X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FJPredClient.java;h=2475fb1ec6ddd587c8ff1d1fab5ee4f07f0f3405;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=d7e75f4ccc3f1ecdf9c546f6c86262d6597670e3;hpb=89a0b775abfaa90242a171ca8133784a424a3d7b;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index d7e75f4..2475fb1 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,688 +1,320 @@ -/* - * 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.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 -{ - AlignFrame parentFrame=null; - /** - * 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) { - wsInfo=setWebService(sh); - this.parentFrame=parentFrame; - startJPredClient(title, msa, alview); - - } - - /** - * startJPredClient - * - * @param title String - * @param msa boolean - * @param alview AlignmentView - */ - private void startJPredClient(String title, boolean msa, - jalview.datamodel.AlignmentView alview) - { - } - - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame) - { - wsInfo = setWebService(sh); - this.parentFrame=parentFrame; - startJPredClient(title, seq); - } - - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame) - { - wsInfo = setWebService(sh); - this.parentFrame=parentFrame; - 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]; - - 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); - wsInfo.setthisService(jthread); - 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"); - 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); - 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 - boolean noMsa = true; // set if no MSA has been returned by JPred - - 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.")); - } - - 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!")); - } - } - - al.setDataset(null); - - jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, - noMsa); - 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) { - this.altitle = altitle; - this.server = server; - this.wsInfo = wsinfo; - } - -// String OutputHeader; -// vamsas.objects.simple.JpredResult result; - - JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq) - { - this(wsinfo, altitle, server); - 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) - { - this(wsinfo, altitle, server); - 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); - } - - 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) - { - if (jobs != null) - { - Alignment res = null; - for (int jn = 0; jn < jobs.length; jn++) - { - Alignment jobres = null; - JPredJob j = (JPredJob) jobs[jn]; - - if (j.hasResults()) - { - 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 - } - } - 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 = new AlignFrame(res); - Desktop.addInternalFrame(af, altitle, - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_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; - } - - } -} - +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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.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 = "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; + } +}