- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(AlignmentI dataset,
+ Map<String, FeatureColourI> featureColours)
if (inFile != null && inFile.length() > 0)
{
new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
if (inFile != null && inFile.length() > 0)
{
new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, String db,
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, String db,
{
this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
OutputHeader = wsInfo.getProgressText();
{
this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
OutputHeader = wsInfo.getProgressText();
public void pollJob(AWsJob job) throws Exception
{
((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
.getJobId());
}
public void pollJob(AWsJob job) throws Exception
{
((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
.getJobId());
}
"label.tree_from", new String[] { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.
"label.tree_from", new String[] { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.