From d32e3804460b3e145f96a1ad68cbed279ac545f4 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 15 Aug 2006 10:59:31 +0000 Subject: [PATCH] first stage of adapting JNet client to hidden regions and new WSClient structure. --- src/jalview/ws/JPredClient.java | 677 +++++++++++++++++++++++++-------------- 1 file changed, 431 insertions(+), 246 deletions(-) diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index ec3f737..2ec8e1e 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -24,42 +24,50 @@ import javax.swing.*; import ext.vamsas.*; import jalview.analysis.*; +import jalview.bin.*; import jalview.datamodel.*; +import jalview.datamodel.Alignment; import jalview.gui.*; -import jalview.io.FormatAdapter; import jalview.io.*; +import jalview.ws.WSThread.*; +import vamsas.objects.simple.*; +import jalview.util.Comparison; public class JPredClient extends WSClient { - ext.vamsas.Jpred server; - String altitle = ""; - java.util.Hashtable SequenceInfo = null; - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) { + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) + { wsInfo = setWebService(sh); startJPredClient(title, seq); } - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) { + + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) + { wsInfo = setWebService(sh); startJPredClient(title, msa); } - public JPredClient(String title, SequenceI[] msf) { + public JPredClient(String title, SequenceI[] msf) + { startJPredClient(title, msf); } - public JPredClient(String title, SequenceI seq) { + public JPredClient(String title, SequenceI seq) + { startJPredClient(title, seq); } private void startJPredClient(String title, SequenceI[] msf) { - if (wsInfo==null) + if (wsInfo == null) + { wsInfo = setWebService(); + } SequenceI seq = msf[0]; - altitle = "JNet prediction on " + seq.getName() + + String altitle = "JNet prediction on " + seq.getName() + " using alignment from " + title; wsInfo.setProgressText("Job details for MSA based prediction (" + @@ -67,40 +75,47 @@ public class JPredClient AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n"); SequenceI aln[] = new SequenceI[msf.length]; - for (int i=0,j=msf.length; i" + seq.getName() + "\n" + AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n"); - altitle = "JNet prediction for sequence " + seq.getName() + " from " + + String altitle = "JNet prediction for sequence " + seq.getName() + " from " + title; - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); - if (!locateWebService()) + Jpred server = locateWebService(); + if (server==null) { return; } - JPredThread jthread = new JPredThread(seq); + JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq); + wsInfo.setthisService(jthread); jthread.start(); } @@ -120,14 +135,14 @@ public class JPredClient return wsInfo; } - private boolean locateWebService() + private ext.vamsas.Jpred locateWebService() { ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default - + ext.vamsas.Jpred server=null; try { - this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties - ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub + server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties + ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE); } @@ -145,164 +160,317 @@ public class JPredClient ex.getMessage()); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - return false; } - return true; + return server; } class JPredThread - extends Thread + extends WSThread + implements WSClientI { - String OutputHeader; - vamsas.objects.simple.JpredResult result; - vamsas.objects.simple.Sequence sequence; - vamsas.objects.simple.Msfalignment msa; - String jobId; - boolean jobComplete = false; - int allowedServerExceptions = 3; // thread dies if too many exceptions. - - JPredThread(SequenceI seq) + class JPredJob + extends WSThread.WSJob { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new vamsas.objects.simple.Sequence(); - this.sequence.setId(seq.getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence())); - } - JPredThread(SequenceI[] msf) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new vamsas.objects.simple.Sequence(); - this.sequence.setId(msf[0].getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ", - msf[0].getSequence())); - - this.msa = new vamsas.objects.simple.Msfalignment(); - jalview.io.PileUpfile pileup = new jalview.io.PileUpfile(); - msa.setMsf(pileup.print(msf)); - } + vamsas.objects.simple.Sequence sequence; + vamsas.objects.simple.Msfalignment