public Vector chainNames;
- String[] chains;
+ /**
+ * array of target chains for seuqences - tied to pdbentry and sequence[]
+ */
+ protected String[][] chains;
boolean colourBySequence = true;
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(),
{
return ("Jalview Jmol Window");
}
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ pdbentry[0].getId());
if (pdbentry[0].getProperty() != null)
*/
public void superposeStructures(AlignmentI alignment)
{
- String[] files = getPdbFile();
+ superposeStructures(alignment, -1, null);
+ }
- StringBuffer command = new StringBuffer();
+ /**
+ * 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();
+
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]);
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++)
+ StringBuffer selcom[] = new StringBuffer[files.length];
+ // 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 = (selcom[pdbfnum] = new StringBuffer());
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
{
- if (s > 0)
+ if (matched[r])
{
- command.append(" | ");
+
+ 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("}");
+ }
+ selectioncom.append("((");
+ selectioncom.append(molsel.subSequence(1, molsel.length()-1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum+1);
+ selectioncom.append(".1)");
+ if (pdbfnum<files.length-1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ }
+
+ 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)
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++)
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);
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
if (loadedInline)
{
// TODO: replace with getData ?
- pdb = ssm.setMapping(sequence, chains,
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
pdbentry[pe].setFile("INLINE" + pdb.id);
}
{
}
;
- pdb = ssm.setMapping(sequence, chains,
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
pdbentry[pe].getFile(), protocol);
}
*/
public abstract void refreshGUI();
-
/**
* @param renderPanel
- * @param jmolfileio - when true will initialise jmol's file IO system (should be false in applet context)
+ * @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(Component renderPanel, boolean jmolfileio, String htmlName,
- URL documentBase, URL codeBase, String commandOptions)
+ public void allocateViewer(Component renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
{
viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null),
- htmlName + ((Object) this).toString(), documentBase, codeBase,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
+ { pdbentry }, new SequenceI[][] { seq }, null, null);
jmb.setLoadingFromArchive(true);
this.ap = ap;
{
if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
{
- topJmol.jmb.addSequence(seq);
+ topJmol.jmb.addSequence(pe, seq);
break;
}
}
}
}
// /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size()>0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements()) {
+ AppJmol topJmol = (AppJmol) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop, "Do you want to add "+
+ pdbentry.getId()+" to the view called\n'"+topJmol.getTitle()
+ + "'\n",
+ "Align to existing structure view"
+ , JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.jmb.addStructure(pdbentry, seq, chains,true);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
+ { pdbentry }, new SequenceI[][]{seq}, null, null);
this.ap = ap;
setSize(400, 400); // probably should be a configurable/dynamic default here
}
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols= new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ AppJmol topJmol = ((AppJmol) frames[i]);
+ if (topJmol.ap==ap2)
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
+ }
+
void initJmol(String command)
{
jmb.setFinishedInit(false);
}
setChainMenuItems(jmb.chainNames);
jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
-
+
this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length>1 && jmb.sequence.length>1) {
+ jmolActionMenu.setVisible(true);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+
+ try {
+ jmb.superposeStructures(ap.av.getAlignment(), -1, ap.av.getColumnSelection());
+ } catch (Exception e)
+ {
+ Cache.log.info("Couldn't align structures in alignframe "+ap.alignFrame.getTitle(),e);
+
+ }
}
public void setJalviewColourScheme(ColourSchemeI ucs)
private AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[] seq, String[] chains, String protocol)
+ SequenceI[][] sequenceIs, String[][] chains, String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
@Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
}
fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
+ .getFeatureRenderer());
}
return fr;
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow!=null && strStatus != null
- )
- // && !strStatus.equals("Script completed"))
- // should we squash the script completed string ?
+ if (appJmolWindow.scriptWindow != null && strStatus != null)
+ // && !strStatus.equals("Script completed"))
+ // should we squash the script completed string ?
{
appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
}
@Override
public void showUrl(String url, String target)
{
- try {
+ try
+ {
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception e) {
+ } catch (Exception e)
+ {
Cache.log.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av)
+ if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
return;
-
+
colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
+ msWalltime);
}
public void showUrl(String url)
{
- showUrl(url,"jmol");
+ showUrl(url, "jmol");
}
public void newJmolPopup(boolean translateLocale, String menuName,
jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
asPopup);
}
- public synchronized void addSequence(SequenceI[] seq)
+
+ /**
+ * add structures and any known sequence associations
+ *
+ * @returns the pdb entries added to the current set.
+ */
+ private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
{
+ int pe = -1;
Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
+ 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;
+ }
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
+ void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
+ 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;
+ }
}
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
-
+
}
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
-
+
}
+
+ /**
+ * add another pdb entry into the view, with associated sequences and chains
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ public synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final boolean align)
+ {
+ PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ if (pe != null)
+ {
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("load APPEND");
+ for (int p = 0; p < pe.length; p++)
+ {
+ cmd.append(" \"");
+ cmd.append(pe[p].getFile());
+ cmd.append("\"");
+ }
+ cmd.append("\n");
+ final String command = cmd.toString();
+ cmd = null;
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ evalStateCommand(command);
+ if (align)
+ {
+ // may need to wait around until script has finished
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
+ }
+ }
+ }).start();
+ }
+ }
+
+ /**
+ * add the given sequences to the mapping scope for the given pdb file handle
+ *
+ * @param pdbFile
+ * - pdbFile identifier
+ * @param seq
+ * - set of sequences it can be mapped to
+ */
+ public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ {
+ for (int pe = 0; pe < pdbentry.length; pe++)
+ {
+ if (pdbentry[pe].getFile().equals(pdbFile))
+ {
+ addSequence(pe, seq);
+ }
+ }
+ }
+
}
\ No newline at end of file
}
for (int s = 0; s < jmol.jmb.sequence.length; s++)
{
- if (jal.findIndex(jmol.jmb.sequence[s]) > -1)
+ for (int smap=0;smap<jmol.jmb.sequence[s].length; smap++)
+ if (jal.findIndex(jmol.jmb.sequence[s][smap]) > -1)
{
pdb.addStructureState(state);
}
StructureSelectionManager.getStructureSelectionManager()
.setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
-
- ((AppJmol) comp).jmb.addSequence(seq);
+
+ ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
}
}
}
jmolHelp_actionPerformed(actionEvent);
}
});
+ alignStructs.setText("Align structures");
+ alignStructs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_actionPerformed(actionEvent);
+ }
+ });
+ jmolActionMenu.setText("Jmol");
menuBar.add(fileMenu);
menuBar.add(viewMenu);
menuBar.add(colourMenu);
+ menuBar.add(jmolActionMenu);
+ jmolActionMenu.setVisible(false);
menuBar.add(helpMenu);
fileMenu.add(savemenu);
fileMenu.add(viewMapping);
colourButtons.add(userColour);
helpMenu.add(jmolHelp);
+ jmolActionMenu.add(alignStructs);
+ }
+
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
}
JMenuBar menuBar = new JMenuBar();
JMenu colourMenu = new JMenu();
+ protected JMenu jmolActionMenu = new JMenu();
+
+ JMenuItem alignStructs = new JMenuItem();
+
JMenuItem backGround = new JMenuItem();
protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
git://source.jalview.org / jalview.git / commitdiff