-/*\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 java.util.*;\r
-\r
-import javax.swing.*;\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.datamodel.AlignmentView;\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.util.*;\r
-import jalview.ws.WSThread.*;\r
-import vamsas.objects.simple.*;\r
-\r
-public class JPredClient\r
- extends WSClient\r
-{\r
- AlignFrame parentFrame=null;\r
- /**\r
- * crate a new GUI JPred Job\r
- * @param sh ServiceHandle\r
- * @param title String\r
- * @param msa boolean - true - submit alignment as a sequence profile\r
- * @param alview AlignmentView\r
- */\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {\r
- wsInfo=setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, msa, alview);\r
-\r
- }\r
-\r
- /**\r
- * startJPredClient\r
- *\r
- * @param title String\r
- * @param msa boolean\r
- * @param alview AlignmentView\r
- */\r
- private void startJPredClient(String title, boolean msa,\r
- jalview.datamodel.AlignmentView alview)\r
- {\r
- }\r
-\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)\r
- {\r
- wsInfo = setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, seq);\r
- }\r
-\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)\r
- {\r
- wsInfo = setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, msa);\r
- }\r
-\r
- public JPredClient(String title, SequenceI[] msf)\r
- {\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
- SequenceI seq = msf[0];\r
-\r
- String altitle = "JNet prediction on " + seq.getName() +\r
- " using alignment from " + title;\r
-\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
-\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(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
- {\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
- 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(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
- return wsInfo;\r
- }\r
-\r
- private ext.vamsas.Jpred locateWebService()\r
- {\r
- ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default\r
- ext.vamsas.Jpred server=null;\r
- try\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
- }\r
- catch (Exception ex)\r
- {\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
- class JPredThread\r
- extends WSThread\r
- implements WSClientI\r
- {\r
- class JPredJob\r
- extends WSThread.WSJob\r
- {\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
- boolean hasValidInput()\r
- {\r
- if (sequence != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\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 (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
- "Unknown format "+format+" for file : \n" +\r
- result.getAligfile()));\r
- }\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
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\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
- 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
-// String OutputHeader;\r
-// vamsas.objects.simple.JpredResult result;\r
-\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
- 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
- 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 (job.jobId != null)\r
- {\r
- if (job.jobId.startsWith("Broken"))\r
- {\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
- job.submitted = true;\r
- job.subjobComplete = false;\r
- Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");\r
- }\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
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
-\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
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
- annotations, min, max, winLength));\r
- }*/\r
-\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
- }\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
- 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
- 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
- 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
- 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
-\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
- 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
- public boolean canMergeResults()\r
- {\r
- return false;\r
- }\r
-\r
- }\r
-}\r
-\r
+/*
+ * 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 java.util.*;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.*;
+import jalview.io.*;
+import jalview.util.*;
+import jalview.ws.WSThread.*;
+import vamsas.objects.simple.*;
+
+public class JPredClient
+ extends WSClient
+{
+ /**
+ * crate a new GUI JPred Job
+ * @param sh ServiceHandle
+ * @param title String
+ * @param msa boolean - true - submit alignment as a sequence profile
+ * @param alview AlignmentView
+ */
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {
+ super();
+ wsInfo=setWebService(sh);
+ startJPredClient(title, msa, alview, parentFrame);
+
+ }
+ /**
+ * startJPredClient
+ * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
+ * TODO: sequence representative support - could submit alignment of representatives as msa.
+ * TODO: msa hidden region prediction - submit each chunk for prediction. concatenate results of each.