msa; + java.util.Hashtable SequenceInfo = null; + /** + * + * @return true if getResultSet will return a valid alignment and prediction result. + */ + public boolean hasResults() + { + if (subjobComplete && result != null && result.isFinished() + && ( (JpredResult) result).getPredfile() != null && + ( (JpredResult) result).getAligfile() != null) + { + return true; + } + return false; + } - public void run() - { - StartJob(); + boolean hasValidInput() + { + if (sequence != null) + { + return true; + } + return false; + } - while (!jobComplete && (allowedServerExceptions > 0)) + public Alignment getResultSet() + throws Exception { - try + if (result == null || !result.isFinished()) + { + return null; + } + Alignment al = null; + int FirstSeq = -1; // the position of the query sequence in Alignment al + boolean noMsa = true; // set if no MSA has been returned by JPred + + JpredResult result = (JpredResult)this.result; + + jalview.bin.Cache.log.debug("Parsing output from JNet job."); + // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File"); + jalview.io.JPredFile prediction = new jalview.io.JPredFile(result. + getPredfile(), + "Paste"); + SequenceI[] preds = prediction.getSeqsAsArray(); + jalview.bin.Cache.log.debug("Got prediction profile."); + + if ( (this.msa != null) && (result.getAligfile() != null)) { - if ( (result = server.getresult(jobId)) == null) + jalview.bin.Cache.log.debug("Getting associated alignment."); + // we ignore the returned alignment if we only predicted on a single sequence + String format = new jalview.io.IdentifyFile().Identify(result. + getAligfile(), + "Paste"); + + if (jalview.io.FormatAdapter.isValidFormat(format)) + { + al = new Alignment(new FormatAdapter().readFile(result.getAligfile(), + "Paste", format)); + SequenceI sqs[] = new SequenceI[al.getHeight()]; + for (int i = 0, j = al.getHeight(); i < j; i++) + { + sqs[i] = al.getSequenceAt(i); + } + if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable) + SequenceInfo, sqs)) + { + throw (new Exception( + "Couldn't recover sequence properties for alignment.")); + } + + noMsa = false; + FirstSeq = 0; + } + else { throw (new Exception( - "Timed out when communicating with server\nTry again later.\n")); + "Unknown format "+format+" for file : \n" + + result.getAligfile())); } - if (result.getState()==0) - jalview.bin.Cache.log.debug("Finished "+jobId); - if (result.isRunning()) + } + else + { + al = new Alignment(preds); + FirstSeq = prediction.getQuerySeqPosition(); + if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( + al.getSequenceAt(FirstSeq), SequenceInfo)) { - wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); + throw (new Exception( + "Couldn't recover sequence properties for JNet Query sequence!")); } - if (result.isQueued()) + } + + al.setDataset(null); + + jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, + noMsa); + return al; // , FirstSeq, noMsa}; + } + public JPredJob(Hashtable SequenceInfo, SequenceI seq) + { + super(); + String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence()); + if (sq.length() >= 20) + { + this.SequenceInfo = SequenceInfo; + sequence = new vamsas.objects.simple.Sequence(); + sequence.setId(seq.getName()); + sequence.setSeq(sq); + } + } + + public JPredJob(Hashtable SequenceInfo, SequenceI[] msf) + { + this(SequenceInfo, msf[0]); + if (sequence != null) + { + if (msf.length > 1) { - wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); + msa = new vamsas.objects.simple.Msfalignment(); + jalview.io.PileUpfile pileup = new jalview.io.PileUpfile(); + msa.setMsf(pileup.print(msf)); } + } + } + } + ext.vamsas.Jpred server; + String altitle = ""; + JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server) { + this.altitle = altitle; + this.server = server; + this.wsInfo = wsinfo; + } - wsInfo.setProgressText(OutputHeader + "\n" + - result.getStatus()); +// String OutputHeader; +// vamsas.objects.simple.JpredResult result; - if (result.isFinished()) + JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq) + { + this(wsinfo, altitle, server); + JPredJob job = new JPredJob(SequenceInfo, seq); + if (job.hasValidInput()) + { + OutputHeader = wsInfo.getProgressText(); + jobs = new WSJob[] + { + job}; + job.jobnum = 0; + } + } + + JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf) + { + this(wsinfo, altitle, server); + JPredJob job = new JPredJob(SequenceInfo, msf); + if (job.hasValidInput()) + { + jobs = new WSJob[] + { + job}; + OutputHeader = wsInfo.getProgressText(); + job.jobnum = 0; + } + } + + /* + public void run() + { + StartJob(); + + while (!jobComplete && (allowedServerExceptions > 0)) { + try + { + if ( (result = server.getresult(jobId)) == null) + { + throw (new Exception( + "Timed out when communicating with server\nTry again later.