// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
+ // todo: could limit trace to cause if this is a SOAPFaultException.
ex.printStackTrace();
if (jobs[j].allowedServerExceptions > 0)
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-package jalview.ws;
+package jalview.ws.jws1;
/**
* <p>
* @author not attributable
* @version 1.0
*/
+
import java.util.*;
import javax.swing.*;
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-package jalview.ws;
+package jalview.ws.jws1;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
- new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af,
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
true);
}
else
if (msa.getSequences().length > 1)
{
// Sequence profile based prediction
- new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af,
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa, af,
true);
}
}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.util.*;\r
-import vamsas.objects.simple.JpredResult;\r
-\r
-class JPredThread extends JWS1Thread implements WSClientI\r
-{\r
- // TODO: put mapping between JPredJob input and input data here -\r
- // JNetAnnotation adding is done after result parsing.\r
- class JPredJob extends WSJob\r
- {\r
- // TODO: make JPredJob deal only with what was sent to and received from a\r
- // JNet service\r
- int[] predMap = null; // mapping from sequence(i) to the original\r
-\r
- // sequence(predMap[i]) being predicted on\r
-\r
- vamsas.objects.simple.Sequence sequence;\r
-\r
- vamsas.objects.simple.Msfalignment msa;\r
-\r
- java.util.Hashtable SequenceInfo = null;\r
-\r
- int msaIndex = 0; // the position of the original sequence in the array of\r
-\r
- // Sequences in the input object that this job holds a\r
- // prediction for\r
-\r
- /**\r
- * \r
- * @return true if getResultSet will return a valid alignment and prediction\r
- * 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 boolean hasValidInput()\r
- {\r
- if (sequence != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- /**\r
- * \r
- * @return null or Object[] { annotated alignment for this prediction,\r
- * ColumnSelection for this prediction} or null if no results\r
- * available.\r
- * @throws Exception\r
- */\r
- public Object[] getResultSet() throws Exception\r
- {\r
- if (result == null || !result.isFinished())\r
- {\r
- return null;\r
- }\r
- Alignment al = null;\r
- ColumnSelection alcsel = null;\r
- int FirstSeq = -1; // the position of the query sequence in Alignment al\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",\r
- // "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result\r
- .getPredfile(), "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\r
- // sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result\r
- .getAligfile(), "Paste");\r
-\r
- if (jalview.io.FormatAdapter.isValidFormat(format))\r
- {\r
- SequenceI sqs[];\r
- if (predMap != null)\r
- {\r
- Object[] alandcolsel = input\r
- .getAlignmentAndColumnSelection(getGapChar());\r
- sqs = (SequenceI[]) alandcolsel[0];\r
- al = new Alignment(sqs);\r
- alcsel = (ColumnSelection) alandcolsel[1];\r
- }\r
- else\r
- {\r
- al = new FormatAdapter().readFile(result.getAligfile(),\r
- "Paste", format);\r
- sqs = new SequenceI[al.getHeight()];\r
-\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(\r
- (Hashtable) SequenceInfo, sqs))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for alignment."));\r
- }\r
- }\r
- FirstSeq = 0;\r
- al.setDataset(null);\r
-\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
- FirstSeq, false, predMap);\r
-\r
- }\r
- else\r
- {\r
- throw (new Exception("Unknown format " + format\r
- + " for file : \n" + result.getAligfile()));\r
- }\r
- }\r
- else\r
- {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- if (predMap != null)\r
- {\r
- char gc = getGapChar();\r
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input\r
- .getAlignmentAndColumnSelection(gc))[0];\r
- if (this.msaIndex >= sqs.length)\r
- {\r
- throw new Error(\r
- "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
- }\r
-\r
- // ///\r
- // Uses RemoveGapsCommand\r
- // ///\r
- new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
- new SequenceI[]\r
- { sqs[msaIndex] }, currentView);\r
-\r
- SequenceI profileseq = al.getSequenceAt(FirstSeq);\r
- profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r
- }\r
-\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al\r
- .getSequenceAt(FirstSeq), SequenceInfo))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\r
- else\r
- {\r
- al.setDataset(null);\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
- FirstSeq, true, predMap);\r
- SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.\r
- alignToProfileSeq(al, profileseq);\r
- if (predMap != null)\r
- {\r
- // Adjust input view for gaps\r
- // propagate insertions into profile\r
- alcsel = propagateInsertions(profileseq, al, input);\r
- }\r
- }\r
- }\r
- return new Object[]\r
- { al, alcsel }; // , FirstSeq, noMsa};\r
- }\r
-\r
- /**\r
- * Given an alignment where all other sequences except profileseq are\r
- * aligned to the ungapped profileseq, insert gaps in the other sequences to\r
- * realign them with the residues in profileseq\r
- * \r
- * @param al\r
- * @param profileseq\r
- */\r
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)\r
- {\r
- char gc = al.getGapCharacter();\r
- int[] gapMap = profileseq.gapMap();\r
- // insert gaps into profile\r
- for (int lp = 0, r = 0; r < gapMap.length; r++)\r
- {\r
- if (gapMap[r] - lp > 1)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 1, ns = al.getHeight(); s < ns; s++)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- int diff = gapMap[r] - sq.length();\r
- if (diff > 0)\r
- {\r
- // pad gaps\r
- sq = sq + sb;\r
- while ((diff = gapMap[r] - sq.length()) > 0)\r
- {\r
- sq = sq\r
- + ((diff >= sb.length()) ? sb.toString() : sb\r
- .substring(0, diff));\r
- }\r
- al.getSequenceAt(s).setSequence(sq);\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(\r
- sq.substring(0, gapMap[r]) + sb.toString()\r
- + sq.substring(gapMap[r]));\r
- }\r
- }\r
- }\r
- lp = gapMap[r];\r
- }\r
- }\r
-\r
- /**\r
- * Add gaps into the sequences aligned to profileseq under the given\r
- * AlignmentView\r
- * \r
- * @param profileseq\r
- * @param al\r
- * @param input\r
- */\r
- private ColumnSelection propagateInsertions(SequenceI profileseq,\r
- Alignment al, AlignmentView input)\r
- {\r
- char gc = al.getGapCharacter();\r
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);\r
- ColumnSelection nview = (ColumnSelection) alandcolsel[1];\r
- SequenceI origseq;\r
- nview.pruneDeletions(ShiftList\r
- .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])\r
- .gapMap())); // recover original prediction sequence's\r
- // mapping to view.\r
- int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());\r
- int spos = 0;\r
- int offset = 0;\r
- // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])\r
- // alandcolsel[0])[0].gapMap()))\r
- // add profile to visible contigs\r
- for (int v = 0; v < viscontigs.length; v += 2)\r
- {\r
- if (viscontigs[v] > spos)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
- {\r
- SequenceI sqobj = al.getSequenceAt(s);\r
- if (sqobj != profileseq)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- if (sq.length() <= spos + offset)\r
- {\r
- // pad sequence\r
- int diff = spos + offset - sq.length() - 1;\r
- if (diff > 0)\r
- {\r
- // pad gaps\r
- sq = sq + sb;\r
- while ((diff = spos + offset - sq.length() - 1) > 0)\r
- {\r
- sq = sq\r
- + ((diff >= sb.length()) ? sb.toString() : sb\r
- .substring(0, diff));\r
- }\r
- }\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(\r
- sq.substring(0, spos + offset) + sb.toString()\r
- + sq.substring(spos + offset));\r
- }\r
- }\r
- }\r
- // offset+=sb.length();\r
- }\r
- spos = viscontigs[v + 1] + 1;\r
- }\r
- if ((offset + spos) < profileseq.getLength())\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 1, ns = al.getHeight(); s < ns; s++)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- // pad sequence\r
- int diff = origseq.getLength() - sq.length();\r
- while (diff > 0)\r
- {\r
- sq = sq\r
- + ((diff >= sb.length()) ? sb.toString() : sb\r
- .substring(0, diff));\r
- diff = origseq.getLength() - sq.length();\r
- }\r
- }\r
- }\r
- return nview;\r
- }\r
-\r
- public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)\r
- {\r
- super();\r
- this.predMap = delMap;\r
- String sq = AlignSeq.extractGaps(Comparison.GapChars, seq\r
- .getSequenceAsString());\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, int[] delMap)\r
- {\r
- this(SequenceInfo, msf[0], delMap);\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
-\r
- ext.vamsas.Jpred server;\r
-\r
- String altitle = "";\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, String wsurl, AlignmentView alview,\r
- AlignFrame alframe)\r
- {\r
- super(alframe, wsinfo, alview, wsurl);\r
- this.altitle = altitle;\r
- this.server = server;\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,\r
- SequenceI seq, int[] delMap, AlignmentView alview,\r
- AlignFrame alframe)\r
- {\r
- this(wsinfo, altitle, server, wsurl, alview, alframe);\r
- JPredJob job = new JPredJob(SequenceInfo, seq, delMap);\r
- if (job.hasValidInput())\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- jobs = new WSJob[]\r
