X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=e6f3899892a6058fff4b0021eb61e9528582b67f;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=2eecf46963f042df7f59b97c9504799cdd451398;hpb=61b0b38d322aef9105cc564d3f5340fd529039ba;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 2eecf46..e6f3899 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,69 +1,128 @@ +/* + * 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.*; -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.*; +import ext.vamsas.*; +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.gui.*; 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(SequenceI[] msf) + public JPredClient(String title, SequenceI[] msf) { - 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 = setWebService(); SequenceI seq = msf[0]; - wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : " - + seq.getName() + "\nSequence : " - + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); + 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"); - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - try { - this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); + SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + + if (!locateWebService()) + { + return; } JPredThread jthread = new JPredThread(msf); jthread.start(); } - public JPredClient(SequenceI seq) + public JPredClient(String title, 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 = 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); - wsInfo.setProgressText("Job details for prediction on sequence :\nName : " - + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); - - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - try { - this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); + if (!locateWebService()) + { + return; } JPredThread jthread = new JPredThread(seq); jthread.start(); } + private WebserviceInfo setWebService() + { + 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; + } + + private boolean locateWebService() + { + 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; + } class JPredThread extends Thread @@ -75,12 +134,13 @@ public class JPredClient 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())); + this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence())); } JPredThread(SequenceI[] msf) @@ -88,28 +148,36 @@ public class JPredClient 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.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)); } - public void run() { - StartJob(); while (!jobComplete && (allowedServerExceptions > 0)) { try { - result = server.getresult(jobId); + 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.isRunning()) + { + wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); + } + else if (result.isQueued()) + { + wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); + } if (result.isFinished()) { @@ -119,12 +187,23 @@ public class JPredClient } else { - wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus()); + wsInfo.setProgressText(OutputHeader + "\n" + + result.getStatus()); + if (! (result.isJobFailed() || result.isServerError())) { - Thread.sleep(5000); + try + { + Thread.sleep(5000); + } + catch (InterruptedException ex1) + { + } + // System.out.println("I'm alive "+seqid+" "+jobid); - } else { + } + else + { wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } } @@ -132,173 +211,271 @@ public class JPredClient catch (Exception ex) { allowedServerExceptions--; - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage()); + wsInfo.appendProgressText("\nJPredWS Server exception!\n" + + ex.getMessage()); + + try + { + if (allowedServerExceptions > 0) + { + Thread.sleep(5000); + } + } + catch (InterruptedException ex1) + { + } } } if (! (result.isJobFailed() || result.isServerError())) + { wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); + } else + { wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + } } void StartJob() { try { - if (msa!=null) { + if (msa != null) + { jobId = server.predictOnMsa(msa); - } else { + } + else + { jobId = server.predict(sequence); } - System.out.println(jobId); + + 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"); + } } catch (Exception e) { - System.out.println("JPredWS Client: Failed to submit the prediction\n" + - e.toString() + "\n"); - e.printStackTrace(); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + allowedServerExceptions = 0; + jobComplete = false; + + wsInfo.appendProgressText("Failed to submit the prediction.\n" + + + "It is most likely that there is a problem with the server.\n" + + "Just close the window\n"); + System.err.println( + "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" + + e.toString() + "\n"); + + // e.printStackTrace(); TODO: JBPNote DEBUG } } - private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) { - + 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); + 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()) { - OutputHeader +="Job failed.\n"; + if (result.isFailed()) + { + OutputHeader += "Job failed.\n"; } - if (result.getStatus()!=null) { - OutputHeader += "\n"+result.getStatus(); + + 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.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(); + + if (result.getAligfile() != null) + { + OutputHeader += ("\n" + result.getAligfile()); } + wsInfo.setProgressText(OutputHeader); - try { + + try + { // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File"); - jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste"); + 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) { + 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"); + 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)); + 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())); + 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; + 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("Jpred 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")); + + 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; + i = 0; + while (i < preds.length) { String id = preds[i].getName().toUpperCase(); - if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) + + 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")) + 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); + { + annotations[gapmap[j]] = new Annotation("", "", + preds[i].getCharAt(j), 0); + } } - else if(id.equals("JNETCONF")) + 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); + 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); + for (int j = 0; j < width; j++) + { + annotations[gapmap[j]] = new Annotation(preds[i].getCharAt( + j) + "", "", ' ', 0); } } - if(id.equals("JNETCONF")) + if (id.equals("JNETCONF")) + { annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", - annotations,0f,10f,1); + "JNet Output", annotations, 0f, + 10f, 1); + } + else + { + annot = new AlignmentAnnotation(preds[i].getName(), + "JNet Output", annotations); + } - 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("JNETPROPH"), + "JnetpropH", "Jnet Helix 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("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, - "JNet Prediction for sequence ", - 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(); + } } - } } -