X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=089b24382672317d66eb780cb6740ebcfb96cd3d;hb=12e7f97678ce85b0238f987d5f4eaf18512a0b94;hp=0d5c22ec9e9c9e3a5f43d823458accaf03e3df9a;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java index 0d5c22e..089b243 100755 --- a/src/jalview/ws/MsaWSClient.java +++ b/src/jalview/ws/MsaWSClient.java @@ -1,468 +1,235 @@ -/* -* 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 ext.vamsas.*; - -import jalview.analysis.AlignSeq; - -import jalview.datamodel.*; - -import jalview.gui.*; - -import java.util.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class MsaWSClient extends WSClient -{ - /** - * server is a WSDL2Java generated stub for an archetypal MsaWSI service. - */ - ext.vamsas.MuscleWS server; - - /** - * Creates a new MsaWSClient object. - * - * @param MsaWSName DOCUMENT ME! - * @param altitle DOCUMENT ME! - * @param msa DOCUMENT ME! - * @param submitGaps DOCUMENT ME! - * @param preserveOrder DOCUMENT ME! - */ - public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, - boolean submitGaps, boolean preserveOrder) - { - if (setWebService(MsaWSName) == false) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The Multiple Sequence Alignment Service named " + MsaWSName + - " is unknown", "Internal Jalview Error", - JOptionPane.WARNING_MESSAGE); - - return; - } - - wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, - WebServiceReference); - - if (!locateWebService()) - { - return; - } - - wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") + - " of " + altitle + "\nJob details\n"); - - MsaWSThread musclethread = new MsaWSThread(WebServiceName + - " alignment of " + altitle, msa, submitGaps, preserveOrder); - wsInfo.setthisService(musclethread); - musclethread.start(); - } - - // JBPNote Nasty object-global state setting methods shouldn't be allowed - private boolean setWebService(String MsaWSName) - { - if (MsaWServices.info.containsKey(MsaWSName)) - { - WebServiceName = MsaWSName; - - String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName); - WsURL = wsinfo[0]; - WebServiceJobTitle = wsinfo[1]; - WebServiceReference = wsinfo[2]; - - return true; - } - else - { - return false; - } - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - private boolean locateWebService() - { - // TODO: MuscleWS transmuted to generic MsaWS client - MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default - - try - { - this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL)); - ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout - } - catch (Exception ex) - { - wsInfo.setProgressText("Serious! " + WebServiceName + - " Service location failed\nfor URL :" + WsURL + "\n" + - ex.getMessage()); - wsInfo.setStatus(wsInfo.ERROR); - ex.printStackTrace(); - - return false; - } - - loc.getEngine().setOption("axis", "1"); - - return true; - } - - protected class MsaWSThread extends Thread implements WSClientI - { - String ServiceName = WebServiceName; - String OutputHeader; - vamsas.objects.simple.MsaResult result = null; - vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet(); - Hashtable SeqNames = null; - boolean submitGaps = false; // and always store and recover sequence order - boolean preserveOrder = true; // and always store and recover sequence order - String jobId; - String alTitle; // name which will be used to form new alignment window. - int allowedServerExceptions = 3; // thread dies if too many exceptions. - boolean jobComplete = false; - - MsaWSThread(String title, SequenceI[] msa, boolean subgaps, - boolean presorder) - { - alTitle = title; - submitGaps = subgaps; - preserveOrder = presorder; - - OutputHeader = wsInfo.getProgressText(); - SeqNames = new Hashtable(); - - vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length]; - - for (int i = 0; i < msa.length; i++) - { - String newname = jalview.analysis.SeqsetUtils.unique_name(i); - - // uniquify as we go - // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation - SeqNames.put(newname, - jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i])); - seqarray[i] = new vamsas.objects.simple.Sequence(); - seqarray[i].setId(newname); - seqarray[i].setSeq((submitGaps) ? msa[i].getSequence() - : AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, msa[i].getSequence())); - } - - this.seqs = new vamsas.objects.simple.SequenceSet(); - this.seqs.setSeqs(seqarray); - } - - public boolean isCancellable() - { - return true; - } - - public void cancelJob() - { - if ((jobId != null) && !jobId.equals("") && !jobComplete) - { - String cancelledMessage = ""; - - try - { - vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId); - - if (cancelledJob.getStatus() == 2) - { - // CANCELLED_JOB - cancelledMessage = "Job cancelled."; - wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK); - jobComplete = true; - jobsRunning--; - result = null; - } - else if (cancelledJob.getStatus() == 3) - { - // VALID UNSTOPPABLE JOB - cancelledMessage += "Server cannot cancel this job. just close the window.