\r
import ext.vamsas.*;\r
import jalview.analysis.*;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
+import jalview.datamodel.Alignment;\r
import jalview.gui.*;\r
-import jalview.io.FormatAdapter;\r
import jalview.io.*;\r
+import jalview.ws.WSThread.*;\r
+import vamsas.objects.simple.*;\r
+import jalview.util.Comparison;\r
\r
public class JPredClient\r
extends WSClient\r
{\r
- ext.vamsas.Jpred server;\r
- String altitle = "";\r
- java.util.Hashtable SequenceInfo = null;\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq)\r
+ {\r
wsInfo = setWebService(sh);\r
startJPredClient(title, seq);\r
}\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) {\r
+\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa)\r
+ {\r
wsInfo = setWebService(sh);\r
startJPredClient(title, msa);\r
}\r
\r
- public JPredClient(String title, SequenceI[] msf) {\r
+ public JPredClient(String title, SequenceI[] msf)\r
+ {\r
startJPredClient(title, msf);\r
}\r
\r
- public JPredClient(String title, SequenceI seq) {\r
+ public JPredClient(String title, SequenceI seq)\r
+ {\r
startJPredClient(title, seq);\r
}\r
\r
private void startJPredClient(String title, SequenceI[] msf)\r
{\r
- if (wsInfo==null)\r
+ if (wsInfo == null)\r
+ {\r
wsInfo = setWebService();\r
+ }\r
\r
SequenceI seq = msf[0];\r
\r
- altitle = "JNet prediction on " + seq.getName() +\r
+ String altitle = "JNet prediction on " + seq.getName() +\r
" using alignment from " + title;\r
\r
wsInfo.setProgressText("Job details for MSA based prediction (" +\r
AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
"\n");\r
SequenceI aln[] = new SequenceI[msf.length];\r
- for (int i=0,j=msf.length; i<j;i++) {\r
- aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
+ for (int i = 0, j = msf.length; i < j; i++)\r
+ {\r
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
}\r
\r
- SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
\r
- if (!locateWebService())\r
+ Jpred server = locateWebService();\r
+ if (server==null)\r
{\r
return;\r
}\r
\r
- JPredThread jthread = new JPredThread(aln);\r
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln);\r
+ wsInfo.setthisService(jthread);\r
jthread.start();\r
}\r
\r
public void startJPredClient(String title, SequenceI seq)\r
{\r
- if (wsInfo==null)\r
+ if (wsInfo == null)\r
+ {\r
wsInfo = setWebService();\r
+ }\r
wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
seq.getName() + "\n" +\r
AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
"\n");\r
- altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+ String altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
title;\r
\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
\r
- if (!locateWebService())\r
+ Jpred server = locateWebService();\r
+ if (server==null)\r
{\r
return;\r
}\r
\r
- JPredThread jthread = new JPredThread(seq);\r
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq);\r
+ wsInfo.setthisService(jthread);\r
jthread.start();\r
}\r
\r
return wsInfo;\r
}\r
\r
- private boolean locateWebService()\r
+ private ext.vamsas.Jpred locateWebService()\r
{\r
ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default\r
-\r
+ ext.vamsas.Jpred server=null;\r
try\r
{\r
- this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
- ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub\r
+ server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+ ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub\r
//((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);\r
\r
}\r
ex.getMessage());\r
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
\r
- return false;\r
}\r
\r
- return true;\r
+ return server;\r
}\r
\r
class JPredThread\r
- extends Thread\r
+ extends WSThread\r
+ implements WSClientI\r
{\r
- String OutputHeader;\r
- vamsas.objects.simple.JpredResult result;\r
- vamsas.objects.simple.Sequence sequence;\r
- vamsas.objects.simple.Msfalignment msa;\r
- String jobId;\r
- boolean jobComplete = false;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
-\r
- JPredThread(SequenceI seq)\r
+ class JPredJob\r
