/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
import jalview.gui.*;
import vamsas.objects.simple.MsaResult;
// order
- class MsaWSJob extends WSThread.WSJob
+ class MsaWSJob
+ extends WSThread.WSJob
{
// hold special input for this
vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
public boolean hasResults()
{
if (subjobComplete && result != null && result.isFinished()
- && ((MsaResult) result).getMsa() != null && ((MsaResult) result).getMsa().getSeqs() != null)
+ && ( (MsaResult) result).getMsa() != null &&
+ ( (MsaResult) result).getMsa().getSeqs() != null)
{
return true;
}
SequenceI[] alseqs = null;
char alseq_gapchar = '-';
int alseq_l = 0;
- if (((MsaResult) result).getMsa() != null)
+ if ( ( (MsaResult) result).getMsa() != null)
{
- alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
- alseq_gapchar = ((MsaResult) result).getMsa().getGapchar().charAt(0);
+ alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
+ alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
alseq_l = alseqs.length;
}
if (emptySeqs.size() > 0)
if (nw > sw)
{
// pad at end
- alseqs[i].setSequence(t_alseqs[i].getSequence() +
+ alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
insbuff.substring(0, sw - nw));
}
}
}
return null;
}
+
/**
* mark subjob as cancelled and set result object appropriatly
*/
- void cancel() {
- cancelled=true;
+ void cancel()
+ {
+ cancelled = true;
subjobComplete = true;
result = null;
}
+
/**
*
* @return boolean true if job can be submitted.
*/
- boolean hasValidInput() {
- if (seqs.getSeqs()!=null)
+ boolean hasValidInput()
+ {
+ if (seqs.getSeqs() != null)
+ {
return true;
+ }
return false;
}
}
-
String alTitle; // name which will be used to form new alignment window.
Alignment dataset; // dataset to which the new alignment will be
AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
+ super(alFrame, wsinfo, alview, wsname, wsUrl);
this.server = server;
- this.WsUrl = wsUrl;
- this.wsInfo = wsinfo;
- this.WebServiceName = wsname;
- this.input = alview;
this.submitGaps = subgaps;
this.preserveOrder = presorder;
- this.alignFrame = alFrame;
}
/**
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
if (njobs > 0)
+ {
wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+ }
wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
}
}
}
+
public boolean isCancellable()
{
return true;
{
// CANCELLED_JOB
cancelledMessage = "Job cancelled.";
- ((MsaWSJob) jobs[job]).cancel();
+ ( (MsaWSJob) jobs[job]).cancel();
wsInfo.setStatus(jobs[job].jobnum,
WebserviceInfo.STATE_CANCELLED_OK);
}
cancelledMessage +=
("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
+ Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
+ exc);
}
wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+ cancelledMessage + "\n");
}
}
}
- void pollJob(WSJob job) throws Exception {
- ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
+
+ void pollJob(WSJob job)
+ throws Exception
+ {
+ ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
}
+
void StartJob(WSJob job)
{
- if (!(job instanceof MsaWSJob)) {
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "+job.getClass());
+ if (! (job instanceof MsaWSJob))
+ {
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
+ job.getClass());
}
MsaWSJob j = (MsaWSJob) job;
if (j.submitted)
j.result = new MsaResult();
j.result.setFinished(true);
j.result.setStatus("Empty Alignment Job");
- ((MsaResult) j.result).setMsa(null);
+ ( (MsaResult) j.result).setMsa(null);
}
try
{
if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
{
results++;
- vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result).getMsa();
+ vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
+ getMsa();
if (valign != null)
{
wsInfo.appendProgressText(jobs[j].jobnum,
}
});
wsInfo.setResultsReady();
- } else
+ }
+ else
+ {
wsInfo.setFinishedNoResults();
+ }
}
void displayResults(boolean newFrame)
{
// view input or result data for each block
Vector alorders = new Vector();
- SequenceI[][] results=new SequenceI[jobs.length][];
+ SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
- for (int j=0; j<jobs.length; j++) {
- if (jobs[j].hasResults()) {
+ for (int j = 0; j < jobs.length; j++)
+ {
+ if (jobs[j].hasResults())
+ {
Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
alorders.add(res[1]);
results[j] = (SequenceI[]) res[0];
orders[j] = (AlignmentOrder) res[1];
// SequenceI[] alignment = input.getUpdated
- } else {
- results[j]=null;
+ }
+ else
+ {
+ results[j] = null;
}
}
- Object[] newview = input.getUpdatedView(results, orders, '-');
+ Object[] newview = input.getUpdatedView(results, orders, getGapChar());
// trash references to original result data
- for (int j=0; j<jobs.length; j++) {
+ for (int j = 0; j < jobs.length; j++)
+ {
results[j] = null;
orders[j] = null;
}
SequenceI[] alignment = (SequenceI[]) newview[0];
ColumnSelection columnselection = (ColumnSelection) newview[1];
Alignment al = new Alignment(alignment);
+
if (dataset != null)
{
al.setDataset(dataset);
}
+ propagateDatasetMappings(al);
// JBNote- TODO: warn user if a block is input rather than aligned data ?
if (newFrame)
{
AlignFrame af = new AlignFrame(al, columnselection,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- // >>>This is a fix for the moment, until a better solution is
- // found!!<<<
+ // initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(
- alignFrame.getFeatureRenderer());
+ this.featureSettings);
// update orders
if (alorders.size() > 0)
{
for (int i = 0, l = alorders.size(); i < l; i++)
{
af.addSortByOrderMenuItem(WebServiceName
- +( (String) names.get(i)) +
+ + ( (String) names.get(i)) +
" Ordering",
(AlignmentOrder) alorders.get(i));
}
git://source.jalview.org / jalview.git / blobdiff