/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
SequenceI[][] seqs)
{
createProgressBar();
+ // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
.getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
+ // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+ // ChimeraViewFrame. Is this even used ???
+
chain = pdbrefs.get(0).getChainCode();
}
}
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
* @param closeChimera
* if true, close any linked Chimera process; if false, prompt first
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
if (jmb != null && jmb.isChimeraRunning())
* Open any newly added PDB structures in Chimera, having first fetched data
* from PDB (if not already saved).
*/
+ @Override
public void run()
{
_started = true;
{
int pos = filePDBpos.get(num).intValue();
long startTime = startProgressBar("Chimera "
- + MessageManager.getString("status.opening_file"));
+ + MessageManager.getString("status.opening_file_for")
+ + " " + pe.getId());
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
alignStructs_withAllAlignPanels();
*/
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
+ // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
}
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);