- { job };\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,\r
- int[] delMap, AlignmentView alview, AlignFrame alframe,\r
- String wsurl)\r
- {\r
- this(wsinfo, altitle, server, wsurl, alview, alframe);\r
- JPredJob job = new JPredJob(SequenceInfo, msf, delMap);\r
- if (job.hasValidInput())\r
- {\r
- jobs = new WSJob[]\r
- { job };\r
- OutputHeader = wsInfo.getProgressText();\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- public void StartJob(AWsJob j)\r
- {\r
- if (!(j instanceof JPredJob))\r
- {\r
- throw new Error(\r
- "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 if (job.sequence != null)\r
- {\r
- job.jobId = server.predict(job.sequence); // debug like : job.jobId =\r
- // "/jobs/www-jpred/jp_Yatat29";//\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
- throw new Exception(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
- } catch (Exception e)\r
- {\r
- // kill the whole job.\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- if (e.getMessage().indexOf("Exception") > -1)\r
- {\r
- wsInfo\r
- .setStatus(j.jobnum,\r
- WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo\r
- .setProgressText(\r
- j.jobnum,\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- + "It is most likely that there is a problem with the server.\n");\r
- System.err\r
- .println("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" + e.getMessage()\r
- + wsInfo.getProgressText());\r
-\r
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum,\r
- e);\r
-\r
- }\r
- j.allowedServerExceptions = -1;\r
- j.subjobComplete = true;\r
- }\r
- }\r
-\r
- public 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\r
- && jobs[j].hasResults())\r
- {\r
- results++;\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(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(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
- // TODO: cope with multiple subjobs.\r
- if (jobs != null)\r
- {\r
- Object[] res = null;\r
- boolean msa = false;\r
- for (int jn = 0; jn < jobs.length; jn++)\r
- {\r
- Object[] jobres = null;\r
- JPredJob j = (JPredJob) jobs[jn];\r
-\r
- if (j.hasResults())\r
- {\r
- // hack - we only deal with all single seuqence predictions or all\r
- // profile predictions\r
- msa = (j.msa != null) ? true : msa;\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
- {\r
- res = jobres;\r
- }\r
- else\r
- {\r
- // do merge with other job results\r
- throw new Error(\r
- "Multiple JNet subjob merging not yet implemented.");\r
- }\r
- } catch (Exception e)\r
- {\r
- jalview.bin.Cache.log.error(\r
- "JNet Client: JPred Annotation Parse Error", e);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- wsInfo.appendProgressText(j.jobnum, OutputHeader + "\n"\r
- + j.result.getStatus()\r
- + "\nInvalid JNet job result data!\n" + e.getMessage());\r
- j.result.setBroken(true);\r
- }\r
- }\r
- }\r
-\r
- if (res != null)\r
- {\r
- if (newWindow)\r
- {\r
- AlignFrame af;\r
- if (input == null)\r
- {\r
- if (res[1] != null)\r
- {\r
- af = new AlignFrame((Alignment) res[0],\r
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- af = new AlignFrame((Alignment) res[0],\r
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
- else\r
- {\r
- /*\r
- * java.lang.Object[] alandcolsel =\r
- * input.getAlignmentAndColumnSelection\r
- * (alignFrame.getViewport().getGapCharacter()); if\r
- * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
- * if (msa) { throw new Error("Implementation Error! ColumnSelection\r
- * from input alignment will not map to result alignment!"); } } if\r
- * (!msa) { // update hidden regions to account for loss of gaps in\r
- * profile. - if any // gapMap returns insert list, interpreted as\r
- * delete list by pruneDeletions //((ColumnSelection)\r
- * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])\r
- * alandcolsel[0])[0].gapMap())); }\r
- */\r
-\r
- af = new AlignFrame((Alignment) res[0],\r
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- Cache.log.info("Append results onto existing alignment.");\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void pollJob(AWsJob job) throws Exception\r
- {\r
- ((JPredJob)job).result = server.getresult(job.jobId);\r
- }\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.jws1;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.*;
+import jalview.util.*;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import vamsas.objects.simple.JpredResult;
+
+class JPredThread extends JWS1Thread implements WSClientI
+{
+ // TODO: put mapping between JPredJob input and input data here -
+ // JNetAnnotation adding is done after result parsing.
