X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=68cc79261c16b4f087d187bce7d588a7c63df8f4;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=1a8fa2de5ed3f0251bdbd9c6d0c6098ad16ddd76;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 1a8fa2d..68cc792 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,8 +23,6 @@ package jalview.ext.jmol;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -32,9 +30,11 @@ import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -43,7 +43,6 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
@@ -56,43 +55,18 @@ import org.jmol.api.JmolViewer;
 import org.jmol.constant.EnumCallback;
 import org.jmol.popup.JmolPopup;
 
-public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding,
-        JmolSelectionListener, ComponentListener,
-        StructureSelectionManagerProvider
-
+public abstract class JalviewJmolBinding extends AAStructureBindingModel
+        implements JmolStatusListener, JmolSelectionListener,
+        ComponentListener
 {
-  /**
-   * set if Jmol state is being restored from some source - instructs binding
-   * not to apply default display style when structure set is updated for first
-   * time.
-   */
-  private boolean loadingFromArchive = false;
-  
-  /**
-   * second flag to indicate if the jmol viewer should ignore sequence colouring
-   * events from the structure manager because the GUI is still setting up
-   */
-  private boolean loadingFinished = true;
-
-  /**
+  /*
    * state flag used to check if the Jmol viewer's paint method can be called
    */
   private boolean finishedInit = false;
 
-  public boolean isFinishedInit()
-  {
-    return finishedInit;
-  }
-
-  public void setFinishedInit(boolean finishedInit)
-  {
-    this.finishedInit = finishedInit;
-  }
-
   boolean allChainsSelected = false;
 
-  /**
+  /*
    * when true, try to search the associated datamodel for sequences that are
    * associated with any unknown structures in the Jmol view.
    */
@@ -104,18 +78,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   Hashtable chainFile;
 
-  /**
-   * array of target chains for seuqences - tied to pdbentry and sequence[]
-   */
-  protected String[][] chains;
-
-  boolean colourBySequence = true;
-
   StringBuffer eval = new StringBuffer();
 
   public String fileLoadingError;
 
-  /**
+  /*
    * the default or current model displayed if the model cannot be identified
    * from the selection message
    */
@@ -134,37 +101,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   String[] modelFileNames = null;
 
-  public PDBEntry[] pdbentry;
-
-  /**
-   * datasource protocol for access to PDBEntrylatest
-   */
-  String protocol = null;
-
   StringBuffer resetLastRes = new StringBuffer();
 
-  /**
-   * sequences mapped to each pdbentry
-   */
-  public SequenceI[][] sequence;
-
-  public StructureSelectionManager ssm;
-
   public JmolViewer viewer;
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
           String protocol)
   {
-    this.ssm = ssm;
-    this.sequence = sequenceIs;
-    this.chains = chains;
-    this.pdbentry = pdbentry;
-    this.protocol = protocol;
-    if (chains == null)
-    {
-      this.chains = new String[pdbentry.length][];
-    }
+    super(ssm, pdbentry, sequenceIs, chains, protocol);
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -175,10 +120,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
   }
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
-          JmolViewer viewer2)
+          SequenceI[][] seqs, JmolViewer theViewer)
   {
-    this.ssm = ssm;
-    viewer = viewer2;
+    super(ssm, seqs);
+
+    viewer = theViewer;
     viewer.setJmolStatusListener(this);
     viewer.addSelectionListener(this);
   }
@@ -191,30 +137,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public String getViewerTitle()
   {
-    if (sequence == null || pdbentry == null || sequence.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());
-
-    if (pdbentry[0].getProperty() != null)
-    {
-      if (pdbentry[0].getProperty().get("method") != null)
-      {
-        title.append(" Method: ");
-        title.append(pdbentry[0].getProperty().get("method"));
-      }
-      if (pdbentry[0].getProperty().get("chains") != null)
-      {
-        title.append(" Chain:");
-        title.append(pdbentry[0].getProperty().get("chains"));
-      }
-    }
-    return title.toString();
+    return getViewerTitle("JMol", true);
   }
 
   /**
@@ -243,7 +166,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
               + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
     }
     if (cmd.length() > 0)
+    {
       cmd.setLength(cmd.length() - 4);
+    }
     evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
   }
 
