- * 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;
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(AlignmentI dataset,
+ Map<String, FeatureColourI> featureColours)
// alseq_gapchar = ( (SeqSearchResult)
// result).getAlignment().getGapchar().charAt(0);
// alseq_l = alseqs.length;
// alseq_gapchar = ( (SeqSearchResult)
// result).getAlignment().getGapchar().charAt(0);
// alseq_l = alseqs.length;
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,
- jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
- inFile, jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile,
+ jalview.io.DataSourceType.PASTE);
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();
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
public void StartJob(AWsJob job)
{
if (!(job instanceof SeqSearchWSJob))
{
throw new Error(MessageManager.formatMessage(
public void StartJob(AWsJob job)
{
if (!(job instanceof SeqSearchWSJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_msawbjob_called",
- new String[] { job.getClass().toString() }));
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
- vamsas.objects.simple.WsJobId jobsubmit = server.search(
- j.seqs.getSeqs()[0], dbArg);
+ vamsas.objects.simple.WsJobId jobsubmit = server
+ .search(j.seqs.getSeqs()[0], dbArg);
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n"
- + e.toString() + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n" + e.toString()
+ + "\n");
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
- af.ShowNewickTree(nf, MessageManager.formatMessage(
- "label.tree_from", new String[] { this.alTitle }));
+ af.showNewickTree(nf,
+ MessageManager.formatMessage("label.tree_from", new String[]
+ { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);