+ class JPredJob extends WSJob
+ {
+ // TODO: make JPredJob deal only with what was sent to and received from a
+ // JNet service
+ int[] predMap = null; // mapping from sequence(i) to the original
+
+ // sequence(predMap[i]) being predicted on
+
+ vamsas.objects.simple.Sequence sequence;
+
+ vamsas.objects.simple.Msfalignment msa;
+
+ java.util.Hashtable SequenceInfo = null;
+
+ int msaIndex = 0; // the position of the original sequence in the array of
+
+ // Sequences in the input object that this job holds a
+ // prediction for
+
+ /**
+ *
+ * @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;
+ }
+
+ public boolean hasValidInput()
+ {
+ if (sequence != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @return null or Object[] { annotated alignment for this prediction,
+ * ColumnSelection for this prediction} or null if no results
+ * available.
+ * @throws Exception
+ */
+ public Object[] getResultSet() throws Exception
+ {
+ if (result == null || !result.isFinished())
+ {
+ return null;
+ }
+ Alignment al = null;
+ ColumnSelection alcsel = 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))
+ {
+ SequenceI sqs[];
+ if (predMap != null)
+ {
+ Object[] alandcolsel = input
+ .getAlignmentAndColumnSelection(getGapChar());
+ sqs = (SequenceI[]) alandcolsel[0];
+ al = new Alignment(sqs);
+ alcsel = (ColumnSelection) alandcolsel[1];
+ }
+ else
+ {
+ al = new FormatAdapter().readFile(result.getAligfile(),
+ "Paste", format);
+ 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, predMap);
+
+ }
+ else
+ {
+ throw (new Exception("Unknown format " + format
+ + " for file : \n" + result.getAligfile()));
+ }
+ }
+ else
+ {
+ al = new Alignment(preds);
+ FirstSeq = prediction.getQuerySeqPosition();
+ if (predMap != null)
+ {
+ char gc = getGapChar();
+ SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
+ .getAlignmentAndColumnSelection(gc))[0];
+ if (this.msaIndex >= sqs.length)
+ {
+ throw new Error(
+ "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+ }
+
+ // ///
+ // Uses RemoveGapsCommand
+ // ///
+ new jalview.commands.RemoveGapsCommand("Remove Gaps",
+ new SequenceI[]
+ { sqs[msaIndex] }, currentView);
+
+ SequenceI profileseq = al.getSequenceAt(FirstSeq);
+ profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
+ }
+
+ 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, predMap);
+ SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
+ alignToProfileSeq(al, profileseq);
+ if (predMap != null)
+ {
+ // Adjust input view for gaps
+ // propagate insertions into profile
+ alcsel = propagateInsertions(profileseq, al, input);
+ }
+ }
+ }
+ return new Object[]
+ { al, alcsel }; // , FirstSeq, noMsa};
+ }
+
+ /**
+ * Given an alignment where all other sequences except profileseq are
+ * aligned to the ungapped profileseq, insert gaps in the other sequences to
+ * realign them with the residues in profileseq
+ *
+ * @param al
+ * @param profileseq
+ */
+ private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ {
+ char gc = al.getGapCharacter();
+ int[] gapMap = profileseq.gapMap();
+ // insert gaps into profile
+ for (int lp = 0, r = 0; r < gapMap.length; r++)
+ {
+ if (gapMap[r] - lp > 1)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 1, ns = al.getHeight(); s < ns; s++)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ int diff = gapMap[r] - sq.length();
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = gapMap[r] - sq.length()) > 0)
+ {
+ sq = sq
+ + ((diff >= sb.length()) ? sb.toString() : sb
+ .substring(0, diff));
+ }
+ al.getSequenceAt(s).setSequence(sq);
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, gapMap[r]) + sb.toString()
+ + sq.substring(gapMap[r]));
+ }
+ }
+ }
+ lp = gapMap[r];
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @param al
+ * @param input
+ */
+ private ColumnSelection propagateInsertions(SequenceI profileseq,
+ Alignment al, AlignmentView input)
+ {
+ char gc = al.getGapCharacter();
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+ SequenceI origseq;
+ nview.pruneDeletions(ShiftList
+ .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])
+ .gapMap())); // recover original prediction sequence's
+ // mapping to view.
