/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.jmol;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+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.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.util.Map;
import java.util.Vector;
+import javajs.awt.Dimension;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
-import org.jmol.constant.EnumCallback;
-import org.jmol.popup.JmolPopup;
-
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-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.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
+import org.jmol.c.CBK;
+import org.jmol.script.T;
+import org.jmol.viewer.JC;
+import org.jmol.viewer.Viewer;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
- /*
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
boolean allChainsSelected = false;
/*
*/
private boolean associateNewStructs = false;
- Vector atomsPicked = new Vector();
-
- public Vector chainNames;
+ Vector<String> atomsPicked = new Vector<String>();
- Hashtable chainFile;
+ public Vector<String> chainNames;
- StringBuffer eval = new StringBuffer();
+ Hashtable<String, String> chainFile;
public String fileLoadingError;
*/
int frameNo = 0;
- protected JmolPopup jmolpopup;
+ // protected JmolGenericPopup jmolpopup; // not used - remove?
String lastCommand;
StringBuffer resetLastRes = new StringBuffer();
- public JmolViewer viewer;
+ public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
}
public JalviewJmolBinding(StructureSelectionManager ssm,
- SequenceI[][] seqs, JmolViewer theViewer)
+ SequenceI[][] seqs, Viewer theViewer)
{
super(ssm, seqs);
*/
public String getViewerTitle()
{
- return getViewerTitle("JMol", true);
+ return getViewerTitle("Jmol", true);
}
/**
* @param chainList
* list of chains to make visible
*/
- public void centerViewer(Vector chainList)
+ public void centerViewer(Vector<String> chainList)
{
- StringBuffer cmd = new StringBuffer();
- String lbl;
+ StringBuilder cmd = new StringBuilder(128);
int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ for (String lbl : chainList)
{
mlength = 0;
- lbl = (String) chainList.elementAt(i);
do
{
p = mlength;
} 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) + " /"
- + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
+ + (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
{
public void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
+ viewer.acm.setModeMouse(JC.MOUSE_NONE);
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getPdbFile());
// and shut down jmol
public void superposeStructures(AlignmentI alignment, int refStructure,
ColumnSelection hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
}
+ /**
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
+ *
+ * @param _alignment
+ * an array of alignments to process
+ * @param _refStructure
+ * an array of corresponding reference structures (index into pdb
+ * file array); if a negative value is passed, the first PDB file
+ * mapped to an alignment sequence is used as the reference for
+ * superposition
+ * @param _hiddenCols
+ * an array of corresponding hidden columns for each alignment
+ */
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
+ while (viewer.isScriptExecuting())
{
- waiting = false;
- for (String file : files)
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
{
- try
- {
- // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
- // every possible exception
- StructureMapping[] sm = getSsm().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)
+ ;
+ }
+ String[] files = getPdbFile();
+ if (!waitForFileLoad(files))
{
- System.err
- .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
return;
}
- StringBuffer selectioncom = new StringBuffer();
+
+ StringBuilder selectioncom = new StringBuilder(256);
// 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 ";
+ nSeconds = " 0.005 ";
}
else
{
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
- nSeconds = " ";
+ // nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
+ refStructure);
refStructure = -1;
}
- if (refStructure < -1)
- {
- refStructure = -1;
- }
- StringBuffer command = new StringBuffer();
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
boolean matched[] = new boolean[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];
- String[] chainNames = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
- 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(MessageManager.getString("error.implementation_error_jmol_getting_data"));
- }
- int lastPos = -1;
- 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() == getSequence()[pdbfnum][s]
- && (sp = alignment.findIndex(getSequence()[pdbfnum][s])) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- 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)))
- {
- // no mapping to gaps in sequence
- continue;
- }
- 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;
- // 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();
- }
- chainNames[pdbfnum] = mapping[m].getPdbId()
- + targetC[pdbfnum];
- // move on to next pdb file
- s = getSequence()[pdbfnum].length;
- break;
- }
- }
- }
+ structures[f] = new SuperposeData(alignment.getWidth());
}
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
String[] selcom = new String[files.length];
int nmatched = 0;
- // generate select statements to select regions to superimpose structures
+ for (boolean b : matched)
+ {
+ if (b)
+ {
+ nmatched++;
+ }
+ }
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
{
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- String chainCd = targetC[pdbfnum];
+ String chainCd = ":" + structures[pdbfnum].chain;
int lpos = -1;
boolean run = false;
- StringBuffer molsel = new StringBuffer();
+ StringBuilder molsel = new StringBuilder();
molsel.append("{");
for (int r = 0; r < matched.length; r++)
{
if (matched[r])
{
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
+ int pdbResNo = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNo - 1)
{
// discontinuity
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
- // molsel.append("} {");
molsel.append("|");
}
+ run = false;
}
else
{
}
run = true;
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ lpos = pdbResNo;
}
}
- // add final selection phrase
+ /*
+ * add final selection phrase
+ */
if (lpos != -1)
{
molsel.append(lpos);
}
}
}
+ StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
}
command.append("echo ");
command.append("\"Superposing (");
- command.append(chainNames[pdbfnum]);
+ command.append(structures[pdbfnum].pdbId);
command.append(") against reference (");
- command.append(chainNames[refStructure]);
+ command.append(structures[refStructure].pdbId);
command.append(")\";\ncompare " + nSeconds);
command.append("{");
- command.append(1 + pdbfnum);
+ command.append(Integer.toString(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(Integer.toString(1 + refStructure));
+ // conformation=1 excludes alternate locations for CA (JAL-1757)
+ command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
+
+ // for (int s = 0; s < 2; s++)
+ // {
+ // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ // }
+ command.append(selcom[pdbfnum]);
+ command.append(selcom[refStructure]);
command.append(" ROTATE TRANSLATE;\n");
}
if (selectioncom.length() > 0)
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
- System.out
- .println("Superimpose command(s):\n" + command.toString());
+ String cmdString = command.toString();
+ System.out.println("Superimpose command(s):\n" + cmdString);
- evalStateCommand(command.toString());
+ evalStateCommand(cmdString);
}
}
if (selectioncom.length() > 0)
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ public void colourBySequence(AlignmentViewPanel alignmentv)
{
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
if (!colourBySequence || !isLoadingFinished())
{
return;
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
for (String cbyseq : cpdbbyseq.commands)
{
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- return JmolCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr,
- alignment);
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
/**
return null;
}
// TODO: verify atomIndex is selecting correct model.
