import javax.swing.JCheckBoxMenuItem;
import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
- boolean leaveColouringToJmol, String loadStatus,
- Rectangle bounds, String viewid)
+ boolean leaveColouringToJmol, String loadStatus, Rectangle bounds,
+ String viewid)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
{
super.initMenus();
- viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
+ viewerActionMenu.setText(MessageManager.getString("label.jmol"));
viewerColour
.setText(MessageManager.getString("label.colour_with_jmol"));
IProgressIndicator progressBar = null;
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
/**
* add a single PDB structure to a new or existing Jmol view
*
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
@Override
protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
{
- List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
+ List<StructureViewerBase> result = new ArrayList<>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
scriptWindow.setVisible(false);
}
- jmb.allocateViewer(renderPanel, true, "", null, null, "",
- scriptWindow, null);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
// jmb.newJmolPopup("Jmol");
if (command == null)
{
jmb.setFinishedInit(true);
}
-
-
boolean allChainsSelected = false;
@Override
void showSelectedChains()
{
- Vector<String> toshow = new Vector<String>();
+ Vector<String> toshow = new Vector<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
int waitFor = 35;
int waitTotal = 0;
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
- .getPdbFile().length == files.size()))
+ : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
+ && jmb.getStructureFiles().length == files.size()))
{
try
{
}
if (waitTotal > waitMax)
{
- System.err
- .println("Timed out waiting for Jmol to load files after "
- + waitTotal + "ms");
-// System.err.println("finished: " + jmb.isFinishedInit()
-// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
-// + "; files: " + files.toString());
- jmb.getPdbFile();
+ System.err.println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+ // System.err.println("finished: " + jmb.isFinishedInit()
+ // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+ // + "; files: " + files.toString());
+ jmb.getStructureFiles();
break;
}
}
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder();
- List<String> files = new ArrayList<String>();
+ List<String> files = new ArrayList<>();
String pdbid = "";
try
{
- String[] filesInViewer = jmb.getPdbFile();
+ String[] filesInViewer = jmb.getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
Pdb pdbclient = new Pdb();
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new String[] { pdbid }), hdl);
+ progressBar.setProgressBar(MessageManager
+ .formatMessage("status.fetching_pdb", new String[]
+ { pdbid }), hdl);
}
try
{
}
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[] { errormsgs.toString() }),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new String[]
+ { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
JvOptionPane.ERROR_MESSAGE);
}
if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
{
lines++;
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
- * g.getFontMetrics().getHeight());
+ g.drawString(sb.toString(), 20, currentSize.height / 2
+ - lines * g.getFontMetrics().getHeight());
}
}
}