\n"; - } - - if (cancelledJob.getJobId() != null) - { - cancelledMessage += ("[" + cancelledJob.getJobId() + - "]"); - } - - cancelledMessage += "\n"; - } - catch (Exception exc) - { - cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" + - exc + "\n"); - exc.printStackTrace(); - } - - wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n"); - } - else - { - if (!jobComplete) - { - wsInfo.setProgressText(OutputHeader + - "Server cannot cancel this job because it has not been submitted properly. just close the window.\n"); - } - } - } - - 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.isRunning()) - { - wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); - } - else if (result.isQueued()) - { - wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); - } - - if (result.isFinished()) - { - parseResult(); - jobComplete = true; - jobsRunning--; - } - else - { - if (result.getStatus() != null) - { - wsInfo.setProgressText(OutputHeader + "\n" + - result.getStatus()); - } - - if (!(result.isJobFailed() || result.isServerError())) - { - Thread.sleep(5000); - - // System.out.println("I'm alive "+seqid+" "+jobid); - } - else - { - break; - } - } - } - catch (Exception ex) - { - allowedServerExceptions--; - wsInfo.appendProgressText("\n" + ServiceName + - " Server exception!\n" + ex.getMessage()); - System.err.println(ServiceName + " Server exception: " + - ex.getMessage()); - - // ex.printStackTrace(); JBPNote Debug - try - { - if (allowedServerExceptions > 0) - { - Thread.sleep(5000); - } - } - catch (InterruptedException ex1) - { - } - } - } - - if (allowedServerExceptions == 0) - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - } - else - { - if (!((result != null) && - (result.isJobFailed() || result.isServerError()))) - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); - } - else - { - if (result.isFailed()) - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - } - - if (result.isServerError()) - { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - } - } - } - } - - void StartJob() - { - try - { - vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs); - - if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) - { - jobId = jobsubmit.getJobId(); - System.out.println(WsURL + " Job Id '" + jobId + "'"); - } - else - { - if (jobsubmit == null) - { - throw new Exception("Server at " + WsURL + - " returned null object, it probably cannot be contacted. Try again later ?"); - } - - throw new Exception(jobsubmit.getJobId()); - } - } - catch (Exception e) - { - // TODO: JBPNote catch timeout or other fault types explicitly - // For unexpected errors - System.err.println(WebServiceName + - "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" + - "When contacting Server:" + WsURL + "\n" + e.toString() + - "\n"); - this.allowedServerExceptions = 0; - wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR); - wsInfo.appendProgressText( - "Failed to submit sequences for alignment.\n" + - "It is most likely that there is a problem with the server.\n" + - "Just close the window\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) - { - 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)); - } - - private jalview.datamodel.Sequence[] getVamsasAlignment( - vamsas.objects.simple.Alignment valign) - { - vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs(); - jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length]; - - for (int i = 0, j = seqs.length; i < j; i++) - msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), - seqs[i].getSeq()); - - return msa; - } - - void parseResult() - { - SequenceI[] seqs = null; - - try - { - // OutputHeader = output.getText(); - if (result.isFailed()) - { - OutputHeader += "Job failed.\n"; - } - - if (result.getStatus() != null) - { - OutputHeader += ("\n" + result.getStatus()); - } - - if (result.getMsa() != null) - { - OutputHeader += "\nAlignment Object Method Notes\n"; - - String[] lines = result.getMsa().getMethod(); - - for (int line = 0; line < lines.length; line++) - OutputHeader += (lines[line] + "\n"); - - // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data - seqs = getVamsasAlignment(result.getMsa()); - } - - wsInfo.setProgressText(OutputHeader); - - if (seqs != null) - { - AlignmentOrder msaorder = new AlignmentOrder(seqs); - - if (preserveOrder) - { - jalview.analysis.AlignmentSorter.recoverOrder(seqs); - } - - jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs); - - Alignment al = new Alignment(seqs); - - // TODO: JBPNote Should also rename the query sequence sometime... - AlignFrame af = new AlignFrame(al); - af.addSortByOrderMenuItem(ServiceName + " Ordering", - msaorder); - - 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 javax.swing.