/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
class MsaWSThread extends JWS1Thread implements WSClientI
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
this.seqs = new vamsas.objects.simple.SequenceSet();
jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- { alseqs, msaorder };
+ return new Object[] { alseqs, msaorder };
}
return null;
}
{
if (!(job instanceof MsaWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+ j.result.setStatus(MessageManager
+ .getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
if (jobsubmit == null)
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.appendProgressText(
- j.getJobnum(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
.getMsa();
if (valign != null)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(),
- MessageManager.getString("info.alignment_object_method_notes"));
+ wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+ .getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{