X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=674743e875533493be242e56dcde215f906158ac;hb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;hp=9f68dca60f6aa918f4994e451b5cbd2ff84b3e91;hpb=7e58cf6fb477265076ae20f33a39e5e1b60a1e0c;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 9f68dca..674743e 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,3 +1,22 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 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 org.apache.axis.client.*; @@ -11,304 +30,424 @@ import java.awt.*; import jalview.analysis.AlignSeq; import ext.vamsas.*; - public class JPredClient + extends WSClient { - int jobsRunning = 0; - ext.vamsas.JpredSoapBindingStub server; - WebserviceInfo wsInfo; + ext.vamsas.JPredWS server; String altitle = ""; java.util.Hashtable SequenceInfo = null; - public JPredClient(String title, SequenceI[] msf) + private WebserviceInfo setWebService() { - 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"); + WebServiceName = "JNetWS"; + WebServiceJobTitle = "JNet secondary structure prediction"; + WebServiceReference = + "\"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\"."; + WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; + WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle, + WebServiceReference); + + return wsInfo; + } - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + private boolean locateWebService() + { - 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()); + JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default + try + { + this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties + ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub + } + 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(wsInfo.STATE_STOPPED_SERVERERROR); + return false; + } + return true; } - 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()); + public JPredClient(String title, SequenceI[] msf) + { + wsInfo = setWebService(); + SequenceI seq = msf[0]; + 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"); + + SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + if (!locateWebService()) + return; + + JPredThread jthread = new JPredThread(msf); + jthread.start(); } - JPredThread jthread = new JPredThread(seq); - jthread.start(); - } + public JPredClient(String title, SequenceI seq) + { + wsInfo = setWebService(); + wsInfo.setProgressText("Job details for prediction on sequence :\n>" + + seq.getName() + "\n" + + AlignSeq.extractGaps("-. ", seq.getSequence()) + + "\n"); + altitle = "JNet prediction for sequence " + seq.getName() + " from " + + title; + SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); - 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())); - } + if (!locateWebService()) + return; - 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)); + JPredThread jthread = new JPredThread(seq); + jthread.start(); } - - public void run() + 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())); + } - StartJob(); + 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.PileUpfile mwrite = new jalview.io.PileUpfile(); + this.msa = new ext.vamsas.Msfalignment(); + msa.setMsf(mwrite.print(msf)); + } - while (!jobComplete && (allowedServerExceptions > 0)) + public void run() { - try - { - result = server.getresult(jobId); - if( result.isRunning() ) - wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); - else if( result.isQueued() ) - wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); + StartJob(); - if (result.isFinished()) + while (!jobComplete && (allowedServerExceptions > 0)) + { + try { - parseResult(); - jobComplete = true; - jobsRunning--; + if ( (result = server.getresult(jobId)) == null) + { + throw (new Exception( + "Timed out when communicating with server\nTry again later.\n")); + } + + 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())) + { + try + { + Thread.sleep(5000); + } + catch (InterruptedException ex1) + { + } + // System.out.println("I'm alive "+seqid+" "+jobid); + } + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + } + } } - else + catch (Exception ex) { - wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus()); - if (! (result.isJobFailed() || result.isServerError())) + allowedServerExceptions--; + wsInfo.appendProgressText("\nJPredWS Server exception!\n" + + ex.getMessage()); + try + { + if (allowedServerExceptions > 0) + { + Thread.sleep(5000); + } + } + catch (InterruptedException ex1) { - Thread.sleep(5000); - // System.out.println("I'm alive "+seqid+" "+jobid); - } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } } } - catch (Exception ex) + + if (! (result.isJobFailed() || result.isServerError())) { - allowedServerExceptions--; - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage()); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); } - } - - 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); + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } - 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++) + void StartJob() { - 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)) + try + { + if (msa != null) { - al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format)); - noMsa = false; - FirstSeq = 0; + jobId = server.predictOnMsa(msa); } else { - throw (new Exception("Unknown format 'format' for file : \n" + - result.getAligfile())); + jobId = server.predict(sequence); + } + if (jobId != null) + { + if (jobId.startsWith("Broken")) + { + throw new Exception("Submission " + jobId); + } + else + { + System.out.println(WsURL + " Job Id '" + jobId + "'"); + } } + else + { + throw new Exception("Server timed out - try again later\n"); - } else { - al = new Alignment(preds); - FirstSeq = prediction.getQuerySeqPosition(); + } } + catch (Exception e) + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + allowedServerExceptions = 0; + jobComplete = false; + wsInfo.appendProgressText("Failed to submit the prediction: " + + e.toString() + "\nJust close the window\n"); + System.err.println( + "JPredWS Client: Failed to submit the prediction\n" + + e.toString() + "\n"); + // e.printStackTrace(); TODO: JBPNote DEBUG + } + } - 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(); - + private void addFloatAnnotations(Alignment al, int[] gapmap, + Vector values, String Symname, + String Visname, float min, float max, + int winLength) + { - int[] gapmap = al.getSequenceAt(FirstSeq).gapMap(); + 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)); + } - 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")); + void parseResult() + { + // OutputHeader = output.getText(); + if (result.isFailed()) + { + OutputHeader += "Job failed.\n"; + } + if (result.getStatus() != null) + { + OutputHeader += "\n" + result.getStatus(); } - // JBPNote Should also rename the query sequence sometime... - i=0; - while (i < preds.length) + if (result.getPredfile() != null) { - String id = preds[i].getName().toUpperCase(); - if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) + 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) { - annotations = new Annotation[al.getWidth()]; - - if(id.equals("JNETPRED") - || id.equals("JNETPSSM") - || id.equals("JNETFREQ") - || id.equals("JNETHMM") - || id.equals("JNETALIGN") - || id.equals("JPRED")) + // 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)) { - for (int j = 0; j < width; j++) - annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0); + al = new Alignment(jalview.io.FormatAdapter.readFile(result. + getAligfile(), "Paste", format)); + noMsa = false; + FirstSeq = 0; } - else if(id.equals("JNETCONF")) + else { - 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); - } + throw (new Exception("Unknown format 'format' for file : \n" + + result.getAligfile())); } - else + + } + 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")) { - for (int j = 0; j < width; j++) { - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0); + 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); } - } - 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]); + else + { + annot = new AlignmentAnnotation(preds[i].getName(), + "JNet Output", + annotations); + } + al.addAnnotation(annot); + if (noMsa) + { + al.deleteSequence(preds[i]); + } + } + i++; } - i++; - } - Hashtable scores = prediction.getScores(); - /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), - "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); + 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("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); + 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(); + } - Desktop.addInternalFrame(af, - altitle, - AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); - }catch(Exception ex){ex.printStackTrace();} + } } - } -} -