X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=2475fb1ec6ddd587c8ff1d1fab5ee4f07f0f3405;hb=ad52f1ddcaefa09c6a3e85329b28dad155613f49;hp=366c90a10f6284a5e5759b614924e5ed835506ab;hpb=998f8c437ca6ea5f76e261ef544e90ebee632f78;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 366c90a..2475fb1 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 @@ -26,30 +26,29 @@ import ext.vamsas.*; import jalview.analysis.*; import jalview.bin.*; import jalview.datamodel.*; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentView; import jalview.gui.*; -import jalview.io.*; -import jalview.util.*; -import jalview.ws.WSThread.*; -import vamsas.objects.simple.*; public class JPredClient extends WSClient { - /** - * crate a new GUI JPred Job - * @param sh ServiceHandle - * @param title String - * @param msa boolean - true - submit alignment as a sequence profile - * @param alview AlignmentView - */ - public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) { + /** + * crate a new GUI JPred Job + * @param sh ServiceHandle + * @param title String + * @param msa boolean - true - submit alignment as a sequence profile + * @param alview AlignmentView + * @param viewonly TODO + */ + public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, + AlignmentView alview, AlignFrame parentFrame, + boolean viewonly) + { super(); - wsInfo=setWebService(sh); - startJPredClient(title, msa, alview, parentFrame); + wsInfo = setWebService(sh); + startJPredClient(title, msa, alview, parentFrame, viewonly); } + /** * startJPredClient * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs @@ -59,9 +58,11 @@ public class JPredClient * @param title String * @param msa boolean * @param alview AlignmentView + * @param viewonly if true then the prediction will be made just on the concatenated visible regions */ private void startJPredClient(String title, boolean msa, - jalview.datamodel.AlignmentView alview, AlignFrame parentFrame) + jalview.datamodel.AlignmentView alview, + AlignFrame parentFrame, boolean viewonly) { AlignmentView input = alview; if (wsInfo == null) @@ -74,20 +75,49 @@ public class JPredClient Cache.log.warn("Couldn't find a Jpred webservice to invoke!"); return; } + SeqCigar[] msf = null; + SequenceI seq = null; + int[] delMap = null; + // original JNetClient behaviour - submit full length of sequence or profile + // and mask result. + msf = input.getSequences(); + seq = msf[0].getSeq('-'); + + if (viewonly) + { + int[] viscontigs = alview.getVisibleContigs(); + int spos = 0; + int i = 0; + if (viscontigs != null) + { + // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence - SeqCigar[] msf = input.getSequences(); - SequenceI seq = msf[0].getSeq('-'); + delMap = new int[seq.getEnd() - seq.getStart() + 1]; + int gapMap[] = seq.gapMap(); + for (int contig = 0; contig < viscontigs.length; contig += 2) + { + + while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) + { + spos++; + } + while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) + { + delMap[i++] = spos++; + } + } + int tmap[] = new int[i]; + System.arraycopy(delMap, 0, tmap, 0, i); + delMap = tmap; + } + } if (msa && msf.length > 1) { - String altitle = "JNet prediction on " + seq.getName() + + String altitle = "JNet prediction on " + (viewonly ? "visible " : "") + + seq.getName() + " using alignment from " + title; - wsInfo.setProgressText("Job details for MSA based prediction (" + - title + ") on sequence :\n>" + seq.getName() + - "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + - "\n"); SequenceI aln[] = new SequenceI[msf.length]; for (int i = 0, j = msf.length; i < j; i++) { @@ -95,41 +125,72 @@ public class JPredClient } Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true); - + if (viewonly) + { + // Remove hidden regions from sequence objects. + String seqs[] = alview.getSequenceStrings('-'); + for (int i = 0, j = msf.length; i < j; i++) + { + aln[i].setSequence(seqs[i]); + } + seq.setSequence(seqs[0]); + } + wsInfo.setProgressText("Job details for " + (viewonly ? "visible " : "") + + "MSA based prediction (" + + title + ") on sequence :\n>" + seq.getName() + + "\n" + + AlignSeq.extractGaps("-. ", + seq.getSequenceAsString()) + + "\n"); JPredThread jthread = new JPredThread(wsInfo, altitle, server, - SequenceInfo, aln, alview, parentFrame); + SequenceInfo, aln, delMap, alview, + parentFrame, WsURL); wsInfo.setthisService(jthread); jthread.start(); } else { - if (!msa && msf.length>1) + if (!msa && msf.length > 1) + { throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported."); - wsInfo.setProgressText("Job details for prediction on sequence :\n>" + - seq.getName() + "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + - "\n"); - String altitle = "JNet prediction for sequence " + seq.getName() + + } + String altitle = "JNet prediction for " + (viewonly ? "visible " : "") + + "sequence " + seq.getName() + " from " + title; - + String seqname = seq.getName(); Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash( seq); - - JPredThread jthread = new JPredThread(wsInfo, altitle, server, - SequenceInfo, seq, alview, parentFrame); + if (viewonly) + { + // Remove hidden regions from input sequence + String seqs[] = alview.getSequenceStrings('-'); + seq.setSequence(seqs[0]); + } + wsInfo.setProgressText("Job details for prediction on " + + (viewonly ? "visible " : "") + "sequence :\n>" + + seqname + "\n" + + AlignSeq.extractGaps("-. ", + seq.getSequenceAsString()) + + "\n"); + JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, + SequenceInfo, seq, delMap, alview, + parentFrame); wsInfo.setthisService(jthread); jthread.start(); } } - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame) + + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, + AlignFrame parentFrame) { super(); wsInfo = setWebService(sh); startJPredClient(title, seq, parentFrame); } - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame) + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, + AlignFrame parentFrame) { wsInfo = setWebService(sh); startJPredClient(title, msa, parentFrame); @@ -145,7 +206,8 @@ public class JPredClient startJPredClient(title, seq, null); } - private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame) + private void startJPredClient(String title, SequenceI[] msf, + AlignFrame parentFrame) { if (wsInfo == null) { @@ -159,7 +221,7 @@ public class JPredClient wsInfo.setProgressText("Job details for MSA based prediction (" + title + ") on sequence :\n>" + seq.getName() + "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n"); SequenceI aln[] = new SequenceI[msf.length]; for (int i = 0, j = msf.length; i < j; i++) @@ -170,17 +232,19 @@ public class JPredClient Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true); Jpred server = locateWebService(); - if (server==null) + if (server == null) { return; } - JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame); + JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, + aln, null, null, parentFrame, WsURL); wsInfo.setthisService(jthread); jthread.start(); } - public void startJPredClient(String title, SequenceI seq, AlignFrame parentFrame) + public void startJPredClient(String title, SequenceI seq, + AlignFrame parentFrame) { if (wsInfo == null) { @@ -188,7 +252,7 @@ public class JPredClient } wsInfo.setProgressText("Job details for prediction on sequence :\n>" + seq.getName() + "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n"); String altitle = "JNet prediction for sequence " + seq.getName() + " from " + title; @@ -196,12 +260,14 @@ public class JPredClient Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); Jpred server = locateWebService(); - if (server==null) + if (server == null) { return; } - JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame); + JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, + SequenceInfo, seq, null, null, + parentFrame); wsInfo.setthisService(jthread); jthread.start(); } @@ -225,11 +291,11 @@ public class JPredClient private ext.vamsas.Jpred locateWebService() { ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default - ext.vamsas.Jpred server=null; + ext.vamsas.Jpred server = null; try { server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties - ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub + ( (JpredSoapBindingStub) server).setTimeout(60000); // one minute stub //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE); } @@ -251,520 +317,4 @@ public class JPredClient return server; } - - class JPredThread - extends WSThread - implements WSClientI - { - class JPredJob - extends WSThread.WSJob - { - - 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; - } - - boolean hasValidInput() - { - if (sequence != null) - { - return true; - } - return false; - } - - public Alignment getResultSet() - throws Exception - { - if (result == null || !result.isFinished()) - { - return null; - } - Alignment al = null; - int FirstSeq = -1; // the position of the query sequence in Alignment al - - 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)) - { - 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.")); - } - - FirstSeq = 0; - al.setDataset(null); - - jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, - false); - - } - else - { - throw (new Exception( - "Unknown format "+format+" for file : \n" + - result.getAligfile())); - } - } - else - { - al = new Alignment(preds); - FirstSeq = prediction.getQuerySeqPosition(); - if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( - al.getSequenceAt(FirstSeq), SequenceInfo)) - { - throw (new Exception( - "Couldn't recover sequence properties for JNet Query sequence!")); - } else { - al.setDataset(null); - jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, - true); - } - } - - 