuffer condenseCommand(String command, int pos)
   {
 
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
+    StringBuffer sb = new StringBuffer(command.substring(0,
+            command.lastIndexOf("select") + 7));
 
     command = command.substring(sb.length());
 
@@ -475,6 +670,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public abstract FeatureRenderer getFeatureRenderer();
 
+  /**
+   * instruct the Jalview binding to update the pdbentries vector if necessary
+   * prior to matching the jmol view's contents to the list of structure files
+   * Jalview knows about.
+   */
+  public abstract void refreshPdbEntries();
+
   private int getModelNum(String modelFileName)
   {
     String[] mfn = getPdbFile();
@@ -490,23 +692,49 @@ 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 String[] getPdbFile()
+  public synchronized String[] getPdbFile()
   {
+    if (viewer == null)
+    {
+      return new String[0];
+    }
     if (modelFileNames == null)
     {
+
       String mset[] = new String[viewer.getModelCount()];
-      for (int i = 0; i < mset.length; i++)
+      _modelFileNameMap = new int[mset.length];
+      int j = 1;
+      mset[0] = viewer.getModelFileName(0);
+      for (int i = 1; i < mset.length; i++)
       {
-        mset[i] = viewer.getModelFileName(i);
+        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++;
+        }
       }
-      modelFileNames = mset;
+      modelFileNames = new String[j];
+      System.arraycopy(mset, 0, modelFileNames, 0, j);
     }
     return modelFileNames;
   }
 
-  public Hashtable getRegistryInfo()
+  /**
+   * map from string to applet
+   */
+  public Map getRegistryInfo()
   {
     // TODO Auto-generated method stub
     return null;
@@ -599,6 +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);
   }
 
@@ -623,8 +859,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String chainId;
 
     if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+              strInfo.indexOf("."));
     else
     {
       chainId = " ";
@@ -660,7 +896,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+      System.err.println("Ignoring additional hover info: " + data
+              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
   }
@@ -713,12 +950,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
     jmolHistory(true);
     // TODO: in application this happens
     //
-//if (scriptWindow != null)
-//    {
-//      scriptWindow.sendConsoleMessage(strInfo);
-//      scriptWindow.sendConsoleMessage("\n");
-//    }
-
+    // if (scriptWindow != null)
+    // {
+    // scriptWindow.sendConsoleMessage(strInfo);
+    // scriptWindow.sendConsoleMessage("\n");
+    // }
 
   }
 
@@ -730,8 +966,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
       {
       case JmolConstants.CALLBACK_LOADSTRUCT:
         notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4], ((Integer) data[5])
-                        .intValue());
+                (String) data[3], (String) data[4],
+                ((Integer) data[5]).intValue());
 
         break;
       case JmolConstants.CALLBACK_PICK:
@@ -743,8 +979,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
                 (String) data[0]);
         break;
       case JmolConstants.CALLBACK_SCRIPT:
-        notifyScriptTermination((String) data[2], ((Integer) data[3])
-                .intValue());
+        notifyScriptTermination((String) data[2],
+                ((Integer) data[3]).intValue());
         break;
       case JmolConstants.CALLBACK_ECHO:
         sendConsoleEcho((String) data[1]);
@@ -758,14 +994,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
         break;
       case JmolConstants.CALLBACK_SYNC:
       case JmolConstants.CALLBACK_RESIZE:
-        updateUI();
+        refreshGUI();
         break;
       case JmolConstants.CALLBACK_MEASURE:
-        
+
       case JmolConstants.CALLBACK_CLICK:
-        
       default:
-        System.err.println("Unhandled callback " + type + " " + data[1].toString());
+        System.err.println("Unhandled callback " + type + " "
+                + data[1].toString());
         break;
       }
     } catch (Exception e)
@@ -797,141 +1033,179 @@ 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)
   {
     if (errorMsg != null)
     {
       fileLoadingError = errorMsg;
-      updateUI();
+      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.
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
+    chainFile = new Hashtable();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
     // first check if we've lost any structures
-    if (oldmodels!=null && oldmodels.length>0)
+    if (oldmodels != null && oldmodels.length > 0)
     {
-      int oldm=0;
-      for (int i=0;i<oldmodels.length;i++)
+      int oldm = 0;
+      for (int i = 0; i < oldmodels.length; i++)
       {
-        for (int n=0;n<modelfilenames.length; n++)
+        for (int n = 0; n < modelfilenames.length; n++)
         {
-          if (modelfilenames[n]==oldmodels[i])
+          if (modelfilenames[n] == oldmodels[i])
           {
-            oldmodels[i]=null;
+            oldmodels[i] = null;
             break;
           }
         }
-        if (oldmodels[i]!=null)
+        if (oldmodels[i] != null)
         {
           oldm++;
         }
       }
-      if (oldm>0)
+      if (oldm > 0)
       {
         String[] oldmfn = new String[oldm];
-        oldm=0;
-        for (int i=0;i<oldmodels.length; i++)
+        oldm = 0;
+        for (int i = 0; i < oldmodels.length; i++)
         {
-          if (oldmodels[i]!=null) {
+          if (oldmodels[i] != null)
+          {
             oldmfn[oldm++] = oldmodels[i];
           }
         }
-        // deregister the Jmol instance for these structures - we'll add 
-        // ourselves again at the end for the current structure set. 
+        // deregister the Jmol instance for these structures - we'll add
+        // ourselves again at the end for the current structure set.
         ssm.removeStructureViewerListener(this, oldmfn);
       }
     }
+    refreshPdbEntries();
     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)
       {
-        // 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++)
         {
-          boolean foundEntry = false;
-          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, chains, 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, chains, 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 (!foundEntry && associateNewStructs)
+          if (matches)
           {
-            // 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
+            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;
+
+      }
     }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
-    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");
+      viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
     }
     setLoadingFromArchive(false);
     // register ourselves as a listener and notify the gui that it needs to
@@ -940,11 +1214,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
     if (notifyLoaded)
     {
       FeatureRenderer fr = getFeatureRenderer();
-      if (fr!=null)
+      if (fr != null)
       {
         fr.featuresAdded();
       }
-      updateUI();
+      refreshGUI();
+      loadNotifiesHandled++;
     }
   }
 
