/*
- * 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
*
* This file is part of Jalview.
*
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.api.FeatureColourI;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
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++)
{
}
boolean valid = nseqs >= 1; // need at least one sequence for valid input
// TODO: generalise
- vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ vamsas.objects.simple.Sequence[] seqarray = (valid)
+ ? new vamsas.objects.simple.Sequence[nseqs]
: null;
boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
// with gaps
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- 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 });
*
* @return true if getAlignment will return a valid alignment result.
*/
+ @Override
public boolean hasResults()
{
- if (subjobComplete
- && result != null
- && result.isFinished()
+ if (subjobComplete && result != null && result.isFinished()
&& ((SeqSearchResult) result).getAlignment() != null
- && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+ && ((SeqSearchResult) result).getAlignment()
+ .getSeqs() != null)
{
return true;
}
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset, Map featureColours)
+ public Object[] getAlignment(AlignmentI dataset,
+ Map<String, FeatureColourI> featureColours)
{
if (result != null && result.isFinished())
// int alseq_l = 0;
if (((SeqSearchResult) result).getAlignment() != null)
{
- alseqs = getVamsasAlignment(((SeqSearchResult) result)
- .getAlignment());
+ alseqs = getVamsasAlignment(
+ ((SeqSearchResult) result).getAlignment());
// 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,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the annotation file associated with the alignment.");
+ System.err.println(
+ "Failed to parse the annotation file associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
inFile = ((SeqSearchResult) result).getFeatures();
if (inFile != null && inFile.length() > 0)
{
- 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);
ff.parse(al, featureColours, false);
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the Features file associated with the alignment.");
+ System.err.println(
+ "Failed to parse the Features file associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
if (!nf.isValid())
{
nf.close();
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the treeFile associated with the alignment.");
+ System.err.println(
+ "Failed to parse the treeFile associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
*
* @return boolean true if job can be submitted.
*/
+ @Override
public boolean hasValidInput()
{
if (seqs.getSeqs() != null)
String alTitle; // name which will be used to form new alignment window.
- Alignment dataset; // dataset to which the new alignment will be
+ AlignmentI dataset; // dataset to which the new alignment will be
// associated.
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, String db,
- Alignment seqset)
+ AlignmentI seqset)
{
this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
OutputHeader = wsInfo.getProgressText();
}
}
+ @Override
public boolean isCancellable()
{
return true;
}
+ @Override
public void cancelJob()
{
if (!jobComplete && jobs != null)
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
}
if (cancelled)
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
- ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
- .getJobId());
+ ((SeqSearchWSJob) job).result = server
+ .getResult(((SeqSearchWSJob) job).getJobId());
}
+ @Override
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() }));
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Console.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
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
{
- vamsas.objects.simple.WsJobId jobsubmit = server.search(
- j.seqs.getSeqs()[0], dbArg);
+ vamsas.objects.simple.WsJobId jobsubmit = server
+ .search(j.seqs.getSeqs()[0], dbArg);
if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
{
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- new String[] { WsUrl }));
+ new String[]
+ { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
{
// TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
- 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(),
return msa;
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
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,
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + alTitle, ex);
+ Console.error(
+ "Unexpected exception when processing results for " + alTitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Map featureColours = new HashMap();
+ Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
* propagateDatasetMappings(al); }
*/
- AlignFrame af = new AlignFrame(al,// columnselection,
+ AlignFrame af = new AlignFrame(al, // columnselection,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- 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);
}
}
+ @Override
public boolean canMergeResults()
{
return false;
git://source.jalview.org / jalview.git / blobdiff