+ extends WSThread.WSJob\r
{\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new vamsas.objects.simple.Sequence();\r
- this.sequence.setId(seq.getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
- }\r
\r
- JPredThread(SequenceI[] msf)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new vamsas.objects.simple.Sequence();\r
- this.sequence.setId(msf[0].getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
- msf[0].getSequence()));\r
-\r
- this.msa = new vamsas.objects.simple.Msfalignment();\r
- jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
- msa.setMsf(pileup.print(msf));\r
- }\r
+ vamsas.objects.simple.Sequence sequence;\r
+ vamsas.objects.simple.Msfalignment msa;\r
+ java.util.Hashtable SequenceInfo = null;\r
+ /**\r
+ *\r
+ * @return true if getResultSet will return a valid alignment and prediction result.\r
+ */\r
+ public boolean hasResults()\r
+ {\r
+ if (subjobComplete && result != null && result.isFinished()\r
+ && ( (JpredResult) result).getPredfile() != null &&\r
+ ( (JpredResult) result).getAligfile() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
\r
- public void run()\r
- {\r
- StartJob();\r
+ boolean hasValidInput()\r
+ {\r
+ if (sequence != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
\r
- while (!jobComplete && (allowedServerExceptions > 0))\r
+ public Alignment getResultSet()\r
+ throws Exception\r
{\r
- try\r
+ if (result == null || !result.isFinished())\r
+ {\r
+ return null;\r
+ }\r
+ Alignment al = null;\r
+ int FirstSeq = -1; // the position of the query sequence in Alignment al\r
+ boolean noMsa = true; // set if no MSA has been returned by JPred\r
+\r
+ JpredResult result = (JpredResult)this.result;\r
+\r
+ jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
+ getPredfile(),\r
+ "Paste");\r
+ SequenceI[] preds = prediction.getSeqsAsArray();\r
+ jalview.bin.Cache.log.debug("Got prediction profile.");\r
+\r
+ if ( (this.msa != null) && (result.getAligfile() != null))\r
{\r
- if ( (result = server.getresult(jobId)) == null)\r
+ jalview.bin.Cache.log.debug("Getting associated alignment.");\r
+ // we ignore the returned alignment if we only predicted on a single sequence\r
+ String format = new jalview.io.IdentifyFile().Identify(result.\r
+ getAligfile(),\r
+ "Paste");\r
+\r
+ if (jalview.io.FormatAdapter.isValidFormat(format))\r
+ {\r
+ al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),\r
+ "Paste", format));\r
+ SequenceI sqs[] = new SequenceI[al.getHeight()];\r
+ for (int i = 0, j = al.getHeight(); i < j; i++)\r
+ {\r
+ sqs[i] = al.getSequenceAt(i);\r
+ }\r
+ if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)\r
+ SequenceInfo, sqs))\r
+ {\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for alignment."));\r
+ }\r
+\r
+ noMsa = false;\r
+ FirstSeq = 0;\r
+ }\r
+ else\r
{\r
throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
+ "Unknown format "+format+" for file : \n" +\r
+ result.getAligfile()));\r
}\r
- if (result.getState()==0)\r
- jalview.bin.Cache.log.debug("Finished "+jobId);\r
- if (result.isRunning())\r
+ }\r
+ else\r
+ {\r
+ al = new Alignment(preds);\r
+ FirstSeq = prediction.getQuerySeqPosition();\r
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
+ al.getSequenceAt(FirstSeq), SequenceInfo))\r
{\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for JNet Query sequence!"));\r
}\r
- if (result.isQueued())\r
+ }\r
+\r
+ al.setDataset(null);\r
+\r
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,\r
+ noMsa);\r
+ return al; // , FirstSeq, noMsa};\r
+ }\r
+ public JPredJob(Hashtable SequenceInfo, SequenceI seq)\r
+ {\r
+ super();\r
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());\r
+ if (sq.length() >= 20)\r
+ {\r
+ this.SequenceInfo = SequenceInfo;\r
+ sequence = new vamsas.objects.simple.Sequence();\r
+ sequence.setId(seq.getName());\r
+ sequence.setSeq(sq);\r
+ }\r
+ }\r
+\r
+ public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)\r
+ {\r
+ this(SequenceInfo, msf[0]);\r
+ if (sequence != null)\r
+ {\r
+ if (msf.length > 1)\r