+ int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+ // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ // alandcolsel[0])[0].gapMap()))
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ sq = sq
+ + ((diff >= sb.length()) ? sb.toString() : sb
+ .substring(0, diff));
+ }
+ }
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 1, ns = al.getHeight(); s < ns; s++)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ sq = sq
+ + ((diff >= sb.length()) ? sb.toString() : sb
+ .substring(0, diff));
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
+ return nview;
+ }
+
+ public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+ {
+ super();
+ this.predMap = delMap;
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
+ .getSequenceAsString());
+ 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, int[] delMap)
+ {
+ this(SequenceInfo, msf[0], delMap);
+ 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, String wsurl, AlignmentView alview,
+ AlignFrame alframe)
+ {
+ super(alframe, wsinfo, alview, wsurl);
+ this.altitle = altitle;
+ this.server = server;
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle,
+ ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+ SequenceI seq, int[] delMap, AlignmentView alview,
+ AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server, wsurl, alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
+ if (job.hasValidInput())
+ {
+ OutputHeader = wsInfo.getProgressText();
+ jobs = new WSJob[]
+ { job };
+ job.setJobnum(0);
+ }
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle,
+ ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
+ int[] delMap, AlignmentView alview, AlignFrame alframe,
+ String wsurl)
+ {
+ this(wsinfo, altitle, server, wsurl, alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
+ if (job.hasValidInput())
+ {
+ jobs = new WSJob[]
+ { job };
+ OutputHeader = wsInfo.getProgressText();
+ job.setJobnum(0);
+ }
+ }
+
+ public void StartJob(AWsJob 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.setJobId(server.predictOnMsa(job.msa));
+ }
+ else if (job.sequence != null)
+ {
+ job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
+ // "/jobs/www-jpred/jp_Yatat29";//
+ }
+
+ if (job.getJobId() != null)
+ {
+ if (job.getJobId().startsWith("Broken"))
+ {
+ job.result = (vamsas.objects.simple.Result) new JpredResult();
+ job.result.setInvalid(true);
+ job.result.setStatus("Submission " + job.getJobId());
+ throw new Exception(job.getJobId());
+ }
+ else
+ {
+ job.setSubmitted(true);
+ job.setSubjobComplete(false);
+ Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ }
+ }
+ else
+ {
+ throw new Exception("Server timed out - try again later\n");
+ }
+ } catch (Exception e)
+ {
+ // kill the whole job.
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ if (e.getMessage().indexOf("Exception") > -1)
+ {
+ wsInfo
+ .setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo
+ .setProgressText(
+ j.getJobnum(),
+ "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.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ // JBPNote - this could be a popup informing the user of the problem.
