/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
import jalview.ws.WSClientI;
import vamsas.objects.simple.MsaResult;
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
class MsaWSThread extends JWS1Thread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
// for
// any
// subjob
- SeqNames.put(newname, jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seqs[i]));
+ SeqNames.put(newname,
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
{
seqarray[n] = new vamsas.objects.simple.Sequence();
if (seqs[i].getEnd() >= seqs[i].getStart())
{
empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
- .getSequenceAsString());
+ .extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[]
{ newname, empty });
}
if (njobs > 0)
{
- wsinfo
- .setProgressName("region " + jobs[j].getJobnum(),
- jobs[j].getJobnum());
+ wsinfo.setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
}
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
}
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
Cache.log.warn(
- "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ "Exception whilst cancelling " + jobs[job].getJobId(),
+ exc);
}
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
{
if (!jobComplete)
{
- wsInfo
- .setProgressText(OutputHeader
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ wsInfo.setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
}
}
}
+ e.toString() + "\n");
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .appendProgressText(
- j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.appendProgressText(
+ j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "It is most likely that there is a problem with the server.\n"
+ + "Just close the window\n");
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
for (int i = 0, j = seqs.length; i < j; i++)
{
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
- .getSeq());
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+ seqs[i].getSeq());
}
return msa;
&& jobs[j].hasResults())
{
results++;
- //if (Cache.log.isDebugEnabled())
- // {
- // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
- // System.out.println(jobs[j].getStatus());
- // }
+ // if (Cache.log.isDebugEnabled())
+ // {
+ // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
+ // System.out.println(jobs[j].getStatus());
+ // }
- vamsas.objects.simple.Alignment valign = ((MsaResult)((MsaWSJob) jobs[j]).result)
+ vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
.getMsa();
if (valign != null)
{
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+ wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
+ + "\n");
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
// when clicked, pop up their corresponding data
-
+
}
}
}
}
for (int i = 0, l = alorders.size(); i < l; i++)
{
- af.addSortByOrderMenuItem(WebServiceName
- + ((String) names.get(i)) + " Ordering",
+ af.addSortByOrderMenuItem(
+ WebServiceName + ((String) names.get(i)) + " Ordering",
(AlignmentOrder) alorders.get(i));
}
}