{\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ msa = new vamsas.objects.simple.Msfalignment();\r
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
+ msa.setMsf(pileup.print(msf));\r
}\r
+ }\r
+ }\r
+ }\r
+ ext.vamsas.Jpred server;\r
+ String altitle = "";\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server) {\r
+ this.altitle = altitle;\r
+ this.server = server;\r
+ this.wsInfo = wsinfo;\r
+ }\r
\r
- wsInfo.setProgressText(OutputHeader + "\n" +\r
- result.getStatus());\r
+// String OutputHeader;\r
+// vamsas.objects.simple.JpredResult result;\r
\r
- if (result.isFinished())\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq)\r
+ {\r
+ this(wsinfo, altitle, server);\r
+ JPredJob job = new JPredJob(SequenceInfo, seq);\r
+ if (job.hasValidInput())\r
+ {\r
+ OutputHeader = wsInfo.getProgressText();\r
+ jobs = new WSJob[]\r
+ {\r
+ job};\r
+ job.jobnum = 0;\r
+ }\r
+ }\r
+\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf)\r
+ {\r
+ this(wsinfo, altitle, server);\r
+ JPredJob job = new JPredJob(SequenceInfo, msf);\r
+ if (job.hasValidInput())\r
+ {\r
+ jobs = new WSJob[]\r
+ {\r
+ job};\r
+ OutputHeader = wsInfo.getProgressText();\r
+ job.jobnum = 0;\r
+ }\r
+ }\r
+\r
+ /*\r
+ public void run()\r
+ {\r
+ StartJob();\r
+\r
+ while (!jobComplete && (allowedServerExceptions > 0))\r
{\r
+ try\r
+ {\r
+ if ( (result = server.getresult(jobId)) == null)\r
+ {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+ if (result.getState()==0)\r
+ jalview.bin.Cache.log.debug("Finished "+jobId);\r
+ if (result.isRunning())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ }\r
+ if (result.isQueued())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- } else {\r
- // catch exceptions\r
- if (! (result.isJobFailed() || result.isServerError()))\r
+ wsInfo.setProgressText(OutputHeader + "\n" +\r
+ result.getStatus());\r
+\r
+ if (result.isFinished())\r
+ {\r
+\r
+ parseResult();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ } else {\r
+ // catch exceptions\r
+ if (! (result.isJobFailed() || result.isServerError()))\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(5000);\r
+ }\r
+ catch (InterruptedException ex1)\r
+ {\r
+ }\r
+\r
+ // System.out.println("I'm alive "+seqid+" "+jobid);\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ jobsRunning--;\r
+ jobComplete = true;\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
{\r
+ allowedServerExceptions--;\r
+\r
+ wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
+ ex.getMessage());\r
+\r
try\r
{\r
- Thread.sleep(5000);\r
+ if (allowedServerExceptions > 0)\r
+ {\r
+ Thread.sleep(5000);\r
+ }\r
}\r
catch (InterruptedException ex1)\r
{\r
}\r
-\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
}\r
- else\r
+ catch (OutOfMemoryError er)\r
{\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- jobsRunning--;\r
jobComplete = true;\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory handling result!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("JPredClient: "+er);\r
+ System.gc();\r
}\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
-\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
- ex.getMessage());\r
-\r
- try\r
- {\r
- if (allowedServerExceptions > 0)\r
+ if (result!=null)\r
+ if (! (result.isJobFailed() || result.isServerError()))\r
{\r
- Thread.sleep(5000);\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
}\r
- }\r
- catch (InterruptedException ex1)\r
- {\r
- }\r
- }\r
- catch (OutOfMemoryError er)\r
- {\r
- jobComplete = true;\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of memory handling result!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("JPredClient: "+er);\r
- System.gc();\r
- }\r
- }\r
- if (result!=null)\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
}\r
- }\r
-\r
- void StartJob()\r
+ */\r
+ void StartJob(WSJob j)\r
{\r
+ if (! (j instanceof JPredJob))\r
+ {\r
+ throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
+ j.getClass());\r
+ }\r
try\r
{\r
- if (msa != null)\r
+ JPredJob job = (JPredJob) j;\r