@@ -251,7 +176,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
     // remove listeners for all structures in viewer
-    ssm.removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getPdbFile());
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
@@ -260,12 +185,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
     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;
@@ -330,16 +249,18 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
     String[] files = getPdbFile();
     // check to see if we are still waiting for Jmol files
-    long starttime=System.currentTimeMillis();
-    boolean waiting=true;
-    do {
-      waiting=false;
-      for (String file:files)
+    long starttime = System.currentTimeMillis();
+    boolean waiting = true;
+    do
+    {
+      waiting = false;
+      for (String file : files)
       {
-        try {
+        try
+        {
           // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
           // every possible exception
-          StructureMapping[] sm = ssm.getMapping(file);
+          StructureMapping[] sm = getSsm().getMapping(file);
           if (sm == null || sm.length == 0)
           {
             waiting = true;
@@ -353,10 +274,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
       }
       // we wait around for a reasonable time before we give up
-    } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime));
+    } while (waiting
+            && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
     if (waiting)
     {
-      System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+      System.err
+              .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
       return;
     }
     StringBuffer selectioncom = new StringBuffer();
@@ -415,20 +338,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
       String[] chainNames = new String[files.length];
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
-        StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+        StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
         // RACE CONDITION - getMapping only returns Jmol loaded filenames once
         // Jmol callback has completed.
         if (mapping == null || mapping.length < 1)
         {
-          throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+          throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
         }
         int lastPos = -1;
-        for (int s = 0; s < sequence[pdbfnum].length; s++)
+        final int sequenceCountForPdbFile = getSequence()[pdbfnum].length;
+        for (int s = 0; s < sequenceCountForPdbFile; s++)
         {
           for (int sp, m = 0; m < mapping.length; m++)
           {
-            if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                    && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+            if (mapping[m].getSequence() == getSequence()[pdbfnum][s]
+                    && (sp = alignment.findIndex(getSequence()[pdbfnum][s])) > -1)
             {
               if (refStructure == -1)
               {
@@ -480,13 +404,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
               chainNames[pdbfnum] = mapping[m].getPdbId()
                       + targetC[pdbfnum];
               // move on to next pdb file
-              s = sequence[pdbfnum].length;
+              s = getSequence()[pdbfnum].length;
               break;
             }
           }
         }
       }
-      
+
       // TODO: consider bailing if nmatched less than 4 because superposition
       // not
       // well defined.
@@ -558,14 +482,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
             {
               selectioncom.append("|");
             }
-          } else {
+          }
+          else
+          {
             selcom[pdbfnum] = null;
           }
         }
       }
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
-        if (pdbfnum == refStructure || selcom[pdbfnum]==null || selcom[refStructure]==null)
+        if (pdbfnum == refStructure || selcom[pdbfnum] == null
+                || selcom[refStructure] == null)
         {
           continue;
         }
@@ -574,7 +501,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         command.append(chainNames[pdbfnum]);
         command.append(") against reference (");
         command.append(chainNames[refStructure]);
-        command.append(")\";\ncompare "+nSeconds);
+        command.append(")\";\ncompare " + nSeconds);
         command.append("{");
         command.append(1 + pdbfnum);
         command.append(".1} {");
@@ -633,9 +560,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void colourBySequence(boolean showFeatures,
           jalview.api.AlignmentViewPanel alignmentv)
   {
-    if (!colourBySequence || !loadingFinished)
+    if (!colourBySequence || !isLoadingFinished())
+    {
       return;
-    if (ssm == null)
+    }
+    if (getSsm() == null)
     {
       return;
     }
@@ -650,23 +579,38 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
-            .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
-                    alignment))
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+    {
       for (String cbyseq : cpdbbyseq.commands)
       {
-        evalStateCommand(cbyseq);
+        executeWhenReady(cbyseq);
       }
+    }
   }
 
-  public boolean isColourBySequence()
+  /**
+   * @param files
+   * @param sr
+   * @param fr
+   * @param alignment
+   * @return
+   */
+  protected StructureMappingcommandSet[] getColourBySequenceCommands(
+          String[] files, SequenceRenderer sr, FeatureRenderer fr,
+          AlignmentI alignment)
   {
-    return colourBySequence;
+    return JmolCommands
+            .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
+                    fr,
+                    alignment);
   }
 
