X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=27130787f8025a217c2dabd41a0e7e67c7d2e980;hb=7be3a744db5213f49e70178ade126d1cc797c762;hp=9f68dca60f6aa918f4994e451b5cbd2ff84b3e91;hpb=7e58cf6fb477265076ae20f33a39e5e1b60a1e0c;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 9f68dca..2713078 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,314 +1,775 @@ -package jalview.ws; - -import org.apache.axis.client.*; -import javax.xml.namespace.QName; -import java.util.*; -import jalview.datamodel.*; -import jalview.gui.*; -import javax.swing.*; -import java.util.*; -import java.awt.*; -import jalview.analysis.AlignSeq; -import ext.vamsas.*; - - -public class JPredClient -{ - int jobsRunning = 0; - ext.vamsas.JpredSoapBindingStub server; - WebserviceInfo wsInfo; - String altitle = ""; - java.util.Hashtable SequenceInfo = null; - public JPredClient(String title, SequenceI[] msf) - { - wsInfo = new WebserviceInfo("JNet secondary structure prediction on "+title, - "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\"."); - - SequenceI seq = msf[0]; - altitle = "JNet prediction on "+seq.getName()+" using "+title; - wsInfo.setProgressText("Job details for MSA based prediction ("+title+") on sequence :\n>" - + seq.getName() + "\n" - + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); - - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); - - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - // JBPNote url will be set from properties - try { - this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred")); - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); - } - - JPredThread jthread = new JPredThread(msf); - jthread.start(); - } - - public JPredClient(SequenceI seq) - { - wsInfo = new WebserviceInfo("JNet secondary structure prediction Job", - "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\"."); - - - wsInfo.setProgressText("Job details for prediction on sequence :\n>" - + seq.getName() + "\n" + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); - altitle = "JNet prediction for sequence "+seq.getName(); - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); -// TODO: put proper url in - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - try { - this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred")); // JBPNote will be set from properties - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); - } - - JPredThread jthread = new JPredThread(seq); - jthread.start(); - } - - - class JPredThread - extends Thread - { - String OutputHeader; - ext.vamsas.JpredResult result; - ext.vamsas.Sequence sequence; - ext.vamsas.Msfalignment msa; - String jobId; - boolean jobComplete = false; - int allowedServerExceptions = 3; // thread dies if too many exceptions. - JPredThread(SequenceI seq) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new ext.vamsas.Sequence(); - this.sequence.setId(seq.getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence())); - } - - JPredThread(SequenceI[] msf) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new ext.vamsas.Sequence(); - this.sequence.setId(msf[0].getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence())); - jalview.io.MSFfile mwrite = new jalview.io.MSFfile(); - this.msa = new ext.vamsas.Msfalignment(); - msa.setMsf(mwrite.print(msf)); - } - - - public void run() - { - - StartJob(); - - while (!jobComplete && (allowedServerExceptions > 0)) - { - try - { - result = server.getresult(jobId); - - if( result.isRunning() ) - wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); - else if( result.isQueued() ) - wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); - - if (result.isFinished()) - { - parseResult(); - jobComplete = true; - jobsRunning--; - } - else - { - wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus()); - if (! (result.isJobFailed() || result.isServerError())) - { - Thread.sleep(5000); - // System.out.println("I'm alive "+seqid+" "+jobid); - } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - } - } - } - catch (Exception ex) - { - allowedServerExceptions--; - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage()); - } - } - - if (! (result.isJobFailed() || result.isServerError())) - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); - else - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - } - - void StartJob() - { - try - { - if (msa!=null) { - jobId = server.predictOnMsa(msa); - } else { - jobId = server.predict(sequence); - } - System.out.println(jobId); - } - catch (Exception e) - { - System.out.println("JPredWS Client: Failed to submit the prediction\n" + - e.toString() + "\n"); - e.printStackTrace(); - } - } - - 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() - { - // OutputHeader = output.getText(); - if (result.isFailed()) { - OutputHeader +="Job failed.\n"; - } - if (result.getStatus()!=null) { - OutputHeader += "\n"+result.getStatus(); - } - if (result.getPredfile()!=null) { - 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 - } - if (result.getAligfile()!=null) { - OutputHeader += "\n"+result.getAligfile(); - } - wsInfo.setProgressText(OutputHeader); - try { - // 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(); - 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) { - // we ignore the returned alignment if we only predicted on a single sequence - String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste"); - if (jalview.io.FormatAdapter.formats.contains(format)) - { - al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format)); - noMsa = false; - FirstSeq = 0; - } - 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!")); - - AlignmentAnnotation annot; - Annotation [] annotations = null; - int i = 0; - int width = preds[0].getSequence().length(); - - - int[] gapmap = al.getSequenceAt(FirstSeq).gapMap(); - - if (gapmap.length!