public class MsaWSClient
+ extends WSClient
{
- int jobsRunning = 0;
- ext.vamsas.MuscleWS server;
- WebserviceInfo wsInfo;
- /**
- * MsaWSClient
- *
- * @param msa SequenceI[]
- */
-
- String WebServiceName;
- String WebServiceJobTitle;
- String WebServiceReference;
- String WsURL;
+ /**
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */
+ ext.vamsas.MuscleWS server;
+
private boolean setWebService(String MsaWSName) {
- if (MsaWServices.info.contains(MsaWSName.toUpperCase())) {
+ if (MsaWServices.info.containsKey(MsaWSName)) {
WebServiceName = MsaWSName;
- String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName.toUpperCase());
+ String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
WsURL = wsinfo[0];
WebServiceJobTitle = wsinfo[1];
WebServiceReference = wsinfo[2];
}
}
-// public MsaWSClient(String MsaWSName, SequenceI[] msa) {
-// MsaWSClient(MsaWSName, msa, true);
-// }
- public MsaWSClient(String MsaWSName, SequenceI[] msa, boolean preserveOrder)
+ 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",
wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
- wsInfo.setProgressText("Job details\n");
+ wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")+" of "+altitle+"\nJob details\n");
// TODO: MuscleWS transmuted to generic MsaWS client
MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
try {
- this.server = (MuscleWS) loc.getMuscleWS(// JBPNote will be set from properties
- new java.net.URL(WsURL));
+ 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 :"
wsInfo.setStatus(wsInfo.ERROR);
ex.printStackTrace();
}
-
- MsaWSThread musclethread = new MsaWSThread(msa);
+ loc.getEngine().setOption("axis","1");
+ MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
wsInfo.setthisService(musclethread);
musclethread.start();
}
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(SequenceI[] msa)
+ 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(msa[i].getName());
- seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));
+ 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);
}
boolean jobComplete = false;
public void cancelJob() {
- if (!jobComplete) {
+ if (jobId!=null && !jobId.equals("") && !jobComplete) {
String cancelledMessage="";
try {
vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
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");
+ }
}
}
{
try
{
- result = server.getResult(jobId);
+ 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.isRunning())
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ else if (result.isQueued())
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
if (result.isFinished())
{
}
else
{
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
+ 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();
+ 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 (! (result!=null && (result.isJobFailed() || result.isServerError())))
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ if (allowedServerExceptions == 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
else
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ {
+ 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.getStatus()==1) {
- System.out.println(jobId=jobsubmit.getJobId());
+ 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)
{
- System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
+ // TODO: JBPNote catch timeout or other fault types explicitly
+ // For unexpected errors
+ System.err.println(WebServiceName + " Client: Failed to submit the sequences for alignment.\n"+WsURL+" : " +
e.toString() + "\n");
- e.printStackTrace();
+ this.allowedServerExceptions=0;
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.appendProgressText("Server problems! "+e.toString()+"\nFailed to submit sequences for alignment. Just close the window\n");
+ // e.printStackTrace(); // TODO: JBPNote DEBUG
}
}
wsInfo.setProgressText(OutputHeader);
if (seqs!=null) {
- Alignment al;
- al = new Alignment(seqs);
+ 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,
- ServiceName + " Alignment",
+ alTitle,
AlignFrame.NEW_WINDOW_WIDTH,
AlignFrame.NEW_WINDOW_HEIGHT);
}
git://source.jalview.org / jalview.git / blobdiff