+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.ws;\r
\r
-import org.apache.axis.client.*;\r
-import javax.xml.namespace.QName;\r
import java.util.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
+\r
import javax.swing.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-import jalview.analysis.AlignSeq;\r
-import ext.vamsas.*;\r
\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.*;\r
+import jalview.ws.WSThread.*;\r
+import vamsas.objects.simple.*;\r
+import jalview.util.Comparison;\r
\r
-public class JPredClient extends WSClient\r
+public class JPredClient\r
+ extends WSClient\r
{\r
- ext.vamsas.JPredWS server;\r
- String altitle = "";\r
- java.util.Hashtable SequenceInfo = null;\r
- private void setWebService() {\r
- WebServiceName = "JNetWS";\r
- WebServiceJobTitle = "JNet secondary structure prediction";\r
- WebServiceReference="\"Cuff J. A and Barton G.J (1999) Application of enhanced "\r
- + "multiple sequence alignment profiles to improve protein secondary structure prediction, "\r
- + "Proteins 40:502-511\".";\r
- WsURL="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq)\r
+ {\r
+ wsInfo = setWebService(sh);\r
+ startJPredClient(title, seq);\r
}\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
{\r
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
- SequenceI seq = msf[0];\r
- altitle = "JNet prediction on "+seq.getName()+" using alignment from "+title;\r
+ startJPredClient(title, msf);\r
+ }\r
+\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
+ {\r
+ wsInfo = setWebService();\r
+ }\r
\r
- wsInfo.setProgressText("Job details for MSA based prediction ("+title+") on sequence :\n>"\r
- + seq.getName() + "\n"\r
- + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
+ SequenceI seq = msf[0];\r
\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+ String altitle = "JNet prediction on " + seq.getName() +\r
+ " using alignment from " + title;\r
\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
- // JBPNote url will be set from properties\r
- try {\r
- this.server = loc.getjpred(new java.net.URL(WsURL));\r
+ wsInfo.setProgressText("Job details for MSA based prediction (" +\r
+ title + ") on sequence :\n>" + seq.getName() + "\n" +\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
+ {\r
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
}\r
- catch (Exception ex) {\r
- JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
- +WebServiceName+" at "+WsURL+" couldn't be located.",\r
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
- wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
- +WsURL+"\n"+ex.getMessage());\r
+\r
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
+\r
+ Jpred server = locateWebService();\r
+ if (server==null)\r
+ {\r
+ return;\r
}\r
\r
- JPredThread jthread = new JPredThread(msf);\r
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln);\r
+ wsInfo.setthisService(jthread);\r
jthread.start();\r
}\r
\r
- public JPredClient(String title, SequenceI seq)\r
+ public void startJPredClient(String title, SequenceI seq)\r
{\r
- setWebService();\r
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
- wsInfo.setProgressText("Job details for prediction on sequence :\n>"\r
- + seq.getName() + "\n" + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
- altitle = "JNet prediction for sequence "+seq.getName()+" from "+title;\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
- try {\r
- this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+ if (wsInfo == null)\r
+ {\r
+ wsInfo = setWebService();\r
}\r
- catch (Exception ex) {\r
- JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
- +WebServiceName+" at "+WsURL+" couldn't be located.",\r
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
- wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
- +WsURL+"\n"+ex.getMessage());\r
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
+ seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+ "\n");\r
+ String altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+ title;\r
+\r
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+\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
+ private WebserviceInfo setWebService()\r
+ {\r
+ WebServiceName = "JNetWS";\r
+ WebServiceJobTitle = "JNet secondary structure prediction";\r
+ WebServiceReference =\r
+ "\"Cuff J. A and Barton G.J (2000) Application of " +\r
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
+ "Proteins 40:502-511\".";\r
+ WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
+\r
+ WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
+ WebServiceReference);\r
\r
- class JPredThread\r
- extends Thread\r
+ return wsInfo;\r
+ }\r
+\r
+ private ext.vamsas.Jpred locateWebService()\r
{\r
- String OutputHeader;\r
- ext.vamsas.JpredResult result;\r
- ext.vamsas.Sequence sequence;\r
- ext.vamsas.Msfalignment msa;\r
- String jobId;\r
- boolean jobComplete = false;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- JPredThread(SequenceI seq)\r
+ ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default\r
+ ext.vamsas.Jpred server=null;\r
+ try\r
{\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(seq.getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));\r
- }\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
- JPredThread(SequenceI[] msf)\r
+ }\r
+ catch (Exception ex)\r
{\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(msf[0].getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));\r
- jalview.io.MSFfile mwrite = new jalview.io.MSFfile();\r
- this.msa = new ext.vamsas.Msfalignment();\r
- msa.setMsf(mwrite.print(msf));\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Secondary Structure Prediction Service named " +\r
+ WebServiceName + " at " + WsURL +\r
+ " couldn't be located.",\r
+ "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ wsInfo.setProgressText("Serious! " + WebServiceName +\r
+ " Service location failed\nfor URL :" + WsURL +\r
+ "\n" +\r
+ ex.getMessage());\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+\r
}\r
\r
+ return server;\r
+ }\r
\r
- public void run()\r
+ class JPredThread\r
+ extends WSThread\r
+ implements WSClientI\r
+ {\r
+ class JPredJob\r
+ extends WSThread.WSJob\r
{\r
\r
- StartJob();\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
- while (!jobComplete && (allowedServerExceptions > 0))\r
+ boolean hasValidInput()\r
{\r
- try\r
+ if (sequence != null)\r
{\r
- result = server.getresult(jobId);\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
\r
- if( result.isRunning() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- else if( result.isQueued() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ public Alignment getResultSet()\r
+ throws Exception\r
+ {\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
+ 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 (result.isFinished())\r
+ if (jalview.io.FormatAdapter.isValidFormat(format))\r
{\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\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
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- Thread.sleep(5000);\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- } else {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
+ throw (new Exception(\r
+ "Unknown format "+format+" for file : \n" +\r
+ result.getAligfile()));\r
}\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\r
+ al = new Alignment(preds);\r
+ FirstSeq = prediction.getQuerySeqPosition();\r
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
+ al.getSequenceAt(FirstSeq), SequenceInfo))\r
+ {\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for JNet Query sequence!"));\r
+ }\r
}\r
- }\r
\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- else\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
+ al.setDataset(null);\r
\r
- void StartJob()\r
- {\r
- try\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
- if (msa!=null) {\r
- jobId = server.predictOnMsa(msa);\r
- } else {\r
- jobId = server.predict(sequence);\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
- System.out.println(WsURL+" Job Id '"+jobId+"'");\r
}\r
- catch (Exception e)\r
+\r
+ public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)\r
{\r
- System.out.println("JPredWS Client: Failed to submit the prediction\n" +\r
- e.toString() + "\n");\r
- e.printStackTrace();\r
+ this(SequenceInfo, msf[0]);\r
+ if (sequence != null)\r
+ {\r
+ if (msf.length > 1)\r
+ {\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
- private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {\r
+// String OutputHeader;\r
+// vamsas.objects.simple.JpredResult result;\r
\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < values.size(); j++)\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
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value+"",' ',value);\r
+ OutputHeader = wsInfo.getProgressText();\r
+ jobs = new WSJob[]\r
+ {\r
+ job};\r
+ job.jobnum = 0;\r
}\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));\r
}\r
\r
- void parseResult()\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf)\r
{\r
- // OutputHeader = output.getText();\r
- if (result.isFailed()) {\r
- OutputHeader +="Job failed.\n";\r
- }\r
- if (result.getStatus()!=null) {\r
- OutputHeader += "\n"+result.getStatus();\r
- }\r
- if (result.getPredfile()!=null) {\r
- OutputHeader += "\n"+result.getPredfile();\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
+ 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
- if (result.getAligfile()!=null) {\r
- OutputHeader += "\n"+result.getAligfile();\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
+ 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
+ if (allowedServerExceptions > 0)\r
+ {\r
+ Thread.sleep(5000);\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(WSJob j)\r
+ {\r
+ if (! (j instanceof JPredJob))\r
+ {\r
+ throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
+ j.getClass());\r
}\r
- wsInfo.setProgressText(OutputHeader);\r
