import java.util.Vector;
public class AppletJmol extends EmbmenuFrame implements
-// StructureListener,
+ // StructureListener,
KeyListener, ActionListener, ItemListener
{
CheckboxMenuItem jmolColour = new CheckboxMenuItem(
MessageManager.getString("action.using_jmol"), false);
- MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
+ MenuItem chain = new MenuItem(
+ MessageManager.getString("action.by_chain"));
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
AlignmentPanel ap;
- List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+ List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
// added to
String fileLoadingError;
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- protocol);
+ new PDBEntry[]
+ { pdbentry }, new SequenceI[][] { seq }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
if (protocol == DataSourceType.PASTE)
{
- pdbentry.setId("PASTED PDB"
- + (chains == null ? "_" : chains.toString()));
+ pdbentry.setId(
+ "PASTED PDB" + (chains == null ? "_" : chains.toString()));
}
else
{
StructureFile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager(
- ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
- protocol);
+ reader = StructureSelectionManager
+ .getStructureSelectionManager(ap.av.applet)
+ .setMapping(seq, chains, pdbentry.getFile(), protocol, null);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
try
{
- jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
- + "_jmol_", ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+ jmb.allocateViewer(renderPanel, true,
+ ap.av.applet.getName() + "_jmol_",
+ ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
+ "-applet", scriptWindow, null);
} catch (Exception e)
{
- System.err
- .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
- + ap.av.applet.getDocumentBase()
- + "\nCodebase="
+ System.err.println(
+ "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+ + ap.av.applet.getDocumentBase() + "\nCodebase="
+ ap.av.applet.getCodeBase());
e.printStackTrace();
dispose();
});
pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
-
+
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Trying to reuse existing PDBfile IO parser.");
}
// re-use the one we opened earlier
freader = reader.getReader();
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Creating new PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Creating new PDBfile IO parser.");
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
}
if (freader == null)
{
- throw new Exception(
- MessageManager
- .getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(MessageManager.getString(
+ "exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
void centerViewer()
{
- Vector<String> toshow = new Vector<String>();
+ Vector<String> toshow = new Vector<>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
} catch (OutOfMemoryError ex)
{
frame.dispose();
- System.err
- .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+ System.err.println(
+ "Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
jalview.bin.JalviewLite.addFrame(frame,
{
try
{
- ap.av.applet.getAppletContext().showDocument(
- new java.net.URL(
+ ap.av.applet.getAppletContext()
+ .showDocument(new java.net.URL(
"http://jmol.sourceforge.net/docs/JmolUserGuide/"),
- "jmolHelp");
+ "jmolHelp");
} catch (java.net.MalformedURLException ex)
{
}