*; + +import ext.vamsas.*; +import jalview.datamodel.*; +import jalview.gui.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class MsaWSClient extends WSClient +{ + /** + * server is a WSDL2Java generated stub for an archetypal MsaWSI service. + */ + ext.vamsas.MuscleWS server; + + AlignFrame alignFrame; + + /** + * Creates a new MsaWSClient object that uses a service given by an externally + * retrieved ServiceHandle + * + * @param sh + * service handle of type AbstractName(MsaWS) + * @param altitle + * DOCUMENT ME! + * @param msa + * DOCUMENT ME! + * @param submitGaps + * DOCUMENT ME! + * @param preserveOrder + * DOCUMENT ME! + */ + + public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, + jalview.datamodel.AlignmentView msa, boolean submitGaps, + boolean preserveOrder, Alignment seqdataset, + AlignFrame _alignFrame) + { + super(); + alignFrame = _alignFrame; + if (!sh.getAbstractName().equals("MsaWS")) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "The Service called \n" + + sh.getName() + + "\nis not a \nMultiple Sequence Alignment Service !", + "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + + return; + } + + if ((wsInfo = setWebService(sh)) == null) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The Multiple Sequence Alignment Service named " + + sh.getName() + " is unknown", + "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + + return; + } + startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); + + } + + public MsaWSClient() + { + super(); + // add a class reference to the list + } + + private void startMsaWSClient(String altitle, AlignmentView msa, + boolean submitGaps, boolean preserveOrder, Alignment seqdataset) + { + if (!locateWebService()) + { + return; + } + + wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") + + " of " + altitle + "\nJob details\n"); + String jobtitle = WebServiceName.toLowerCase(); + if (jobtitle.endsWith("alignment")) + { + if (submitGaps + && (!jobtitle.endsWith("realignment") || jobtitle + .indexOf("profile") == -1)) + { + int pos = jobtitle.indexOf("alignment"); + jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " + + altitle; + } + else + { + jobtitle = WebServiceName + " of " + altitle; + } + } + else + { + jobtitle = WebServiceName + (submitGaps ? " re" : " ") + + "alignment of " + altitle; + } + + MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, + alignFrame, WebServiceName, jobtitle, msa, submitGaps, + preserveOrder, seqdataset); + wsInfo.setthisService(msathread); + msathread.start(); + } + + /** + * Initializes the server field with a valid service implementation. + * + * @return true if service was located. + */ + private boolean locateWebService() + { + // TODO: MuscleWS transmuted to generic MsaWS client + MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default + + try + { + this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL)); + ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute + // timeout + } catch (Exception ex) + { + wsInfo.setProgressText("Serious! " + WebServiceName + + " Service location failed\nfor URL :" + WsURL + "\n" + + ex.getMessage()); + wsInfo.setStatus(WebserviceInfo.ERROR); + ex.printStackTrace(); + + return false; + } + + loc.getEngine().setOption("axis", "1"); + + return true; + } + + protected String getServiceActionKey() + { + return "MsaWS"; + } + + protected String getServiceActionDescription() + { + return "Multiple Sequence Alignment"; + } + + /** + * look at ourselves and work out if we are a service that can take a profile + * and align to it + * + * @return true if we can send gapped sequences to the alignment service + */ + private boolean canSubmitGaps() + { + // TODO: query service or extract service handle props to check if we can + // realign + return (WebServiceName.indexOf("lustal") > -1); // cheat! + } + + public void attachWSMenuEntry(JMenu msawsmenu, + final ServiceHandle serviceHandle, final AlignFrame alignFrame) + { + setWebService(serviceHandle, true); // headless + JMenuItem method = new JMenuItem(WebServiceName); + method.setToolTipText(WsURL); + method.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + AlignmentView msa = alignFrame.gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(), + msa, false, true, alignFrame.getViewport().getAlignment() + .getDataset(), alignFrame); + + } + + }); + msawsmenu.add(method); + if (canSubmitGaps()) + { + // We know that ClustalWS can accept partial alignments for refinement. + final JMenuItem methodR = new JMenuItem(serviceHandle.getName() + + " Realign"); + methodR.setToolTipText(WsURL); + methodR.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + AlignmentView msa = alignFrame.gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(), + msa, true, true, alignFrame.getViewport().getAlignment() + .getDataset(), alignFrame); + + } + + }); + msawsmenu.add(methodR); + + } + + } +}