- return new Color(viewer.getAtomArgb(atomIndex));
+ // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
+ return new Color(colour);
}
/**
// ////////////////////////////////
// /StructureListener
+ @Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
}
if (modelFileNames == null)
{
-
- String mset[] = new String[viewer.getModelCount()];
+ String mset[] = new String[viewer.ms.mc];
_modelFileNameMap = new int[mset.length];
- int j = 1;
- String m = viewer.getModelFileName(0);
+ String m = viewer.ms.getModelFileName(0);
if (m != null)
{
+ mset[0] = m;
try
{
mset[0] = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
- // usually not allowed to do this in applet, so keep raw handle
+ // usually not allowed to do this in applet
+ System.err
+ .println("jmolBinding: Using local file string from Jmol: "
+ + m);
+ }
+ if (mset[0].indexOf("/file:") != -1)
+ {
+ // applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
}
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
+ int j = 1;
for (int i = 1; i < mset.length; i++)
{
- m = viewer.getModelFileName(i);
+ m = viewer.ms.getModelFileName(i);
+ mset[j] = m;
if (m != null)
{
try
} 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);
}
}
public void handlePopupMenu(int x, int y)
{
- jmolpopup.show(x, y);
+ // jmolpopup.show(x, y);
+ // jmolpopup.jpiShow(x, y);
+ }
+
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ if (atoms != null)
+ {
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
}
// jmol/ssm only
// look up file model number for this pdbfile
int mdlNum = 0;
- String fn;
// may need to adjust for URLencoding here - we don't worry about that yet.
while (mdlNum < modelFileNames.length
&& !pdbfile.equals(modelFileNames[mdlNum]))
{
- // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
mdlNum++;
}
if (mdlNum == modelFileNames.length)
viewer.evalStringQuiet(resetLastRes.toString());
}
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
+ StringBuilder cmd = new StringBuilder(64);
+ cmd.append("select " + pdbResNum); // +modelNum
resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
+ cmd.append(":");
resetLastRes.append(":");
if (!chain.equals(" "))
{
- eval.append(chain);
+ cmd.append(chain);
resetLastRes.append(chain);
}
{
- eval.append(" /" + (mdlNum + 1));
+ cmd.append(" /" + (mdlNum + 1));
resetLastRes.append("/" + (mdlNum + 1));
}
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+ cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ " and not hetero; spacefill 0;");
- eval.append("spacefill 200;select none");
+ cmd.append("spacefill 200;select none");
- viewer.evalStringQuiet(eval.toString());
+ viewer.evalStringQuiet(cmd.toString());
jmolHistory(true);
}
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
- pdbfilename = new File(viewer.getModelFileName(mnumber))
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ picked += strInfo.substring(p, strInfo.indexOf("."));
}
if ((p = strInfo.indexOf("/")) > -1)
}
@Override
- public void notifyCallback(EnumCallback type, Object[] data)
+ public void notifyCallback(CBK type, Object[] data)
{
try
{
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
case HOVER:
case ERROR:
return true;
- case RESIZE:
- case SYNC:
- case CLICK:
- case ANIMFRAME:
- case MINIMIZATION:
+ default:
+ return false;
}
- return false;
}
// incremented every time a load notification is successfully handled -
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
- chainFile = new Hashtable();
+ chainNames = new Vector<String>();
+ chainFile = new Hashtable<String, String>();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
// first check if we've lost any structures
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
MCview.PDBfile pdb = null;
- String pdbfile = null, pdbfhash = null;
+ String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
// 'best guess'
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
- pdbfhash = "" + pdbfile.hashCode();
}
- // search pdbentries and sequences to find correct pdbentry for this
- // model
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
}
else
{
- File fl;
- if (matches = (fl = new File(getPdbEntry(pe).getFile()))
- .equals(new File(fileName)))
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
{
foundEntry = true;
// TODO: Jmol can in principle retrieve from CLASSLOADER but
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
- if (jmolpopup != null)
- {
- // potential for deadlock here:
- // 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 *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
{
commandOptions = "";
}
- viewer = JmolViewer.allocateViewer(renderPanel,
+ viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
}
protected abstract JmolAppConsoleInterface createJmolConsole(
- JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+ Container consolePanel, String buttonsToShow);
protected org.jmol.api.JmolAppConsoleInterface console = null;
jmolHistory(true);
}
- /**
- *
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
- */
- public String printMapping(String pdbfile)
- {
- return getSsm().printMapping(pdbfile);
- }
-
@Override
- public void resizeInnerPanel(String data)
+ public Dimension resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
-
- }
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
+ return null;
}
/**
git://source.jalview.org / jalview.git / blobdiff