+ wsInfo.appendProgressText(j.getJobnum(),
+ "Failed to submit the prediction:\n" + e.getMessage()
+ + wsInfo.getProgressText());
+
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.getJobnum(),
+ e);
+
+ }
+ j.setAllowedServerExceptions(-1);
+ j.setSubjobComplete(true);
+ }
+ }
+
+ public 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].isSubmitted() && jobs[j].isSubjobComplete()
+ && 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)
+ {
+ Object[] res = null;
+ boolean msa = false;
+ for (int jn = 0; jn < jobs.length; jn++)
+ {
+ Object[] 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.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendProgressText(j.getJobnum(), 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)
+ {
+ if (res[1] != null)
+ {
+ af = new AlignFrame((Alignment) res[0],
+ (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ else
+ {
+ af = new AlignFrame((Alignment) res[0],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ 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!"); } } if
+ * (!msa) { // update hidden regions to account for loss of gaps in
+ * profile. - if any // gapMap returns insert list, interpreted as
+ * delete list by pruneDeletions //((ColumnSelection)
+ * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ * alandcolsel[0])[0].gapMap())); }
+ */
+
+ af = new AlignFrame((Alignment) res[0],
+ (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ else
+ {
+ Cache.log.info("Append results onto existing alignment.");
+ }
+ }
+ }
+ }
+
+ public void pollJob(AWsJob job) throws Exception
+ {
+ ((JPredJob)job).result = server.getresult(job.getJobId());
+ }
+
+ public boolean isCancellable()
+ {
+ return false;
+ }
+
+ public void cancelJob()
+ {
+ throw new Error("Implementation error!");
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+}
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-package jalview.ws;
+package jalview.ws.jws1;
import javax.swing.*;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.ws.AWSThread;
/**
* specific methods for Jalview WS1 web service jobs
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-package jalview.ws;
+package jalview.ws.jws1;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+ new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame.getTitle(),
msa, false, true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+ new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame.getTitle(),
msa, true, true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import vamsas.objects.simple.MsaResult;\r
-\r
-/**\r
- * <p>\r
- * Title:\r
- * </p>\r
- * \r
- * <p>\r
- * Description:\r
- * </p>\r
- * \r
- * <p>\r
- * Copyright: Copyright (c) 2004\r
- * </p>\r
- * \r
- * <p>\r
- * Company: Dundee University\r
- * </p>\r
- * \r
- * @author not attributable\r
- * @version 1.0\r
- */\r
-class MsaWSThread extends JWS1Thread implements WSClientI\r
-{\r
- boolean submitGaps = false; // pass sequences including gaps to alignment\r
-\r
- // service\r
-\r
- boolean preserveOrder = true; // and always store and recover sequence\r
-\r
- // order\r
-\r
- class MsaWSJob extends WSJob\r
- {\r
- // hold special input for this\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
-\r
- /**\r
- * MsaWSJob\r
- * \r
- * @param jobNum\r
- * int\r
- * @param jobId\r
- * String\r
- */\r
- public MsaWSJob(int jobNum, SequenceI[] inSeqs)\r
- {\r
- this.jobnum = jobNum;\r
- if (!prepareInput(inSeqs, 2))\r
- {\r
- submitted = true;\r
- subjobComplete = true;\r
- result = new MsaResult();\r
- result.setFinished(true);\r
- result.setStatus("Job never ran - input returned to user.");\r
- }\r
-\r
- }\r
-\r
- Hashtable SeqNames = new Hashtable();\r
-\r
- Vector emptySeqs = new Vector();\r
-\r
- /**\r
- * prepare input sequences for MsaWS service\r
- * \r
- * @param seqs\r
- * jalview sequences to be prepared\r
- * @param minlen\r
- * minimum number of residues required for this MsaWS service\r
- * @return true if seqs contains sequences to be submitted to service.\r
- */\r
- private boolean prepareInput(SequenceI[] seqs, int minlen)\r
- {\r
- int nseqs = 0;\r
- if (minlen < 0)\r
- {\r
- throw new Error(\r
- "Implementation error: minlen must be zero or more.");\r
- }\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