+ * TODO: single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs)
+ * @param title String
+ * @param msa boolean
+ * @param alview AlignmentView
+ */
+ private void startJPredClient(String title, boolean msa,
+ jalview.datamodel.AlignmentView alview, AlignFrame parentFrame)
+ {
+ AlignmentView input = alview;
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ Jpred server = locateWebService();
+ if (server == null)
+ {
+ Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ return;
+ }
+
+ SeqCigar[] msf = input.getSequences();
+ SequenceI seq = msf[0].getSeq('-');
+ if (msa && msf.length > 1)
+ {
+
+ String altitle = "JNet prediction on " + seq.getName() +
+ " using alignment from " + title;
+
+ wsInfo.setProgressText("Job details for MSA based prediction (" +
+ title + ") on sequence :\n>" + seq.getName() +
+ "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = msf[i].getSeq('-');
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, aln, alview, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ else
+ {
+ if (!msa && msf.length>1)
+ throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+ seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName() +
+ " from " +
+ title;
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
+ seq);
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, seq, alview, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ }
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)
+ {
+ super();
+ wsInfo = setWebService(sh);
+ startJPredClient(title, seq, parentFrame);
+ }
+
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)
+ {
+ wsInfo = setWebService(sh);
+ startJPredClient(title, msa, parentFrame);
+ }
+
+ public JPredClient(String title, SequenceI[] msf)
+ {
+ startJPredClient(title, msf, null);
+ }
+
+ public JPredClient(String title, SequenceI seq)
+ {
+ startJPredClient(title, seq, null);
+ }
+
+ private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+
+ SequenceI seq = msf[0];
+
+ String altitle = "JNet prediction on " + seq.getName() +
+ " using alignment from " + title;
+
+ wsInfo.setProgressText("Job details for MSA based prediction (" +
+ title + ") on sequence :\n>" + seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+ Jpred server = locateWebService();
+ if (server==null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ public void startJPredClient(String title, SequenceI seq, AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+ seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
+ title;
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+
+ Jpred server = locateWebService();
+ if (server==null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ private WebserviceInfo setWebService()
+ {
+ WebServiceName = "JNetWS";
+ WebServiceJobTitle = "JNet secondary structure prediction";
+ WebServiceReference =
+ "\"Cuff J. A and Barton G.J (2000) Application of " +
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
+ "Proteins 40:502-511\".";
+ WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+ WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceReference);
+
+ return wsInfo;
+ }
+
+ private ext.vamsas.Jpred locateWebService()
+ {
+ ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
+ ext.vamsas.Jpred server=null;
+ try
+ {
+ server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
+ ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub
+ //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
+
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The Secondary Structure Prediction Service named " +
+ WebServiceName + " at " + WsURL +
+ " couldn't be located.",
+ "Internal Jalview Error",
+ JOptionPane.WARNING_MESSAGE);
+ wsInfo.setProgressText("Serious! " + WebServiceName +
+ " Service location failed\nfor URL :" + WsURL +
+ "\n" +
+ ex.getMessage());
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
+ }
+
+ return server;
+ }
+
+ class JPredThread
+ extends WSThread
+ implements WSClientI
+ {
+ class JPredJob
+ extends WSThread.WSJob
+ {
+
+ vamsas.objects.simple.Sequence sequence;
+ vamsas.objects.simple.Msfalignment msa;
+ java.util.Hashtable SequenceInfo = null;
+ /**
+ *
+ * @return true if getResultSet will return a valid alignment and prediction result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete && result != null && result.isFinished()
+ && ( (JpredResult) result).getPredfile() != null &&
+ ( (JpredResult) result).getAligfile() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ boolean hasValidInput()
+ {
+ if (sequence != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public Alignment getResultSet()
+ throws Exception
+ {
+ if (result == null || !result.isFinished())
+ {
+ return null;
+ }
+ Alignment al = null;
+ int FirstSeq = -1; // the position of the query sequence in Alignment al
+
+ JpredResult result = (JpredResult)this.result;
+
+ jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
+ getPredfile(),
+ "Paste");
+ SequenceI[] preds = prediction.getSeqsAsArray();
+ jalview.bin.Cache.log.debug("Got prediction profile.");
+
+ if ( (this.msa != null) && (result.getAligfile() != null))
+ {
+ jalview.bin.Cache.log.debug("Getting associated alignment.");
+ // we ignore the returned alignment if we only predicted on a single sequence
+ String format = new jalview.io.IdentifyFile().Identify(result.