\n")); + } + if (result.getState()==0) + jalview.bin.Cache.log.debug("Finished "+jobId); + if (result.isRunning()) + { + wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); + } + if (result.isQueued()) + { + wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); + } - parseResult(); - jobComplete = true; - jobsRunning--; - } else { - // catch exceptions - if (! (result.isJobFailed() || result.isServerError())) + wsInfo.setProgressText(OutputHeader + "\n" + + result.getStatus()); + + if (result.isFinished()) + { + + parseResult(); + jobComplete = true; + jobsRunning--; + } else { + // catch exceptions + if (! (result.isJobFailed() || result.isServerError())) + { + try + { + Thread.sleep(5000); + } + catch (InterruptedException ex1) + { + } + + // System.out.println("I'm alive "+seqid+" "+jobid); + } + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + jobsRunning--; + jobComplete = true; + } + } + } + catch (Exception ex) { + allowedServerExceptions--; + + wsInfo.appendProgressText("\nJPredWS Server exception!\n" + + ex.getMessage()); + try { - Thread.sleep(5000); + if (allowedServerExceptions > 0) + { + Thread.sleep(5000); + } } catch (InterruptedException ex1) { } - - // System.out.println("I'm alive "+seqid+" "+jobid); } - else + catch (OutOfMemoryError er) { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - jobsRunning--; jobComplete = true; + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory handling result!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + JOptionPane.WARNING_MESSAGE); + System.out.println("JPredClient: "+er); + System.gc(); } } - } - catch (Exception ex) - { - allowedServerExceptions--; - - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + - ex.getMessage()); - - try - { - if (allowedServerExceptions > 0) + if (result!=null) + if (! (result.isJobFailed() || result.isServerError())) { - Thread.sleep(5000); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); + } + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } - } - catch (InterruptedException ex1) - { - } - } - catch (OutOfMemoryError er) - { - jobComplete = true; - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory handling result!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - JOptionPane.WARNING_MESSAGE); - System.out.println("JPredClient: "+er); - System.gc(); - } - } - if (result!=null) - if (! (result.isJobFailed() || result.isServerError())) - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); - } - else - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } - } - - void StartJob() + */ + void StartJob(WSJob j) { + if (! (j instanceof JPredJob)) + { + throw new Error("Implementation error - StartJob(JpredJob) called on " + + j.getClass()); + } try { - if (msa != null) + JPredJob job = (JPredJob) j; + if (job.msa != null) { - jobId = server.predictOnMsa(msa); + job.jobId = server.predictOnMsa(job.msa); } else - { - jobId = server.predict(sequence); - } + if (job.sequence!=null) + { + job.jobId = server.predict(job.sequence); + } - if (jobId != null) + if (job.jobId != null) { - if (jobId.startsWith("Broken")) + if (job.jobId.startsWith("Broken")) { - throw new Exception("Submission " + jobId); + job.result = (vamsas.objects.simple.Result)new JpredResult(); + job.result.setInvalid(true); + job.result.setStatus("Submission " + job.jobId); } else { - System.out.println(WsURL + " Job Id '" + jobId + "'"); + job.submitted = true; + job.subjobComplete = false; + Cache.log.info(WsURL + " Job Id '" + job.jobId + "'"); } } else @@ -312,158 +480,175 @@ public class JPredClient } catch (Exception e) { - if (e.getMessage().indexOf("Exception")>-1) { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - wsInfo.setProgressText( - "Failed to submit the prediction. (Just close the window)\n" - + - "It is most likely that there is a problem with the server.\n"); + if (e.getMessage().indexOf("Exception") > -1) + { + wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR); + wsInfo.setProgressText(j.jobnum, + "Failed to submit the prediction. (Just close the window)\n" + + + "It is most likely that there is a problem with the server.