=width) { - throw (new Exception("Jnet Client Error\nNumber of residues in supposed query sequence :\n" - +al.getSequenceAt(FirstSeq).getName()+"\n" - +al.getSequenceAt(FirstSeq).getSequence() - +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n")); - } - // JBPNote Should also rename the query sequence sometime... - i=0; - while (i < preds.length) - { - String id = preds[i].getName().toUpperCase(); - if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) - { - annotations = new Annotation[al.getWidth()]; - - if(id.equals("JNETPRED") - || id.equals("JNETPSSM") - || id.equals("JNETFREQ") - || id.equals("JNETHMM") - || id.equals("JNETALIGN") - || id.equals("JPRED")) - { - for (int j = 0; j < width; j++) - annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0); - } - else if(id.equals("JNETCONF")) - { - for (int j = 0; j < width; j++) - { - float value = Float.parseFloat(preds[i].getCharAt(j)+""); - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value); - } - } - else - { - for (int j = 0; j < width; j++) { - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0); - } - } - - if(id.equals("JNETCONF")) - annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", - annotations,0f,10f,1); - - else annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", - annotations); - al.addAnnotation(annot); - if (noMsa) - al.deleteSequence(preds[i]); - } - i++; - } - - Hashtable scores = prediction.getScores(); - /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), - "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); - - addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"), - "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1); - - addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"), - "JnetpropC", "Jnet Coil Propensity", 0f,1f,1); - */ - AlignFrame af = new AlignFrame(al); - - - Desktop.addInternalFrame(af, - altitle, - AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); - }catch(Exception ex){ex.printStackTrace();} - - } - - } -} - +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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 + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.ws; + +import java.util.*; + +import javax.swing.*; + +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) { + super(); + wsInfo=setWebService(sh); + startJPredClient(title, msa, alview, parentFrame); + + } + /** + * startJPredClient + * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs + * TODO: sequence representative support - could submit alignment of representatives as msa. + * TODO: msa hidden region prediction - submit each chunk for prediction. concatenate results of each. + * TODO: single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs) + * @param title String + * @param msa boolean + * @param alview AlignmentView + */ + private void startJPredClient(String title, boolean msa, + jalview.datamodel.AlignmentView alview, AlignFrame parentFrame) + { + AlignmentView input = alview; + if (wsInfo == null) + { + wsInfo = setWebService(); + } + Jpred server = locateWebService(); + if (server == null) + { + Cache.log.warn("Couldn't find a Jpred webservice to invoke!"); + return; + } + + SeqCigar[] msf = input.getSequences(); + SequenceI seq = msf[0].getSeq('-'); + if (msa && msf.length > 1) + { + + String altitle = "JNet prediction on " + 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++) + { + aln[i] = msf[i].getSeq('-'); + } + + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true); + + JPredThread jthread = new JPredThread(wsInfo, altitle, server, + SequenceInfo, aln, alview, parentFrame); + wsInfo.setthisService(jthread); + jthread.start(); + } + else + { + 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() + + " from " + + title; + + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash( + seq); + + JPredThread jthread = new JPredThread(wsInfo, altitle, server, + SequenceInfo, seq, alview, parentFrame); + wsInfo.setthisService(jthread); + jthread.start(); + } + } + 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) + { + wsInfo = setWebService(sh); + startJPredClient(title, msa, parentFrame); + } + + public JPredClient(String title, SequenceI[] msf) + { + startJPredClient(title, msf, null); + } + + public JPredClient(String title, SequenceI seq) + { + startJPredClient(title, seq, null); + } + + private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame) + { + if (wsInfo == null) + { + wsInfo = setWebService(); + } + + SequenceI seq = msf[0]; + + String altitle = "JNet prediction on " + 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++) + { + aln[i] = new jalview.datamodel.Sequence(msf[i]); + } + + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true); + + Jpred server = locateWebService(); + if (server==null) + { + return; + } + + JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame); + wsInfo.setthisService(jthread); + jthread.start(); + } + + public void startJPredClient(String title, SequenceI seq, AlignFrame parentFrame) + { + if (wsInfo == null) + { + wsInfo = setWebService(); + } + 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() + " from " + + title; + + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + + Jpred server = locateWebService(); + if (server==null) + { + return; + } + + JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame); + wsInfo.setthisService(jthread); + jthread.start(); + } + + private WebserviceInfo setWebService() + { + WebServiceName = "JNetWS"; + WebServiceJobTitle = "JNet secondary structure prediction"; + WebServiceReference = + "\"Cuff J. A and Barton G.J (2000) Application of " + + "multiple sequence alignment profiles to improve protein secondary structure prediction, " + + "Proteins 40:502-511\"."; + WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; + + WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle, + WebServiceReference); + + return wsInfo; + } + + private ext.vamsas.Jpred locateWebService() + { + ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default + 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)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE); + + } + catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The Secondary Structure Prediction Service named " + + WebServiceName + " at " + WsURL + + " couldn't be located.", + "Internal Jalview Error", + JOptionPane.WARNING_MESSAGE); + wsInfo.setProgressText("Serious! " + WebServiceName + + " Service location failed\nfor URL :" + WsURL + + "\n" + + ex.getMessage()); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + + } + + 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); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";// + } + + 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, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + } 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]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));//gapMap returns insert list, interpreted as delete list by pruneDeletions + } + } + af = new AlignFrame(res, (ColumnSelection) alandcolsel[1], + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + Desktop.addInternalFrame(af, altitle, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_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; + } + + } +} +