+++ /dev/null
-package jalview.ws.jws2;
-
-import javax.swing.JMenuItem;
-
-import jalview.analysis.SeqsetUtils;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.ws.WSClient;
-import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.api.JPredServiceI;
-import jalview.ws.api.ServiceWithParameters;
-
-public class JPredClient extends WSClient
-{
- JPredServiceI server;
-
- public JPredClient(ServiceWithParameters sh, String title,
- AlignmentView alView, AlignFrame alFrame, boolean viewOnly)
- {
- server = (JPredServiceI) sh.getEndpoint();
- wsInfo = setWebService(sh, false);
- startClient(title, alView, alFrame, viewOnly);
- }
-
- private void startClient(String title, AlignmentView view,
- AlignFrame frame, boolean viewOnly)
- {
- var msf = view.getSequences();
- var seq = msf[0].getSeq('-');
- int[] delMap = null;
- if (viewOnly)
- delMap = view.getVisibleContigMapFor(seq.gapMap());
- var aln = new SequenceI[msf.length];
- for (int i = 0; i < msf.length; i++)
- {
- aln[i] = msf[i].getSeq('-');
- }
- var sequenceInfo = msf.length > 1 ? SeqsetUtils.uniquify(aln, true)
- : SeqsetUtils.SeqCharacterHash(seq);
- if (viewOnly)
- {
- String seqs[] = view.getSequenceStrings('-');
- for (int i = 0; i < msf.length; i++)
- aln[i].setSequence(seqs[i]);
- seq.setSequence(seqs[0]);
- }
- var thread = new JPredThread(wsInfo, title, server, sequenceInfo, aln,
- delMap, view, frame, WsURL);
- wsInfo.setthisService(thread);
- wsInfo.setVisible(true);
- thread.start();
- }
-
- // sh parameter should be moved to the WSMenuEntryProvider interface
- public static WSMenuEntryProviderI getMenuEntryProvider(ServiceWithParameters sh)
- {
- return (menu, frame) -> {
- final JMenuItem mi = new JMenuItem(sh.getName());
- mi.setToolTipText(sh.getHostURL());
- mi.addActionListener((event) -> {
- var view = frame.gatherSeqOrMsaForSecStrPrediction();
- new JPredClient(sh, frame.getTitle(), view, frame, true);
- });
- menu.add(mi);
- };
- }
-}
+++ /dev/null
-package jalview.ws.jws2;
-
-import static java.lang.String.format;
-
-import java.util.Hashtable;
-import java.util.List;
-
-import jalview.analysis.SeqsetUtils;
-import jalview.bin.Cache;
-import jalview.commands.RemoveGapsCommand;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.WebserviceInfo;
-import jalview.io.JPredFile;
-import jalview.io.JnetAnnotationMaker;
-import jalview.util.MessageManager;
-import jalview.ws.AWSThread;
-import jalview.ws.AWsJob;
-import jalview.ws.JobStateSummary;
-import jalview.ws.WSClientI;
-import jalview.ws.api.CancellableI;
-import jalview.ws.api.JPredServiceI;
-import jalview.ws.gui.WsJob;
-import jalview.ws.gui.WsJob.JobState;
-
-
-public class JPredThread extends AWSThread implements WSClientI
-{
-
- private static class JPredJob extends WsJob
- {
- private final Hashtable<?, ?> sequenceInfo;
- private final List<SequenceI> msf;
- private final int[] delMap;
- private AlignmentI alignment = null;
- private HiddenColumns hiddenCols = null;
-
- private JPredJob(Hashtable<?, ?> sequenceInfo, SequenceI[] msf, int[] delMap)
- {
- this.sequenceInfo = sequenceInfo;
- this.msf = List.of(msf);
- this.delMap = delMap;
- }
-
- @Override
- public boolean hasValidInput()
- {
- return true;
- }
-
- @Override
- public boolean hasResults()
- {
- return (isSubjobComplete() && alignment != null);
- }
-
- public boolean isMSA()
- {
- return msf.size() > 1;
- }
- }
-
-
- private JPredServiceI server;
- private String title;
- private Hashtable<?, ?> sequenceInfo;
- private SequenceI[] msf;
- private int[] delMap;
-
- public JPredThread(WebserviceInfo wsInfo, String title,
- JPredServiceI server, Hashtable<?, ?> sequenceInfo,
- SequenceI[] msf, int[] delMap, AlignmentView view, AlignFrame frame,
- String wsURL)
- {
- super(frame, wsInfo, view, wsURL);
- this.server = server;
- this.title = title;
- this.sequenceInfo = sequenceInfo;
- this.msf = msf;
- this.delMap = delMap;
- JPredJob job = new JPredJob(sequenceInfo, msf, delMap);
