{
super();
}
+
/**
*
* @param ap2
}
// otherwise, start adding the structure.
getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
- new SequenceI[][] { seqs }, new String[][] { chains });
+ new SequenceI[][]
+ { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
alignAddedStructures = align;
{
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[] { pdbId, view.getTitle() }),
+ new Object[]
+ { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
JvOptionPane.YES_NO_CANCEL_OPTION);
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(
- apanel);
+ apanel.getStructureSelectionManager()
+ .sequenceColoursChanged(apanel);
break;
}
}
*/
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed",
- new Object[] { pdbId }), MessageManager
- .formatMessage(
- "label.map_sequences_to_visible_window",
- new Object[] { pdbId }),
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }),
+ MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }),
JvOptionPane.YES_NO_CANCEL_OPTION);
if (option == JvOptionPane.CANCEL_OPTION)
{
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourSchemeName, al, null);
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, al, null);
getBinding().setJalviewColourScheme(cs);
}
}
@Override
- public void setJalviewColourScheme(ColourSchemeI cs) {
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
getBinding().setJalviewColourScheme(cs);
}
* the operation.
*/
@Override
- protected String alignStructs_actionPerformed(
- ActionEvent actionEvent)
+ protected String alignStructs_actionPerformed(ActionEvent actionEvent)
{
return alignStructs_withAllAlignPanels();
}
{
return null;
}
-
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
-
+
String reply = null;
try
{
HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
-
+
for (AlignmentPanel ap : _alignwith)
{
als[a] = ap.av.getAlignment();
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
{
- String text = MessageManager.formatMessage(
- "error.superposition_failed", reply);
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
statusBar.setText(text);
}
} catch (Exception e)
getBinding().setBackgroundColour(col);
}
}
+
@Override
public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
getBinding().setColourBySequence(false);
}
}
+
@Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
+
@Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
+
@Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
}
}
}
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
-
+
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
+
int value = chooser.showSaveDialog(this);
-
+
if (value == JalviewFileChooser.APPROVE_OPTION)
{
BufferedReader in = null;
in = new BufferedReader(
new FileReader(getBinding().getStructureFiles()[0]));
File outFile = chooser.getSelectedFile();
-
+
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
}
}
}
+
@Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
return;
}
setChainMenuItems(binding.getChainNames());
-
+
this.setTitle(binding.getViewerTitle(getViewerName(), true));
/*