public void run()
{
final long sttime = System.currentTimeMillis();
- alignFrame.setProgressBar(
- MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from", new Object[]
+ { source }), sttime);
try
{
AlignmentI alignment = alignFrame.getViewport().getAlignment();
+ " now searching for " + (dna ? "DNA" : "Protein")
+ " Context.");
}
- AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
- source, dna);
+ AlignmentI xrefs = new CrossRef(sel, dataset)
+ .findXrefSequences(source, dna);
if (xrefs == null)
{
return;
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
- JOptionPane.showMessageDialog(alignFrame,
+ JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("label.cant_map_cds"),
MessageManager.getString("label.operation_failed"),
- JOptionPane.OK_OPTION);
+ JvOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
if (copyAlignment.getHeight() <= 0)
{
- System.err.println("No Sequences generated for xRef type "
- + source);
+ System.err.println(
+ "No Sequences generated for xRef type " + source);
return;
}
/*
String linkedTitle = MessageManager
.getString("label.linked_view_title");
Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
- sf.adjustDivider();
+ sf.adjustInitialLayout();
// finally add the top, then bottom frame to the view list
xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
+ "status.finished_searching_for_sequences_from", new Object[]
+ { source }), sttime);
}
}
for (int s = 0; s < sprods.length; s++)
{
sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ if (dataset.getSequences() == null || !dataset.getSequences()
+ .contains(sprods[s].getDatasetSequence()))
{
dataset.addSequence(sprods[s].getDatasetSequence());
}