@@ -953,7 +1228,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     notifyAtomPicked(iatom, strMeasure, null);
   }
 
-  public abstract void notifyScriptTermination(String strStatus, int msWalltime);
+  public abstract void notifyScriptTermination(String strStatus,
+          int msWalltime);
 
   /**
    * display a message echoed from the jmol viewer
@@ -1033,14 +1309,94 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * state change. this could be because structures were loaded, or because an
    * error has occured.
    */
-  public abstract void updateUI();
+  public abstract void refreshGUI();
+
+  /**
+   * called to show or hide the associated console window container.
+   * 
+   * @param show
+   */
+  public abstract void showConsole(boolean show);
 
-  public void allocateViewer(Component renderPanel, String htmlName,
-          URL documentBase, URL codeBase, String commandOptions)
+  /**
+   * @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
+   */
+  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,
-            new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
+            (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)
@@ -1052,6 +1408,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     return loadingFromArchive;
   }
+
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);
@@ -1059,4 +1416,142 @@ public abstract class JalviewJmolBinding implements StructureListener,
             + col.getGreen() + "," + col.getBlue() + "];");
     jmolHistory(true);
   }
+
+  /**
+   * add structures and any known sequence associations
+   * 
+   * @returns the pdb entries added to the current set.
+   */
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
+  {
+    int pe = -1;
+    Vector v = new Vector();
+    Vector rtn = new Vector();
+    for (int i = 0; i < pdbentry.length; i++)
+    {
+      v.addElement(pdbentry[i]);
+    }
+    for (int i = 0; i < pdbe.length; i++)
+    {
+      int r = v.indexOf(pdbe[i]);
+      if (r == -1 || r >= pdbentry.length)
+      {
+        rtn.addElement(new int[]
+        { v.size(), i });
+        v.addElement(pdbe[i]);
+      }
+      else
+      {
+        // just make sure the sequence/chain entries are all up to date
+        addSequenceAndChain(r, seq[i], chns[i]);
+      }
+    }
+    pdbe = new PDBEntry[v.size()];
+    v.copyInto(pdbe);
+    pdbentry = pdbe;
+    if (rtn.size() > 0)
+    {
+      // expand the tied seuqence[] and string[] arrays
+      SequenceI[][] sqs = new SequenceI[pdbentry.length][];
+      String[][] sch = new String[pdbentry.length][];
+      System.arraycopy(sequence, 0, sqs, 0, sequence.length);
+      System.arraycopy(chains, 0, sch, 0, this.chains.length);
+      sequence = sqs;
+      chains = sch;
+      pdbe = new PDBEntry[rtn.size()];
+      for (int r = 0; r < pdbe.length; r++)
+      {
+        int[] stri = ((int[]) rtn.elementAt(r));
+        // record the pdb file as a new addition
+        pdbe[r] = pdbentry[stri[0]];
+        // and add the new sequence/chain entries
+        addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+      }
+    }
+    else
+    {
+      pdbe = null;
+    }
+    return pdbe;
+  }
+
+  public void addSequence(int pe, SequenceI[] seq)
+  {
+    // add sequences to the pe'th pdbentry's seuqence set.
+    addSequenceAndChain(pe, seq, null);
+  }
+
+  private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+  {
+    if (pe < 0 || pe >= pdbentry.length)
+    {
+      throw new Error(
+              "Implementation error - no corresponding pdbentry (for index "
+                      + pe + ") to add sequences mappings to");
+    }
+    final String nullChain = "TheNullChain";
+    Vector s = new Vector();
+    Vector c = new Vector();
+    if (chains == null)
+    {
+      chains = new String[pdbentry.length][];
+    }
+    if (sequence[pe] != null)
+    {
+      for (int i = 0; i < sequence[pe].length; i++)
+      {
+        s.addElement(sequence[pe][i]);
+        if (chains[pe] != null)
+        {
+          if (i < chains[pe].length)
+          {
+            c.addElement(chains[pe][i]);
+          }
+          else
+          {
+            c.addElement(nullChain);
+          }
+        }
+        else
+        {
+          if (tchain != null && tchain.length > 0)
+          {
+            c.addElement(nullChain);
+          }
+        }
+      }
+    }
+    for (int i = 0; i < seq.length; i++)
+    {
+      if (!s.contains(seq[i]))
+      {
+        s.addElement(seq[i]);
+        if (tchain != null && i < tchain.length)
+        {
+          c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+        }
+      }
+    }
+    SequenceI[] tmp = new SequenceI[s.size()];
+    s.copyInto(tmp);
+    sequence[pe] = tmp;
+    if (c.size() > 0)
+    {
+      String[] tch = new String[c.size()];
+      c.copyInto(tch);
+      for (int i = 0; i < tch.length; i++)
+      {
+        if (tch[i] == nullChain)
+        {
+          tch[i] = null;
+        }
+      }
+      chains[pe] = tch;
+    }
+    else
+    {
+      chains[pe] = null;
+    }
+  }
 }