// TODO: JAL-1102 - should have a warning message in dialog, not simply
// overwrite the broken input data with the exception
textarea.setText(MessageManager.formatMessage(
- "label.could_not_parse_newick_file", new Object[]
- { ex.getMessage() }));
+ "label.could_not_parse_newick_file",
+ new Object[] { ex.getMessage() }));
return false;
}
return false;
*/
protected boolean openSplitFrame(AlignmentI al, String format)
{
- final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+ final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+ .getAlignment();
if (thisAlignment.isNucleotide() == al.isNucleotide())
{
// both nucleotide or both protein
dialog.setMainPanel(question);
dialog.setVisible(true);
dialog.toFront();
-
+
if (!dialog.accept)
{
return false;
AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
"Cut & Paste input - " + format, false, false);
AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
- AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
- : newFrame;
+ AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
sf.addToDisplay(false, applet);
return true;
jalview.io.AppletFormatAdapter.PASTE);
if (tcf.isValid())
{
- if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
- true))
+ if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
{
alignFrame.tcoffeeColour.setEnabled(true);
alignFrame.alignPanel.fontChanged();
// file valid but didn't get added to alignment for some reason
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.failed_add_tcoffee_scores",
- new Object[]
- { (tcf.getWarningMessage() != null ? tcf
+ new Object[] { (tcf.getWarningMessage() != null ? tcf
.getWarningMessage() : "") }));
}
}
if (tcf == null)
{
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
+ textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
if (alignFrame.alignPanel.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
else
{
- new MCview.AppletPDBViewer(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
}