\n"); System.err.println( "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" + e.getMessage() + "\n"); - jalview.bin.Cache.log.warn("Server Exception",e); - } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + jalview.bin.Cache.log.warn("Server Exception", e); + } + else + { + wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR); // JBPNote - this could be a popup informing the user of the problem. - wsInfo.setProgressText("Failed to submit the prediction:\n" - +e.getMessage()+ - wsInfo.getProgressText()); + wsInfo.appendProgressText(j.jobnum, + "Failed to submit the prediction:\n" + + e.getMessage() + + wsInfo.getProgressText()); - jalview.bin.Cache.log.debug("Failed Submission",e); + jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e); } - allowedServerExceptions = -1; - jobComplete = true; - + j.allowedServerExceptions = -1; + j.subjobComplete = true; } } - - - /* private void addFloatAnnotations(Alignment al, int[] gapmap, - Vector values, String Symname, - String Visname, float min, - float max, int winLength) - { - Annotation[] annotations = new Annotation[al.getWidth()]; - - for (int j = 0; j < values.size(); j++) + /* private void addFloatAnnotations(Alignment al, int[] gapmap, + Vector values, String Symname, + String Visname, float min, + float max, int winLength) { - float value = Float.parseFloat(values.get(j).toString()); - annotations[gapmap[j]] = new Annotation("", value + "", ' ', - value); - } + Annotation[] annotations = new Annotation[al.getWidth()]; + + for (int j = 0; j < values.size(); j++) + { + float value = Float.parseFloat(values.get(j).toString()); + annotations[gapmap[j]] = new Annotation("", value + "", ' ', + value); + } - al.addAnnotation(new AlignmentAnnotation(Symname, Visname, - annotations, min, max, winLength)); - }*/ + al.addAnnotation(new AlignmentAnnotation(Symname, Visname, + annotations, min, max, winLength)); + }*/ void parseResult() { - // OutputHeader = output.getText(); - if (result.isFailed()) + int results = 0; // number of result sets received + JobStateSummary finalState = new JobStateSummary(); + try { - OutputHeader += "Job failed.\n"; + for (int j = 0; j < jobs.length; j++) + { + finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]); + if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults()) + { + results++; + } + } } - - if (result.getStatus() != null) + catch (Exception ex) { - OutputHeader += ("\n" + result.getStatus()); - } - if (result.getPredfile() != null) + Cache.log.error("Unexpected exception when processing results for " + + altitle, ex); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + } + if (results > 0) { - OutputHeader += ("\n" + result.getPredfile()); - - // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data + wsInfo.showResultsNewFrame + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed( + java.awt.event.ActionEvent evt) + { + displayResults(true); + } + }); + wsInfo.mergeResults + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed( + java.awt.event.ActionEvent evt) + { + displayResults(false); + } + }); + wsInfo.setResultsReady(); } - - if (result.getAligfile() != null) + else { - OutputHeader += ("\n" + result.getAligfile()); + wsInfo.setFinishedNoResults(); } + } - wsInfo.setProgressText(OutputHeader+"Parsing..."); - - try + void displayResults(boolean newWindow) + { + if (jobs != null) { - jalview.bin.Cache.log.debug("Parsing output from JNet job."); - // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File"); - jalview.io.JPredFile prediction = new jalview.io.JPredFile(result. - getPredfile(), - "Paste"); - SequenceI[] preds = prediction.getSeqsAsArray(); - jalview.bin.Cache.log.debug("Got prediction profile."); - Alignment al; - int FirstSeq; // the position of the query sequence in Alignment al - boolean noMsa = true; // set if no MSA has been returned by JPred - - if ( (this.msa != null) && (result.getAligfile() != null)) + Alignment res = null; + for (int jn = 0; jn < jobs.length; jn++) { - jalview.bin.Cache.log.debug("Getting associated alignment."); - // we ignore the returned alignment if we only predicted on a single sequence - String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(), - "Paste"); + Alignment jobres = null; + JPredJob j = (JPredJob) jobs[jn]; - if (jalview.io.FormatAdapter.isValidFormat(format)) + if (j.hasResults()) { - al = new Alignment(new FormatAdapter().readFile( - result.getAligfile(), "Paste", format)); - SequenceI sqs[] = new SequenceI[al.getHeight()]; - for (int i=0, j=al.getHeight(); i