X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=3add58d8f47341ea3d6ce7e5a44e939b192d9dbf;hb=7d4f1d8e997964bef5c351d04fbdafe4401cf5d7;hp=9f68dca60f6aa918f4994e451b5cbd2ff84b3e91;hpb=7e58cf6fb477265076ae20f33a39e5e1b60a1e0c;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 9f68dca..3add58d 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,314 +1,391 @@ -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 (Version 2.4) + * Copyright (C) 2008 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.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.*; + +import javax.swing.*; + +import ext.vamsas.*; +import jalview.analysis.*; +import jalview.bin.*; +import jalview.datamodel.*; +import jalview.gui.*; + +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 + * @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, viewonly); + + } + + /** + * 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 + * @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, + boolean viewonly) + { + 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 = 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 + + 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 = getPredictionName(WebServiceName) + " on " + + (viewonly ? "visible " : "") + seq.getName() + + " using alignment from " + title; + + 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); + 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, delMap, alview, parentFrame, WsURL); + 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."); + } + + String altitle = getPredictionName(WebServiceName) + " for " + + (viewonly ? "visible " : "") + "sequence " + seq.getName() + + " from " + title; + String seqname = seq.getName(); + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils + .SeqCharacterHash(seq); + 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(); + } + } + + private String getPredictionName(String webServiceName) + { + if (webServiceName.toLowerCase().indexOf( + "secondary structure prediction") > -1) + { + return webServiceName; + } + else + { + return webServiceName + "secondary structure prediction"; + } + } + + 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); + } + + public JPredClient() + { + + super(); + // add a class reference to the list + } + + 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.getSequenceAsString()) + + "\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, null, parentFrame, WsURL); + 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.getSequenceAsString()) + + "\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, WsURL, + SequenceInfo, seq, null, 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; + } + + public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, + final AlignFrame af) + { + final JMenuItem method = new JMenuItem(sh.getName()); + method.setToolTipText(sh.getEndpointURL()); + method.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction(); + if (msa.getSequences().length == 1) + { + // Single Sequence prediction + new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af, + true); + } + else + { + if (msa.getSequences().length > 1) + { + // Sequence profile based prediction + new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af, + true); + } + } + } + }); + wsmenu.add(method); + } +}