+ getAligfile(),
+ "Paste");
+
+ if (jalview.io.FormatAdapter.isValidFormat(format))
+ {
+ al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
+ "Paste", format));
+ SequenceI sqs[] = new SequenceI[al.getHeight()];
+ for (int i = 0, j = al.getHeight(); i < j; i++)
+ {
+ sqs[i] = al.getSequenceAt(i);
+ }
+ if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
+ SequenceInfo, sqs))
+ {
+ throw (new Exception(
+ "Couldn't recover sequence properties for alignment."));
+ }
+
+ FirstSeq = 0;
+ al.setDataset(null);
+
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+ false);
+
+ }
+ else
+ {
+ throw (new Exception(
+ "Unknown format "+format+" for file : \n" +
+ result.getAligfile()));
+ }
+ }
+ else
+ {
+ al = new Alignment(preds);
+ FirstSeq = prediction.getQuerySeqPosition();
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+ al.getSequenceAt(FirstSeq), SequenceInfo))
+ {
+ throw (new Exception(
+ "Couldn't recover sequence properties for JNet Query sequence!"));
+ } else {
+ al.setDataset(null);
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+ true);
+ }
+ }
+
+ return al; // , FirstSeq, noMsa};
+ }
+ public JPredJob(Hashtable SequenceInfo, SequenceI seq)
+ {
+ super();
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
+ if (sq.length() >= 20)
+ {
+ this.SequenceInfo = SequenceInfo;
+ sequence = new vamsas.objects.simple.Sequence();
+ sequence.setId(seq.getName());
+ sequence.setSeq(sq);
+ }
+ }
+
+ public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
+ {
+ this(SequenceInfo, msf[0]);
+ if (sequence != null)
+ {
+ if (msf.length > 1)
+ {
+ msa = new vamsas.objects.simple.Msfalignment();
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+ msa.setMsf(pileup.print(msf));
+ }
+ }
+ }
+ }
+ ext.vamsas.Jpred server;
+ String altitle = "";
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, AlignmentView alview, AlignFrame alframe) {
+ this.altitle = altitle;
+ this.server = server;
+ this.wsInfo = wsinfo;
+ this.input = alview;
+ this.alignFrame = alframe;
+ }
+
+// String OutputHeader;
+// vamsas.objects.simple.JpredResult result;
+
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq, AlignmentView alview, AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server,alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, seq);
+ if (job.hasValidInput())
+ {
+ OutputHeader = wsInfo.getProgressText();
+ jobs = new WSJob[]
+ {
+ job};
+ job.jobnum = 0;
+ }
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf, AlignmentView alview, AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server,alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, msf);
+ if (job.hasValidInput())
+ {
+ jobs = new WSJob[]
+ {
+ job};
+ OutputHeader = wsInfo.getProgressText();
+ job.jobnum = 0;
+ }
+ }
+
+ /*
+ 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.getState()==0)
+ jalview.bin.Cache.log.debug("Finished "+jobId);
+ if (result.isRunning())
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ if (result.isQueued())
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+
+ wsInfo.setProgressText(OutputHeader + "\n" +
+ result.getStatus());
+
+ if (result.isFinished())
+ {
+
+ parseResult();
+ jobComplete = true;
+ jobsRunning--;
+ } else {
+ // catch exceptions
+ if (! (result.isJobFailed() || result.isServerError()))
+ {
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+
+ // System.out.println("I'm alive "+seqid+" "+jobid);
+ }
+ else
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ jobsRunning--;
+ jobComplete = true;
+ }
+ }
+ }
+ catch (Exception ex)
+ {
+ allowedServerExceptions--;
+
+ wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
+ ex.getMessage());
+
+ try
+ {
+ if (allowedServerExceptions > 0)
+ {
+ Thread.sleep(5000);
+ }
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+ }
+ catch (OutOfMemoryError er)
+ {
+ jobComplete = true;
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory handling result!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ JOptionPane.WARNING_MESSAGE);
+ System.out.println("JPredClient: "+er);
+ System.gc();
+ }
+ }
+ if (result!=null)
+ if (! (result.isJobFailed() || result.isServerError()))
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ }
+ */
+ void StartJob(WSJob j)
+ {
+ if (! (j instanceof JPredJob))
+ {
+ throw new Error("Implementation error - StartJob(JpredJob) called on " +
+ j.getClass());
+ }
+ try
+ {
+ JPredJob job = (JPredJob) j;
+ if (job.msa != null)
+ {
+ job.jobId = server.predictOnMsa(job.msa);
+ }
+ else
+ if (job.sequence!=null)
+ {
+ job.jobId = server.predict(job.sequence);
+ }
+
+ if (job.jobId != null)
+ {
+ if (job.jobId.startsWith("Broken"))
+ {
+ job.result = (vamsas.objects.simple.Result)new JpredResult();
+ job.result.setInvalid(true);
+ job.result.setStatus("Submission " + job.jobId);
+ }
+ else
+ {
+ job.submitted = true;
+ job.subjobComplete = false;
+ Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
+ }
+ }
+ else
+ {
+ throw new Exception("Server timed out - try again later\n");
+ }
+ }
+ catch (Exception e)
+ {
+ if (e.getMessage().indexOf("Exception") > -1)
+ {
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setProgressText(j.jobnum,
+ "Failed to submit the prediction. (Just close the window)\n"
+ +
+ "It is most likely that there is a problem with the server.\n");
+ System.err.println(
+ "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
+ e.getMessage() + "\n");
+
+ jalview.bin.Cache.log.warn("Server Exception", e);
+ }
+ else
+ {
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ // JBPNote - this could be a popup informing the user of the problem.