-  public void setColourBySequence(boolean colourBySequence)
+  /**
+   * @param command
+   */
+  protected void executeWhenReady(String command)
   {
-    this.colourBySequence = colourBySequence;
+    evalStateCommand(command);
   }
 
   public void createImage(String file, String type, int quality)
@@ -706,7 +650,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
           String pdbfile)
   {
     if (getModelNum(pdbfile) < 0)
+    {
       return null;
+    }
     // TODO: verify atomIndex is selecting correct model.
     return new Color(viewer.getAtomArgb(atomIndex));
   }
@@ -739,7 +685,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
     for (int i = 0; i < mfn.length; i++)
     {
       if (mfn[i].equalsIgnoreCase(modelFileName))
+      {
         return i;
+      }
     }
     return -1;
   }
@@ -810,7 +758,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   /**
    * map from string to applet
    */
-  public Map getRegistryInfo()
+  @Override
+  public Map<String, Object> getRegistryInfo()
   {
     // TODO Auto-generated method stub
     return null;
@@ -948,8 +897,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String chainId;
 
     if (strInfo.indexOf(":") > -1)
+    {
       chainId = strInfo.substring(strInfo.indexOf(":") + 1,
               strInfo.indexOf("."));
+    }
     else
     {
       chainId = " ";
@@ -987,7 +938,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
       ;
     }
     if (lastMessage == null || !lastMessage.equals(strInfo))
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+    {
+      getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+    }
 
     lastMessage = strInfo;
   }
@@ -1021,13 +974,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
     int chainSeparator = strInfo.indexOf(":");
     int p = 0;
     if (chainSeparator == -1)
+    {
       chainSeparator = strInfo.indexOf(".");
+    }
 
     String picked = strInfo.substring(strInfo.indexOf("]") + 1,
             chainSeparator);
     String mdlString = "";
     if ((p = strInfo.indexOf(":")) > -1)
+    {
       picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+    }
 
     if ((p = strInfo.indexOf("/")) > -1)
     {
@@ -1199,7 +1156,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
         // deregister the Jmol instance for these structures - we'll add
         // ourselves again at the end for the current structure set.
-        ssm.removeStructureViewerListener(this, oldmfn);
+        getSsm().removeStructureViewerListener(this, oldmfn);
       }
     }
     refreshPdbEntries();
@@ -1219,70 +1176,68 @@ public abstract class JalviewJmolBinding implements StructureListener,
                 + ".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 < getPdbCount(); pe++)
+      {
+        boolean matches = false;
+        if (fileName == null)
         {
-          boolean matches = false;
-          if (fileName == null)
+          if (false)
+          // see JAL-623 - need method of matching pasted data up
           {
-            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;
-            }
+            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+                    pdbfile, AppletFormatAdapter.PASTE);
+            getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+            matches = true;
+            foundEntry = true;
           }
-          else
+        }
+        else
+        {
+          File fl;
+          if (matches = (fl = new File(getPdbEntry(pe).getFile()))
+                  .equals(new File(fileName)))
           {
-            File fl;
-            if (matches = (fl = new File(pdbentry[pe].getFile()))
-                    .equals(new File(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
             {
-              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
-              {
-                if (fl.exists())
-                {
-                  protocol = AppletFormatAdapter.FILE;
-                }
-              } catch (Exception e)
-              {
-              } catch (Error e)
+              if (fl.exists())
               {
+                protocol = AppletFormatAdapter.FILE;
               }
-              // Explicitly map to the filename used by Jmol ;
-              pdb = ssm.setMapping(sequence[pe], chains[pe], fileName,
-                      protocol);
-              // pdbentry[pe].getFile(), protocol);
-
+            } catch (Exception e)
+            {
+            } catch (Error e)
+            {
             }
+            // Explicitly map to the filename used by Jmol ;
+            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+                    fileName, protocol);
+            // pdbentry[pe].getFile(), protocol);
+
           }
-          if (matches)
+        }
+        if (matches)
+        {
+          // add an entry for every chain in the model
+          for (int i = 0; i < pdb.chains.size(); i++)
           {
-            // 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, fileName);
-              chainNames.addElement(chid);
-            }
-            notifyLoaded = true;
+            String chid = new String(pdb.id + ":"
+                    + pdb.chains.elementAt(i).id);
+            chainFile.put(chid, fileName);
+            chainNames.addElement(chid);
           }
+          notifyLoaded = true;
         }
       }
+
       if (!foundEntry && associateNewStructs)
       {
         // this is a foreign pdb file that jalview doesn't know about - add
@@ -1311,7 +1266,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
     // register ourselves as a listener and notify the gui that it needs to
     // update itself.
-    ssm.addStructureViewerListener(this);
+    getSsm().addStructureViewerListener(this);
     if (notifyLoaded)
     {
       FeatureRenderer fr = getFeatureRenderer(null);
@@ -1368,21 +1323,23 @@ public abstract class JalviewJmolBinding implements StructureListener,
     colourBySequence = false;
 
     if (cs == null)
+    {
       return;
+    }
 
-    String res;
     int index;
     Color col;
     jmolHistory(false);
     // TODO: Switch between nucleotide or aa selection expressions
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
+    StringBuilder command = new StringBuilder(128);
+    command.append("select *;color white;");
+    for (String res : ResidueProperties.aa3Hash.keySet())
     {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+      index = ResidueProperties.aa3Hash.get(res).intValue();
       if (index > 20)
+      {
         continue;
+      }
 
