+/*
+ * 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 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 vamsas.objects.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+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;
-
- 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;
- }
- }
-
-
- public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
+ /**
+ * 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)
{
- if (setWebService(MsaWSName)==false) {
- JOptionPane.showMessageDialog(Desktop.desktop, "The Multiple Sequence Alignment Service named "+MsaWSName+" is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ 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;
}
- wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
-
- wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")+" of "+altitle+"\nJob details\n");
+ 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);
- // TODO: MuscleWS transmuted to generic MsaWS client
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
- try {
- this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
- }
- catch (Exception ex) {
- wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
- +WsURL+"\n"+ex.getMessage());
- wsInfo.setStatus(wsInfo.ERROR);
- ex.printStackTrace();
- }
+ return;
+ }
+ startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
- MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
- wsInfo.setthisService(musclethread);
- musclethread.start();
}
- protected class MsaWSThread extends Thread implements WSClientI
+ private void startMsaWSClient(String altitle, AlignmentView msa,
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
{
- String ServiceName = WebServiceName;
-
- public boolean isCancellable()
- {
- return true;
- }
-
- String OutputHeader;
- vamsas.objects.simple.MsaResult result = null;
-
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
- SequenceSet();
-
- Hashtable SeqNames = null;
- boolean submitGaps = false,// default is to strip gaps from sequences
- 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.
- MsaWSThread(String title, SequenceI[] msa, boolean subgaps, boolean presorder)
+ if (!locateWebService())
{
- 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);
+ return;
}
- boolean jobComplete = false;
-
- public void cancelJob() {
- if (!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( ( (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;
}
- wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
- }
+ } else {
+ jobtitle = WebServiceName+(submitGaps? " re" : " ") +"alignment of "+altitle;
}
- public void run()
- {
-
- StartJob();
-
- while (!jobComplete && (allowedServerExceptions > 0))
- {
- try
- {
- result = server.getResult(jobId);
+ MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
+ WebServiceName,
+ jobtitle,
+ msa,
+ submitGaps, preserveOrder, seqdataset);
+ wsInfo.setthisService(msathread);
+ msathread.start();
+ }
- if (result.isRunning())
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- else if (result.isQueued())
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ /**
+ * 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
- 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());
- ex.printStackTrace();
- }
- }
- 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
{
- try
- {
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
- if (jobsubmit.getStatus()==1) {
- jobId=jobsubmit.getJobId();
- System.out.println(WsURL+" Job Id '"+jobId+"'");
- } else {
- throw new Exception(jobsubmit.getJobId());
- }
- }
- catch (Exception e)
- {
- System.err.println(ServiceName + " 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));
- }
- 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;
+ this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+ ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
}
- void parseResult()
+ catch (Exception ex)
{
- 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);
+ wsInfo.setProgressText("Serious! " + WebServiceName +
+ " Service location failed\nfor URL :" + WsURL +
+ "\n" +
+ ex.getMessage());
+ wsInfo.setStatus(WebserviceInfo.ERROR);
+ ex.printStackTrace();
- Alignment al = new Alignment(seqs);
+ return false;
+ }
- // TODO: JBPNote Should also rename the query sequence sometime...
- AlignFrame af = new AlignFrame(al);
- af.addSortByOrderMenuItem(ServiceName+" Ordering", msaorder);
+ loc.getEngine().setOption("axis", "1");
- Desktop.addInternalFrame(af,
- alTitle,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- }
- }catch(Exception ex){ex.printStackTrace();}
+ return true;
+ }
- }
+ protected String getServiceActionKey()
+ {
+ return "MsaWS";
+ }
+ protected String getServiceActionDescription()
+ {
+ return "Multiple Sequence Alignment";
}
}
-
-
git://source.jalview.org / jalview.git / blobdiff