- this.jobs = new JPredJob[] { job };
- }
-
- @Override
- public boolean isCancellable()
- {
- return server instanceof CancellableI;
- }
-
- @Override
- public boolean canMergeResults()
- {
- return false;
- }
-
- @Override
- public void cancelJob()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void pollJob(AWsJob job_) throws Exception
- {
- var job = (JPredJob) job_;
- server.updateStatus(job);
- server.updateJobProgress(job);
- }
-
- @Override
- public void StartJob(AWsJob job_)
- {
- if (!(job_ instanceof JPredJob))
- throw new RuntimeException("Invalid job type");
- var job = (JPredJob) job_;
- if (job.isSubmitted())
- {
- return;
- }
- try {
- try
- {
- var jobHandle = server.predict(job.msf, job.isMSA());
- if (jobHandle != null)
- job.setJobHandle(jobHandle);
- }
- catch (Throwable th) {
- if (!server.handleSubmitError(th, job, wsInfo)) {
- throw th;
- }
- }
- if (job.getJobId() != null) {
- job.setSubmitted(true);
- job.setSubjobComplete(false);
- return;
- }
- else {
- throw new Exception(MessageManager.formatMessage(
- "exception.web_service_returned_null_try_later",
- new String[]
- { WsUrl }));
- }
- }
- catch (Throwable th)
- {
- // 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");
- th.printStackTrace(System.err);
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(job.getJobnum(),
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
-
- }
- finally
- {
- if (!job.isSubmitted())
- {
- job.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(job.getJobnum(), MessageManager.getString(
- "info.failed_to_submit_sequences_for_alignment"));
- }
- }
- }
-
- @Override
- public void parseResult()
- {
- long progbar = (long) (Math.random() * ~(1L << 63));
- wsInfo.setProgressBar(
- MessageManager.getString("status.collecting_job_results"), progbar);
- int results = 0;
- var finalState = new JobStateSummary();
- try
- {
- for (int i = 0; i < jobs.length; i++) {
- final var job = (JPredJob) jobs[i];
- finalState.updateJobPanelState(wsInfo, OutputHeader, job);
- if (job.isFinished()) {
- try {
- server.updateJobProgress(job);
- }
- catch (Exception e) {
- Cache.log.warn(format(
- "Exception when retrieving remaining Job progress data " +
- "for job %s on server %s", job.getJobId(), WsUrl));
- e.printStackTrace();
- }
- // removed the waiting loop
- Cache.log.debug(format("Job Execution file for job: %s " +
- "on server %s%n%s", job.getJobId(), WsUrl, job.getStatus()));
- try {
- prepareJobResult(job);
- }
- catch (Exception e) {
- if (!server.handleCollectionException(e, job, wsInfo)) {
- Cache.log.error("Could not get alignment for job.", e);
- job.setState(JobState.SERVERERROR);
- }
- }
- }
- finalState.updateJobPanelState(wsInfo, OutputHeader, job);
- if (job.isSubmitted() && job.isSubjobComplete() && job.hasResults()) {
- results++;
- }
- }
- }
- catch (Exception e) {
- Cache.log.error(
- "Unexpected exception when processing results for " + title, e);
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- if (results > 0) {
- wsInfo.showResultsNewFrame.addActionListener(
- (evt) -> displayResults(true));
- wsInfo.mergeResults.addActionListener(
- (evt) -> displayResults(false));
- wsInfo.setResultsReady();
- }
- else {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendInfoText("No jobs ran.");
- wsInfo.setFinishedNoResults();
- }
- updateGlobalStatus(finalState);
- wsInfo.removeProgressBar(progbar);
- }
-
- static final int msaIndex = 0;
-
- private void prepareJobResult(JPredJob job) throws Exception
- {
- HiddenColumns hiddenCols = null;
- int firstSeq = -1;
- AlignmentI alignment;
- var prediction = server.getPrediction(job.getJobHandle());
- var preds = prediction.getSeqsAsArray();
-
- if (job.msf.size() > 1)
- {
- if (job.delMap != null)
- {
- Object[] alandcolsel = input
- .getAlignmentAndHiddenColumns(getGapChar());
- alignment = new Alignment((SequenceI[]) alandcolsel[0]);
- hiddenCols = (HiddenColumns) alandcolsel[1];
- }
- else