+ wsInfo.appendProgressText(j.jobnum,
+ "Failed to submit the prediction:\n"
+ + e.getMessage() +
+ wsInfo.getProgressText());
+
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
+
+ }
+ j.allowedServerExceptions = -1;
+ j.subjobComplete = true;
+ }
+ }
+
+ /* 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));
+ }*/
+
+ void parseResult()
+ {
+ int results = 0; // number of result sets received
+ JobStateSummary finalState = new JobStateSummary();
+ try
+ {
+ for (int j = 0; j < jobs.length; j++)
+ {
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+ {
+ results++;
+ }
+ }
+ }
+ catch (Exception ex)
+ {
+
+ Cache.log.error("Unexpected exception when processing results for " +
+ altitle, ex);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ if (results > 0)
+ {
+ wsInfo.showResultsNewFrame
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(
+ java.awt.event.ActionEvent evt)
+ {
+ displayResults(true);
+ }
+ });
+ wsInfo.mergeResults
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(
+ java.awt.event.ActionEvent evt)
+ {
+ displayResults(false);
+ }
+ });
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+ void displayResults(boolean newWindow)
+ {
+ // TODO: cope with multiple subjobs.
+ if (jobs != null)
+ {
+ Alignment res = null;
+ boolean msa=false;
+ for (int jn = 0; jn < jobs.length; jn++)
+ {
+ Alignment jobres = null;
+ JPredJob j = (JPredJob) jobs[jn];
+
+ if (j.hasResults())
+ {
+ // hack - we only deal with all single seuqence predictions or all profile predictions
+ msa = (j.msa!=null) ? true : msa;
+ try
+ {
+ jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ jobres = j.getResultSet();
+ jalview.bin.Cache.log.debug("Finished parsing output.");
+ if (jobs.length==1)
+ res = jobres;
+ else {
+ // do merge with other job results
+ throw new Error("Multiple JNet subjob merging not yet implemented.");
+ }
+ }
+ catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "JNet Client: JPred Annotation Parse Error",
+ e);
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendProgressText(j.jobnum,
+ OutputHeader + "\n" +
+ j.result.getStatus() +
+ "\nInvalid JNet job result data!\n" +
+ e.getMessage());
+ j.result.setBroken(true);
+ }
+ }
+ }
+
+ if (res != null)
+ {
+ if (newWindow)
+ {
+ AlignFrame af;
+ if (input==null) {
+ af = new AlignFrame(res);
+ } else {
+ java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
+
+ if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
+ if (msa) {
+ throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
+ } else {
+ // test this.
+ ((ColumnSelection) alandcolsel[1]).compensateForEdits(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
+ }
+ }
+ af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);
+ }
+ Desktop.addInternalFrame(af, altitle,
+ AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+ }
+ else
+ {
+ Cache.log.info("Append results onto existing alignment.");
+ }
+ }
+ }
+ }
+ void pollJob(WSJob job)
+ throws Exception
+ {
+ job.result = server.getresult(job.jobId);
+ }
+ public boolean isCancellable()
+ {
+ return false;
+ }
+
+ public void cancelJob()
+ {
+ throw new Error("Implementation error!");
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+ }
+}
+
git://source.jalview.org / jalview.git / blobdiff