+ if (job.msa != null)\r
{\r
- jobId = server.predictOnMsa(msa);\r
+ job.jobId = server.predictOnMsa(job.msa);\r
}\r
else\r
- {\r
- jobId = server.predict(sequence);\r
- }\r
+ if (job.sequence!=null)\r
+ {\r
+ job.jobId = server.predict(job.sequence);\r
+ }\r
\r
- if (jobId != null)\r
+ if (job.jobId != null)\r
{\r
- if (jobId.startsWith("Broken"))\r
+ if (job.jobId.startsWith("Broken"))\r
{\r
- throw new Exception("Submission " + jobId);\r
+ job.result = (vamsas.objects.simple.Result)new JpredResult();\r
+ job.result.setInvalid(true);\r
+ job.result.setStatus("Submission " + job.jobId);\r
}\r
else\r
{\r
- System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ job.submitted = true;\r
+ job.subjobComplete = false;\r
+ Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");\r
}\r
}\r
else\r
}\r
catch (Exception e)\r
{\r
- if (e.getMessage().indexOf("Exception")>-1) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setProgressText(\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- +\r
- "It is most likely that there is a problem with the server.\n");\r
+ if (e.getMessage().indexOf("Exception") > -1)\r
+ {\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.setProgressText(j.jobnum,\r
+ "Failed to submit the prediction. (Just close the window)\n"\r
+ +\r
+ "It is most likely that there is a problem with the server.\n");\r
System.err.println(\r
"JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +\r
e.getMessage() + "\n");\r
\r
- jalview.bin.Cache.log.warn("Server Exception",e);\r
- } else {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ jalview.bin.Cache.log.warn("Server Exception", e);\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
// JBPNote - this could be a popup informing the user of the problem.\r
- wsInfo.setProgressText("Failed to submit the prediction:\n"\r
- +e.getMessage()+\r
- wsInfo.getProgressText());\r
+ wsInfo.appendProgressText(j.jobnum,\r
+ "Failed to submit the prediction:\n"\r
+ + e.getMessage() +\r
+ wsInfo.getProgressText());\r
\r
- jalview.bin.Cache.log.debug("Failed Submission",e);\r
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
\r
}\r
- allowedServerExceptions = -1;\r
- jobComplete = true;\r
-\r
+ j.allowedServerExceptions = -1;\r
+ j.subjobComplete = true;\r
}\r
}\r
\r
-\r
-\r
- /* private void addFloatAnnotations(Alignment al, int[] gapmap,\r
- Vector values, String Symname,\r
- String Visname, float min,\r
- float max, int winLength)\r
- {\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
-\r
- for (int j = 0; j < values.size(); j++)\r
+ /* private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+ Vector values, String Symname,\r
+ String Visname, float min,\r
+ float max, int winLength)\r
{\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
- value);\r
- }\r
+ Annotation[] annotations = new Annotation[al.getWidth()];\r
+\r
+ for (int j = 0; j < values.size(); j++)\r
+ {\r
+ float value = Float.parseFloat(values.get(j).toString());\r
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
+ value);\r
+ }\r
\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
- annotations, min, max, winLength));\r
- }*/\r
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
+ annotations, min, max, winLength));\r
+ }*/\r
\r
void parseResult()\r
{\r
- // OutputHeader = output.getText();\r
- if (result.isFailed())\r
+ int results = 0; // number of result sets received\r
+ JobStateSummary finalState = new JobStateSummary();\r
+ try\r
{\r
- OutputHeader += "Job failed.\n";\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
+ if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())\r
+ {\r
+ results++;\r
+ }\r
+ }\r
}\r
-\r
- if (result.getStatus() != null)\r
+ catch (Exception ex)\r
{\r
- OutputHeader += ("\n" + result.getStatus());\r
- }\r
\r
- if (result.getPredfile() != null)\r
+ Cache.log.error("Unexpected exception when processing results for " +\r
+ altitle, ex);\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ if (results > 0)\r
{\r
- OutputHeader += ("\n" + result.getPredfile());\r