- try {\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\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
+ try\r
+ {\r
+ JPredJob job = (JPredJob) j;\r
+ if (job.msa != null)\r
+ {\r
+ job.jobId = server.predictOnMsa(job.msa);\r
+ }\r
+ else\r
+ if (job.sequence!=null)\r
+ {\r
+ job.jobId = server.predict(job.sequence);\r
+ }\r
\r
- if (this.msa!=null && result.getAligfile()!=null) {\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");\r
- if (jalview.io.FormatAdapter.formats.contains(format))\r
+ if (job.jobId != null)\r
+ {\r
+ if (job.jobId.startsWith("Broken"))\r
{\r
- al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));\r
- noMsa = false;\r
- FirstSeq = 0;\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
- throw (new Exception("Unknown format 'format' for file : \n" +\r
- result.getAligfile()));\r
+ job.submitted = true;\r
+ job.subjobComplete = false;\r
+ Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");\r
}\r
-\r
- } else {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
}\r
+ else\r
+ {\r
+ throw new Exception("Server timed out - try again later\n");\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\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
+ }\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.appendProgressText(j.jobnum,\r
+ "Failed to submit the prediction:\n"\r
+ + e.getMessage() +\r
+ wsInfo.getProgressText());\r
\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(FirstSeq), SequenceInfo))\r
- throw (new Exception("Couldn't recover sequence properties for JNet Query sequence!"));\r
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
\r
- AlignmentAnnotation annot;\r
- Annotation [] annotations = null;\r
- int i = 0;\r
- int width = preds[0].getSequence().length();\r
+ }\r
+ j.allowedServerExceptions = -1;\r
+ j.subjobComplete = true;\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
+ {\r
+ float value = Float.parseFloat(values.get(j).toString());\r
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
+ value);\r
+ }\r
\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
+ annotations, min, max, winLength));\r
+ }*/\r
\r
- if (gapmap.length!=width) {\r
- throw (new Exception("Jnet Client Error\nNumber of residues in supposed query sequence :\n"\r
- +al.getSequenceAt(FirstSeq).getName()+"\n"\r
- +al.getSequenceAt(FirstSeq).getSequence()\r
- +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n"));\r
+ void parseResult()\r
+ {\r
+ int results = 0; // number of result sets received\r
+ JobStateSummary finalState = new JobStateSummary();\r
+ try\r
+ {\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
- // JBPNote Should also rename the query sequence sometime...\r
- i=0;\r
- while (i < preds.length)\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+\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
+ wsInfo.showResultsNewFrame\r
+ .addActionListener(new java.awt.event.ActionListener()\r
{\r
- String id = preds[i].getName().toUpperCase();\r
- if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))\r
+ public void actionPerformed(\r
+ java.awt.event.ActionEvent evt)\r
{\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if(id.equals("JNETPRED")\r
- || id.equals("JNETPSSM")\r
- || id.equals("JNETFREQ")\r
- || id.equals("JNETHMM")\r
- || id.equals("JNETALIGN")\r
- || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0);\r
- }\r
- else if(id.equals("JNETCONF"))\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
+ else\r
+ {\r
+ wsInfo.setFinishedNoResults();\r
+ }\r
+ }\r
+\r
+ void displayResults(boolean newWindow)\r
+ {\r
+ if (jobs != null)\r
+ {\r
+ Alignment res = null;\r
+ for (int jn = 0; jn < jobs.length; jn++)\r
+ {\r
+ Alignment jobres = null;\r
+ JPredJob j = (JPredJob) jobs[jn];\r
+\r
+ if (j.hasResults())\r
+ {\r
+ try\r
{\r
- for (int j = 0; j < width; j++)\r
- {\r
- float value = Float.parseFloat(preds[i].getCharAt(j)+"");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);\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
- else\r
+ catch (Exception e)\r
{\r
- for (int j = 0; j < width; j++) {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);\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
- if(id.equals("JNETCONF"))\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations,0f,10f,1);\r
-\r
- else annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations);\r
- al.addAnnotation(annot);\r
- if (noMsa)\r
- al.deleteSequence(preds[i]);\r
}\r
- i++;\r
}\r
\r
- Hashtable scores = prediction.getScores();\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
- AlignFrame af = new AlignFrame(al);\r
-\r
+ if (res != null)\r
+ {\r
+ if (newWindow)\r
+ {\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
- Desktop.addInternalFrame(af,\r
- altitle,\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- }catch(Exception ex){ex.printStackTrace();}\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
+ public void cancelJob()\r
+ {\r
+ throw new Error("Implementation error!");\r
}\r
\r
}\r