- {
- alignment = server.getAlignment(job.getJobHandle());
- var seqs = new SequenceI[alignment.getHeight()];
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- seqs[i] = alignment.getSequenceAt(i);
- }
- if (!SeqsetUtils.deuniquify(sequenceInfo, seqs))
- {
- throw (new Exception(MessageManager.getString(
- "exception.couldnt_recover_sequence_properties_for_alignment")));
- }
- }
- firstSeq = 0;
- if (currentView.getDataset() != null)
- {
- alignment.setDataset(currentView.getDataset());
- }
- else
- {
- alignment.setDataset(null);
- }
- JnetAnnotationMaker.add_annotation(prediction, alignment, firstSeq, false,
- job.delMap);
- }
- else
- {
- alignment = new Alignment(preds);
- firstSeq = prediction.getQuerySeqPosition();
- if (job.delMap != null)
- {
- Object[] alanndcolsel = input.getAlignmentAndHiddenColumns(getGapChar());
- SequenceI[] seqs = (SequenceI[]) alanndcolsel[0];
- new RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
- new SequenceI[] {seqs[msaIndex]}, currentView);
- SequenceI profileSeq = alignment.getSequenceAt(firstSeq);
- profileSeq.setSequence(seqs[msaIndex].getSequenceAsString());
- }
- if (!SeqsetUtils.SeqCharacterUnhash(
- alignment.getSequenceAt(firstSeq), sequenceInfo))
- {
- throw new Exception(MessageManager.getString(
- "exception.couldnt_recover_sequence_props_for_jnet_query"));
- }
- alignment.setDataset(currentView.getDataset());
- JnetAnnotationMaker.add_annotation(prediction, alignment, firstSeq, true,
- job.delMap);
- SequenceI profileSeq = alignment.getSequenceAt(0);
- alignToProfileSeq(alignment, profileSeq);
- if (job.delMap != null)
- {
- hiddenCols = alignment.propagateInsertions(profileSeq, input);
- }
- }
-
- for (var annot : alignment.getAlignmentAnnotation())
- {
- if (annot.sequenceRef != null)
- {
- replaceAnnotationOnAlignmentWith(annot, annot.label,
- "jalview.ws.JPred", annot.sequenceRef);
- }
- }
- job.alignment = alignment;
- job.hiddenCols = hiddenCols;
- }
-
- private static void replaceAnnotationOnAlignmentWith(
- AlignmentAnnotation newAnnot, String typeName, String calcId,
- SequenceI aSeq)
- {
- SequenceI dsseq = aSeq.getDatasetSequence();
- while (dsseq.getDatasetSequence() != null)
- {
- dsseq = dsseq.getDatasetSequence();
- }
- // look for same annotation on dataset and lift this one over
- List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
- typeName);
- if (dsan != null && dsan.size() > 0)
- {
- for (AlignmentAnnotation dssan : dsan)
- {
- dsseq.removeAlignmentAnnotation(dssan);
- }
- }
- AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
- dsseq.addAlignmentAnnotation(dssan);
- dssan.adjustForAlignment();
- }
-
- private static void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
- {
- char gc = al.getGapCharacter();
- int[] gapMap = profileseq.gapMap();
- // insert gaps into profile
- for (int lp = 0, r = 0; r < gapMap.length; r++)
- {
- if (gapMap[r] - lp > 1)
- {
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 1, ns = al.getHeight(); s < ns; s++)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- int diff = gapMap[r] - sq.length();
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = gapMap[r] - sq.length()) > 0)
- {
- sq = sq + ((diff >= sb.length()) ? sb.toString()
- : sb.substring(0, diff));
- }
- al.getSequenceAt(s).setSequence(sq);
- }
- else
- {
- al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
- + sb.toString() + sq.substring(gapMap[r]));
- }
- }
- }
- lp = gapMap[r];
- }
- }
-
- private void displayResults(boolean newWindow)
- {
- if (jobs == null || jobs.length == 0)
- {
- return;
- }
- var job = (JPredJob) jobs[0];
- if (job.hasResults() && newWindow)
- {
- job.alignment.setSeqrep(job.alignment.getSequenceAt(0));
- AlignFrame frame = new AlignFrame(job.alignment, job.hiddenCols,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(frame, title, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
- }
-
-}
git://source.jalview.org / jalview.git / commitdiff