X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=9187912d12ca05f25437280bc99979faf23cc912;hb=5f090b7d1cb8836903474f8f4d5e475be142d30c;hp=67327c13b26aed3f956a86c4c5b7bbf9e3c251e6;hpb=2da92b61300307562cb8bec70a72f0b0527aa3b3;p=jalview.git
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 67327c1..9187912 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,61 +1,70 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+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.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+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;
-import org.jmol.api.*;
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,
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolSelectionListener;
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.popup.JmolPopup;
+
+public abstract class JalviewJmolBinding extends SequenceStructureBindingModel implements StructureListener,
JmolStatusListener, SequenceStructureBinding,
- JmolSelectionListener, ComponentListener
+ JmolSelectionListener, ComponentListener,
+ StructureSelectionManagerProvider
{
/**
- * 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;
-
- /**
* state flag used to check if the Jmol viewer's paint method can be called
*/
private boolean finishedInit = false;
@@ -128,13 +137,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public SequenceI[][] sequence;
- StructureSelectionManager ssm;
+ public StructureSelectionManager ssm;
public JmolViewer viewer;
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String[][] chains, String protocol)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
+ this.ssm = ssm;
this.sequence = sequenceIs;
this.chains = chains;
this.pdbentry = pdbentry;
@@ -152,8 +163,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
}
- public JalviewJmolBinding(JmolViewer viewer2)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ JmolViewer viewer2)
{
+ this.ssm = ssm;
viewer = viewer2;
viewer.setJmolStatusListener(this);
viewer.addSelectionListener(this);
@@ -227,8 +240,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
// remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, this.getPdbFile());
+ ssm.removeStructureViewerListener(this, this.getPdbFile());
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
@@ -303,9 +315,59 @@ public abstract class JalviewJmolBinding implements StructureListener,
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
+ assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
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)
+ {
+ try
+ {
+ // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+ // every possible exception
+ StructureMapping[] sm = ssm.getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Exception x)
+ {
+ waiting = true;
+ } catch (Error q)
+ {
+ waiting = true;
+ }
+ }
+ // we wait around for a reasonable time before we give up
+ } 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.");
+ return;
+ }
StringBuffer selectioncom = new StringBuffer();
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
+ {
+ nSeconds = " 0.00001 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
@@ -347,10 +409,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
+ // RACE CONDITION - getMapping only returns Jmol loaded filenames once
+ // Jmol callback has completed.
if (mapping == null || mapping.length < 1)
- continue;
-
+ {
+ throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
@@ -415,6 +479,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
}
}
+
+ // TODO: consider bailing if nmatched less than 4 because superposition
+ // not
+ // well defined.
+ // TODO: refactor superposable position search (above) from jmol selection
+ // construction (below)
+
String[] selcom = new String[files.length];
int nmatched = 0;
// generate select statements to select regions to superimpose structures
@@ -467,27 +538,30 @@ public abstract class JalviewJmolBinding implements StructureListener,
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)
+ if (molsel.length() > 1)
+ {
+ 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("|");
+ }
+ }
+ else
{
- selectioncom.append("|");
+ selcom[pdbfnum] = null;
}
}
}
- // 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)
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
{
continue;
}
@@ -496,7 +570,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
command.append(chainNames[pdbfnum]);
command.append(") against reference (");
command.append(chainNames[refStructure]);
- command.append(")\";\ncompare ");
+ command.append(")\";\ncompare " + nSeconds);
command.append("{");
command.append(1 + pdbfnum);
command.append(".1} {");
@@ -511,13 +585,17 @@ 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; ");
- // selcom.append("; ribbons; ");
- System.out.println("Superimpose command(s):\n" + command.toString());
-
- evalStateCommand(command.toString());
+ if (selectioncom.length() > 0)
+ {
+ 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());
+ }
}
if (selectioncom.length() > 0)
{// finally, mark all regions that were superposed.