- {\r
- nseqs++;\r
- }\r
- }\r
- boolean valid = nseqs > 1; // need at least two seqs\r
- vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
- : null;\r
- for (int i = 0, n = 0; i < seqs.length; i++)\r
- {\r
-\r
- String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same\r
- // for\r
- // any\r
- // subjob\r
- SeqNames.put(newname, jalview.analysis.SeqsetUtils\r
- .SeqCharacterHash(seqs[i]));\r
- if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
- {\r
- seqarray[n] = new vamsas.objects.simple.Sequence();\r
- seqarray[n].setId(newname);\r
- seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()\r
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,\r
- seqs[i].getSequenceAsString()));\r
- }\r
- else\r
- {\r
- String empty = null;\r
- if (seqs[i].getEnd() >= seqs[i].getStart())\r
- {\r
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq\r
- .extractGaps(jalview.util.Comparison.GapChars, seqs[i]\r
- .getSequenceAsString());\r
- }\r
- emptySeqs.add(new String[]\r
- { newname, empty });\r
- }\r
- }\r
- this.seqs = new vamsas.objects.simple.SequenceSet();\r
- this.seqs.setSeqs(seqarray);\r
- return valid;\r
- }\r
-\r
- /**\r
- * \r
- * @return true if getAlignment will return a valid alignment result.\r
- */\r
- public boolean hasResults()\r
- {\r
- if (subjobComplete && result != null && result.isFinished()\r
- && ((MsaResult) result).getMsa() != null\r
- && ((MsaResult) result).getMsa().getSeqs() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- public Object[] getAlignment()\r
- {\r
-\r
- if (result != null && result.isFinished())\r
- {\r
- SequenceI[] alseqs = null;\r
- char alseq_gapchar = '-';\r
- int alseq_l = 0;\r
- if (((MsaResult) result).getMsa() != null)\r
- {\r
- alseqs = getVamsasAlignment(((MsaResult) result).getMsa());\r
- alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()\r
- .charAt(0);\r
- alseq_l = alseqs.length;\r
- }\r
- if (emptySeqs.size() > 0)\r
- {\r
- SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];\r
- // get width\r
- int i, w = 0;\r
- if (alseq_l > 0)\r
- {\r
- for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)\r
- {\r
- if (w < alseqs[i].getLength())\r
- {\r
- w = alseqs[i].getLength();\r
- }\r
- t_alseqs[i] = alseqs[i];\r
- alseqs[i] = null;\r
- }\r
- }\r
- // check that aligned width is at least as wide as emptySeqs width.\r
- int ow = w, nw = w;\r
- for (i = 0, w = emptySeqs.size(); i < w; i++)\r
- {\r
- String[] es = (String[]) emptySeqs.get(i);\r
- if (es != null && es[1] != null)\r
- {\r
- int sw = es[1].length();\r
- if (nw < sw)\r
- {\r
- nw = sw;\r
- }\r
- }\r
- }\r
- // make a gapped string.\r
- StringBuffer insbuff = new StringBuffer(w);\r
- for (i = 0; i < nw; i++)\r
- {\r
- insbuff.append(alseq_gapchar);\r
- }\r
- if (ow < nw)\r
- {\r
- for (i = 0; i < alseq_l; i++)\r
- {\r
- int sw = t_alseqs[i].getLength();\r
- if (nw > sw)\r
- {\r
- // pad at end\r
- alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()\r
- + insbuff.substring(0, sw - nw));\r
- }\r
- }\r
- }\r
- for (i = 0, w = emptySeqs.size(); i < w; i++)\r
- {\r
- String[] es = (String[]) emptySeqs.get(i);\r
- if (es[1] == null)\r
- {\r
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],\r
- insbuff.toString(), 1, 0);\r
- }\r
- else\r
- {\r
- if (es[1].length() < nw)\r
- {\r
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
- es[0],\r
- es[1] + insbuff.substring(0, nw - es[1].length()),\r
- 1, 1 + es[1].length());\r
- }\r
- else\r
- {\r
- t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
- es[0], es[1]);\r
- }\r
- }\r
- }\r
- alseqs = t_alseqs;\r
- }\r
- AlignmentOrder msaorder = new AlignmentOrder(alseqs);\r
- // always recover the order - makes parseResult()'s life easier.\r
- jalview.analysis.AlignmentSorter.recoverOrder(alseqs);\r
- // account for any missing sequences\r
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);\r
- return new Object[]\r
- { alseqs, msaorder };\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * mark subjob as cancelled and set result object appropriatly\r
- */\r
- void cancel()\r
- {\r
- cancelled = true;\r
- subjobComplete = true;\r
- result = null;\r
- }\r
-\r
- /**\r
- * \r
- * @return boolean true if job can be submitted.\r
- */\r
- public boolean hasValidInput()\r