-\r
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
+ wsInfo.showResultsNewFrame\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(\r
+ java.awt.event.ActionEvent evt)\r
+ {\r
+ displayResults(true);\r
+ }\r
+ });\r
+ wsInfo.mergeResults\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(\r
+ java.awt.event.ActionEvent evt)\r
+ {\r
+ displayResults(false);\r
+ }\r
+ });\r
+ wsInfo.setResultsReady();\r
}\r
-\r
- if (result.getAligfile() != null)\r
+ else\r
{\r
- OutputHeader += ("\n" + result.getAligfile());\r
+ wsInfo.setFinishedNoResults();\r
}\r
+ }\r
\r
- wsInfo.setProgressText(OutputHeader+"Parsing...");\r
-\r
- try\r
+ void displayResults(boolean newWindow)\r
+ {\r
+ if (jobs != null)\r
{\r
- jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
- getPredfile(),\r
- "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- jalview.bin.Cache.log.debug("Got prediction profile.");\r
- Alignment al;\r
- int FirstSeq; // the position of the query sequence in Alignment al\r
- boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
- if ( (this.msa != null) && (result.getAligfile() != null))\r
+ Alignment res = null;\r
+ for (int jn = 0; jn < jobs.length; jn++)\r
{\r
- jalview.bin.Cache.log.debug("Getting associated alignment.");\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),\r
- "Paste");\r
+ Alignment jobres = null;\r
+ JPredJob j = (JPredJob) jobs[jn];\r
\r
- if (jalview.io.FormatAdapter.isValidFormat(format))\r
+ if (j.hasResults())\r
{\r
- al = new Alignment(new FormatAdapter().readFile(\r
- result.getAligfile(), "Paste", format));\r
- SequenceI sqs[] = new SequenceI[al.getHeight()];\r
- for (int i=0, j=al.getHeight(); i<j; i++) {\r
- sqs[i] = al.getSequenceAt(i);\r
- }\r
- if (!jalview.analysis.SeqsetUtils.deuniquify(\r
- (Hashtable) SequenceInfo,sqs))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for alignment."));\r
+ try\r
+ {\r
+ jalview.bin.Cache.log.debug("Parsing output of job " + jn);\r
+ jobres = j.getResultSet();\r
+ jalview.bin.Cache.log.debug("Finished parsing output.");\r
+ if (jobs.length==1)\r
+ res = jobres;\r
+ else {\r
+ // do merge with other job results\r
}\r
-\r
- noMsa = false;\r
- FirstSeq = 0;\r
- }\r
- else\r
- {\r
- throw (new Exception(\r
- "Unknown format 'format' for file : \n" +\r
- result.getAligfile()));\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ jalview.bin.Cache.log.error(\r
+ "JNet Client: JPred Annotation Parse Error",\r
+ e);\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
+ wsInfo.appendProgressText(j.jobnum,\r
+ OutputHeader + "\n" +\r
+ j.result.getStatus() +\r
+ "\nInvalid JNet job result data!\n" +\r
+ e.getMessage());\r
+ j.result.setBroken(true);\r
+ }\r
}\r
}\r
- else\r
+\r
+ if (res != null)\r
{\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
- al.getSequenceAt(FirstSeq), SequenceInfo))\r
+ if (newWindow)\r
{\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
+ AlignFrame af = new AlignFrame(res);\r
+ Desktop.addInternalFrame(af, altitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ Cache.log.info("Append results onto existing alignment.");\r
}\r
}\r
+ }\r
+ }\r
\r
- al.setDataset(null);\r
-\r
- try {\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,\r
- noMsa);\r
- }\r
- catch (Exception e) {\r
- jalview.bin.Cache.log.error("JNet Client: JPred Annotation Parse Error", e);\r
- }\r
- wsInfo.setProgressText(OutputHeader);\r
- jalview.bin.Cache.log.debug("Finished parsing output.");\r
- AlignFrame af = new AlignFrame(al);\r
+ void pollJob(WSJob job)\r
+ throws Exception\r
+ {\r
+ job.result = server.getresult(job.jobId);\r
+ }\r
+ public boolean isCancellable()\r
+ {\r
+ return false;\r
+ }\r
\r
- Desktop.addInternalFrame(af, altitle,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
- catch (Exception ex)\r
- {\r
- jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);\r
- }\r
+ public void cancelJob()\r
+ {\r
+ throw new Error("Implementation error!");\r
}\r
+\r
}\r
}\r
+\r
git://source.jalview.org / jalview.git / commitdiff