@@ -551,7 +629,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
public void colourBySequence(boolean showFeatures,
jalview.api.AlignmentViewPanel alignmentv)
{
- if (!colourBySequence)
+ if (!colourBySequence || !isLoadingFinished())
return;
if (ssm == null)
{
@@ -567,70 +645,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
fr = getFeatureRenderer(alignmentv);
}
AlignmentI alignment = alignmentv.getAlignment();
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
+ .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
+ alignment))
+ for (String cbyseq : cpdbbyseq.commands)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- 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++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (showFeatures && fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
+ evalStateCommand(cbyseq);
}
- }
- evalStateCommand(command.toString());
}
public boolean isColourBySequence()
@@ -643,30 +665,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
this.colourBySequence = colourBySequence;
}
- StringBuffer condenseCommand(String command, int pos)
- {
-
- StringBuffer sb = new StringBuffer(command.substring(0,
- command.lastIndexOf("select") + 7));
-
- command = command.substring(sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
public void createImage(String file, String type, int quality)
{
System.out.println("JMOL CREATE IMAGE");
@@ -763,10 +761,34 @@ public abstract class JalviewJmolBinding implements StructureListener,
String mset[] = new String[viewer.getModelCount()];
_modelFileNameMap = new int[mset.length];
int j = 1;
- mset[0] = viewer.getModelFileName(0);
+ String m = viewer.getModelFileName(0);
+ if (m != null)
+ {
+ try
+ {
+ mset[0] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ mset[0] = m;
+ // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ }
+ }
for (int i = 1; i < mset.length; i++)
{
- mset[j] = viewer.getModelFileName(i);
+ m = viewer.getModelFileName(i);
+ if (m != null)
+ {
+ try
+ {
+ mset[j] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ mset[j] = m;
+ // 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]
@@ -942,8 +964,19 @@ public abstract class JalviewJmolBinding implements StructureListener,
try
{
// recover PDB filename for the model hovered over.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
+ int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
+ .intValue() - 1;
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
+ if (pdbfilename == null)
+ {
+ pdbfilename = new File(viewer.getModelFileName(mnumber))
+ .getAbsolutePath();
+ }
+
} catch (Exception e)
{
}
@@ -1021,47 +1054,48 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
- public void notifyCallback(int type, Object[] data)
+ @Override
+ public void notifyCallback(EnumCallback type, Object[] data)
{
try
{
switch (type)
{
- case JmolConstants.CALLBACK_LOADSTRUCT:
+ case LOADSTRUCT:
notifyFileLoaded((String) data[1], (String) data[2],
(String) data[3], (String) data[4],
((Integer) data[5]).intValue());
break;
- case JmolConstants.CALLBACK_PICK:
+ case PICK:
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
+ case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
break;
- case JmolConstants.CALLBACK_SCRIPT:
+ case SCRIPT:
notifyScriptTermination((String) data[2],
((Integer) data[3]).intValue());
break;
- case JmolConstants.CALLBACK_ECHO:
+ case ECHO:
sendConsoleEcho((String) data[1]);
break;
- case JmolConstants.CALLBACK_MESSAGE:
+ case MESSAGE:
sendConsoleMessage((data == null) ? ((String) null)
: (String) data[1]);
break;
- case JmolConstants.CALLBACK_ERROR:
+ case ERROR:
// System.err.println("Ignoring error callback.");
break;
- case JmolConstants.CALLBACK_SYNC:
- case JmolConstants.CALLBACK_RESIZE:
+ case SYNC:
+ case RESIZE:
refreshGUI();
break;
- case JmolConstants.CALLBACK_MEASURE:
+ case MEASURE:
- case JmolConstants.CALLBACK_CLICK:
+ case CLICK:
default:
System.err.println("Unhandled callback " + type + " "
+ data[1].toString());
@@ -1074,24 +1108,25 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
}
- public boolean notifyEnabled(int callbackPick)
+ @Override
+ public boolean notifyEnabled(EnumCallback callbackPick)
{
switch (callbackPick)
{
- case JmolConstants.CALLBACK_ECHO:
- case JmolConstants.CALLBACK_LOADSTRUCT:
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_MESSAGE:
- case JmolConstants.CALLBACK_PICK:
- case JmolConstants.CALLBACK_SCRIPT:
- case JmolConstants.CALLBACK_HOVER:
- case JmolConstants.CALLBACK_ERROR:
+ case ECHO:
+ case LOADSTRUCT:
+ case MEASURE:
+ case MESSAGE:
+ case PICK:
+ case SCRIPT:
+ case HOVER:
+ case ERROR:
return true;
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
- case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
- case JmolConstants.CALLBACK_MINIMIZATION:
+ case RESIZE:
+ case SYNC:
+ case CLICK:
+ case ANIMFRAME:
+ case MINIMIZATION:
}
return false;
}
@@ -1128,7 +1163,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
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)
{
@@ -1202,7 +1236,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
else
{
- if (matches = pdbentry[pe].getFile().equals(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
@@ -1213,7 +1249,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
String protocol = AppletFormatAdapter.URL;
try
{
- File fl = new java.io.File(pdbentry[pe].getFile());
if (fl.exists())
{
protocol = AppletFormatAdapter.FILE;
@@ -1223,21 +1258,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
} catch (Error e)
{
}
- ;
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), protocol);
+ // Explicitly map to the filename used by Jmol ;
+ pdb = ssm.setMapping(sequence[pe], chains[pe], fileName,
+ protocol);
+ // 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());
+ chainFile.put(chid, fileName);
chainNames.addElement(chid);
}
notifyLoaded = true;
@@ -1270,7 +1305,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
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
// update itself.
ssm.addStructureViewerListener(this);
@@ -1284,6 +1318,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
refreshGUI();
loadNotifiesHandled++;
}
+ setLoadingFromArchive(false);
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
@@ -1419,6 +1454,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
+ if (commandOptions == null)
+ {
+ commandOptions = "";
+ }
viewer = JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
@@ -1458,16 +1497,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
showConsole(false);
}
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
- }
-
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive;
- }
-
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
@@ -1545,9 +1574,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
if (pe < 0 || pe >= pdbentry.length)
{
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_no_pdbentry_from_index", new String[]{Integer.valueOf(pe).toString()}));
}
final String nullChain = "TheNullChain";
Vector s = new Vector();
@@ -1613,4 +1640,22 @@ public abstract class JalviewJmolBinding implements StructureListener,
chains[pe] = null;
}
}
+
+ /**
+ *
+ * @param pdbfile
+ * @return text report of alignment between pdbfile and any associated
+ * alignment sequences
+ */
+ public String printMapping(String pdbfile)
+ {
+ return ssm.printMapping(pdbfile);
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // Jalview doesn't honour resize panel requests
+
+ }
}