X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=863e80e2c166f7de7471fa331ac92207239bcb02;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=04a6101f3196bd7a77884f81ee625a2b3660a8ae;hpb=cbccf5d4e522cfcbe4f61609cee61f7128f183ec;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 04a6101..863e80e 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,505 +1,299 @@ -/* - * 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 java.util.*; - -import javax.swing.*; - -import ext.vamsas.*; -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.gui.*; - -public class JPredClient - extends WSClient -{ - ext.vamsas.Jpred server; - String altitle = ""; - java.util.Hashtable SequenceInfo = null; - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) { - wsInfo = setWebService(sh); - startJPredClient(title, seq); - } - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) { - wsInfo = setWebService(sh); - startJPredClient(title, msa); - } - - public JPredClient(String title, SequenceI[] msf) { - startJPredClient(title, msf); - } - - public JPredClient(String title, SequenceI seq) { - startJPredClient(title, seq); - } - - private void startJPredClient(String title, SequenceI[] msf) - { - if (wsInfo==null) - 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(); - } - - public void startJPredClient(String title, SequenceI seq) - { - if (wsInfo==null) - 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); - - 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() - { - ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // 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 - { - String OutputHeader; - vamsas.objects.simple.JpredResult result; - vamsas.objects.simple.Sequence sequence; - vamsas.objects.simple.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 vamsas.objects.simple.Sequence(); - this.sequence.setId(seq.getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence())); - } - - JPredThread(SequenceI[] msf) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new vamsas.objects.simple.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 vamsas.objects.simple.Msfalignment(); - msa.setMsf(mwrite.print(msf)); - } - - 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.Jalview.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) - { - } - } - } - - 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); - } - - 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) - { - 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"); - - jalview.bin.Jalview.log.debug("Failed Submission",e); - } - } - - - - 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) - { - jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction."); - jalview.bin.Jalview.log.debug(ex); - } - } - } -} +/* + * 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 + * @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 1) + { + + String altitle = "JNet prediction 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 = "JNet prediction 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(); + } + } + 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.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; + } +} +