       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
@@ -1481,211 +1438,93 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
-  public void componentResized(ComponentEvent e)
-  {
-
-  }
-
-  public void componentMoved(ComponentEvent e)
+  public void setBackgroundColour(java.awt.Color col)
   {
-
+    jmolHistory(false);
+    viewer.evalStringQuiet("background [" + col.getRed() + ","
+            + col.getGreen() + "," + col.getBlue() + "];");
+    jmolHistory(true);
   }
 
-  public void componentShown(ComponentEvent e)
+  /**
+   * 
+   * @param pdbfile
+   * @return text report of alignment between pdbfile and any associated
+   *         alignment sequences
+   */
+  public String printMapping(String pdbfile)
   {
-    showConsole(true);
+    return getSsm().printMapping(pdbfile);
   }
 
-  public void componentHidden(ComponentEvent e)
+  @Override
+  public void resizeInnerPanel(String data)
   {
-    showConsole(false);
-  }
+    // Jalview doesn't honour resize panel requests
 
-  public void setLoadingFromArchive(boolean loadingFromArchive)
-  {
-    this.loadingFromArchive = loadingFromArchive;
-  }
-  
-  /**
-   * 
-   * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive)
-   */
-  public boolean isLoadingFromArchive()
-  {
-    return loadingFromArchive && !loadingFinished;
   }
 
-  /**
-   * modify flag which controls if sequence colouring events are honoured by the binding. 
-   * Should be true for normal operation
-   * @param finishedLoading
-   */
-  public void setFinishedLoadingFromArchive(boolean finishedLoading)
+  public boolean isFinishedInit()
   {
-    loadingFinished = finishedLoading;
+    return finishedInit;
   }
 
-  public void setBackgroundColour(java.awt.Color col)
+  public void setFinishedInit(boolean finishedInit)
   {
-    jmolHistory(false);
-    viewer.evalStringQuiet("background [" + col.getRed() + ","
-            + col.getGreen() + "," + col.getBlue() + "];");
-    jmolHistory(true);
+    this.finishedInit = finishedInit;
   }
 
   /**
-   * 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)
+  protected void closeConsole()
   {
-    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++)
+    if (console != null)
     {
-      int r = v.indexOf(pdbe[i]);
-      if (r == -1 || r >= pdbentry.length)
+      try
       {
-        rtn.addElement(new int[]
-        { v.size(), i });
-        v.addElement(pdbe[i]);
-      }
-      else
+        console.setVisible(false);
+      } catch (Error e)
       {
-        // 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++)
+      } catch (Exception x)
       {
-        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]]);
       }
+      ;
+      console = null;
     }
-    else
-    {
-      pdbe = null;
-    }
-    return pdbe;
   }
 
-  public void addSequence(int pe, SequenceI[] seq)
+  /**
+   * ComponentListener method
+   */
+  @Override
+  public void componentMoved(ComponentEvent e)
   {
-    // add sequences to the pe'th pdbentry's seuqence set.
-    addSequenceAndChain(pe, seq, null);
   }
 
-  private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+  /**
+   * ComponentListener method
+   */
+  @Override
+  public void componentResized(ComponentEvent e)
   {
-    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;
-    }
   }
 
   /**
-   * 
-   * @param pdbfile
-   * @return text report of alignment between pdbfile and any associated
-   *         alignment sequences
+   * ComponentListener method
    */
-  public String printMapping(String pdbfile)
+  @Override
+  public void componentShown(ComponentEvent e)
   {
-    return ssm.printMapping(pdbfile);
+    showConsole(true);
   }
 
+  /**
+   * ComponentListener method
+   */
   @Override
-  public void resizeInnerPanel(String data)
+  public void componentHidden(ComponentEvent e)
   {
-    // Jalview doesn't honour resize panel requests
-
+    showConsole(false);
   }
 }