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) - { - 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, AlignmentView alview, AlignFrame alframe) { - this.altitle = altitle; - this.server = server; - this.wsInfo = wsinfo; - this.input = alview; - this.alignFrame = alframe; - } - -// String OutputHeader; -// vamsas.objects.simple.JpredResult result; - - JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq, AlignmentView alview, AlignFrame alframe) - { - this(wsinfo, altitle, server,alview, alframe); - 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, AlignmentView alview, AlignFrame alframe) - { - this(wsinfo, altitle, server,alview, alframe); - 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); - } - - 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 - { - if (allowedServerExceptions > 0) - { - Thread.sleep(5000); - } - } - 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(WSJob j) - { - if (! (j instanceof JPredJob)) - { - throw new Error("Implementation error - StartJob(JpredJob) called on " + - j.getClass()); - } - try - { - JPredJob job = (JPredJob) j; - if (job.msa != null) - { - job.jobId = server.predictOnMsa(job.msa); - } - else - if (job.sequence!=null) - { - job.jobId = server.predict(job.sequence); - } - - if (job.jobId != null) - { - if (job.jobId.startsWith("Broken")) - { - job.result = (vamsas.objects.simple.Result)new JpredResult(); - job.result.setInvalid(true); - job.result.setStatus("Submission " + job.jobId); - } - else - { - job.submitted = true; - job.subjobComplete = false; - Cache.log.info(WsURL + " Job Id '" + job.jobId + "'"); - } - } - else - { - throw new Exception("Server timed out - try again later\n"); - } - } - catch (Exception e) - { - 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(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR); - // JBPNote - this could be a popup informing the user of the problem. - wsInfo.appendProgressText(j.jobnum, - "Failed to submit the prediction:\n" - + e.getMessage() + - wsInfo.getProgressText()); - - jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e); - - } - 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++) - { - 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)); - }*/ - - void parseResult() - { - int results = 0; // number of result sets received - JobStateSummary finalState = new JobStateSummary(); - try - { - 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++; - } - } - } - catch (Exception ex) - { - - Cache.log.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() - { - 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(); - } - else - { - wsInfo.setFinishedNoResults(); - } - } - - void displayResults(boolean newWindow) - { - // TODO: cope with multiple subjobs. - if (jobs != null) - { - Alignment res = null; - boolean msa=false; - for (int jn = 0; jn < jobs.length; jn++) - { - Alignment jobres = null; - JPredJob j = (JPredJob) jobs[jn]; - - if (j.hasResults()) - { - // hack - we only deal with all single seuqence predictions or all profile predictions - msa = (j.msa!=null) ? true : msa; - try - { - jalview.bin.Cache.log.debug("Parsing output of job " + jn); - jobres = j.getResultSet(); - jalview.bin.Cache.log.debug("Finished parsing output."); - if (jobs.length==1) - res = jobres; - else { - // do merge with other job results - throw new Error("Multiple JNet subjob merging not yet implemented."); - } - } - catch (Exception e) - { - jalview.bin.Cache.log.error( - "JNet Client: JPred Annotation Parse Error", - e); - wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR); - wsInfo.appendProgressText(j.jobnum, - OutputHeader + "\n" + - j.result.getStatus() + - "\nInvalid JNet job result data!\n" + - e.getMessage()); - j.result.setBroken(true); - } - } - } - - if (res != null) - { - if (newWindow) - { - AlignFrame af; - if (input==null) { - af = new AlignFrame(res); - } else { - java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter()); - - if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) { - if (msa) { - throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!"); - } else { - // test this. - ((ColumnSelection) alandcolsel[1]).compensateForEdits(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap())); - } - } - af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]); - } - Desktop.addInternalFrame(af, altitle, - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); - } - else - { - Cache.log.info("Append results onto existing alignment."); - } - } - } - } - void pollJob(WSJob job) - throws Exception - { - job.result = server.getresult(job.jobId); - } - public boolean isCancellable() - { - return false; - } - - public void cancelJob() - { - throw new Error("Implementation error!"); - } - - public boolean canMergeResults() - { - return false; - } - - } } -