- {\r
- if (seqs.getSeqs() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
- }\r
-\r
- String alTitle; // name which will be used to form new alignment window.\r
-\r
- Alignment dataset; // dataset to which the new alignment will be\r
-\r
- // associated.\r
-\r
- ext.vamsas.MuscleWS server = null;\r
-\r
- /**\r
- * set basic options for this (group) of Msa jobs\r
- * \r
- * @param subgaps\r
- * boolean\r
- * @param presorder\r
- * boolean\r
- */\r
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- AlignmentView alview, String wsname, boolean subgaps,\r
- boolean presorder)\r
- {\r
- super(alFrame, wsinfo, alview, wsname, wsUrl);\r
- this.server = server;\r
- this.submitGaps = subgaps;\r
- this.preserveOrder = presorder;\r
- }\r
-\r
- /**\r
- * create one or more Msa jobs to align visible seuqences in _msa\r
- * \r
- * @param title\r
- * String\r
- * @param _msa\r
- * AlignmentView\r
- * @param subgaps\r
- * boolean\r
- * @param presorder\r
- * boolean\r
- * @param seqset\r
- * Alignment\r
- */\r
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- String wsname, String title, AlignmentView _msa, boolean subgaps,\r
- boolean presorder, Alignment seqset)\r
- {\r
- this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);\r
- OutputHeader = wsInfo.getProgressText();\r
- alTitle = title;\r
- dataset = seqset;\r
-\r
- SequenceI[][] conmsa = _msa.getVisibleContigs('-');\r
- if (conmsa != null)\r
- {\r
- int njobs = conmsa.length;\r
- jobs = new MsaWSJob[njobs];\r
- for (int j = 0; j < njobs; j++)\r
- {\r
- if (j != 0)\r
- {\r
- jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);\r
- }\r
- else\r
- {\r
- jobs[j] = new MsaWSJob(0, conmsa[j]);\r
- }\r
- if (njobs > 0)\r
- {\r
- wsinfo\r
- .setProgressName("region " + jobs[j].jobnum,\r
- jobs[j].jobnum);\r
- }\r
- wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);\r
- }\r
- }\r
- }\r
-\r
- public boolean isCancellable()\r
- {\r
- return true;\r
- }\r
-\r
- public void cancelJob()\r
- {\r
- if (!jobComplete && jobs != null)\r
- {\r
- boolean cancelled = true;\r
- for (int job = 0; job < jobs.length; job++)\r
- {\r
- if (jobs[job].submitted && !jobs[job].subjobComplete)\r
- {\r
- String cancelledMessage = "";\r
- try\r
- {\r
- vamsas.objects.simple.WsJobId cancelledJob = server\r
- .cancel(jobs[job].jobId);\r
- if (cancelledJob.getStatus() == 2)\r
- {\r
- // CANCELLED_JOB\r
- cancelledMessage = "Job cancelled.";\r
- ((MsaWSJob) jobs[job]).cancel();\r
- wsInfo.setStatus(jobs[job].jobnum,\r
- WebserviceInfo.STATE_CANCELLED_OK);\r
- }\r
- else if (cancelledJob.getStatus() == 3)\r
- {\r
- // VALID UNSTOPPABLE JOB\r
- cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
- cancelled = false;\r
- // wsInfo.setStatus(jobs[job].jobnum,\r
- // WebserviceInfo.STATE_RUNNING);\r
- }\r
-\r
- if (cancelledJob.getJobId() != null)\r
- {\r
- cancelledMessage += ("[" + cancelledJob.getJobId() + "]");\r
- }\r
-\r
- cancelledMessage += "\n";\r
- } catch (Exception exc)\r
- {\r
- cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"\r
- + exc + "\n");\r
- Cache.log.warn(\r
- "Exception whilst cancelling " + jobs[job].jobId, exc);\r
- }\r
- wsInfo.setProgressText(jobs[job].jobnum, OutputHeader\r
- + cancelledMessage + "\n");\r
- }\r
- }\r
- if (cancelled)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
- jobComplete = true;\r
- }\r
- this.interrupt(); // kick thread to update job states.\r
- }\r
- else\r
- {\r
- if (!jobComplete)\r
- {\r
- wsInfo\r
- .setProgressText(OutputHeader\r
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
- }\r
- }\r
- }\r
-\r
- public void pollJob(AWsJob job) throws Exception\r
- {\r
- ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);\r
- }\r
-\r
- public void StartJob(AWsJob job)\r
- {\r
- if (!(job instanceof MsaWSJob))\r
- {\r
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "\r
- + job.getClass());\r
- }\r
- MsaWSJob j = (MsaWSJob) job;\r
- if (j.submitted)\r
- {\r
- if (Cache.log.isDebugEnabled())\r
- {\r
- Cache.log.debug("Tried to submit an already submitted job "\r
- + j.jobId);\r
- }\r
- return;\r
- }\r
- if (j.seqs.getSeqs() == null)\r
- {\r
- // special case - selection consisted entirely of empty sequences...\r
- j.submitted = true;\r
- j.result = new MsaResult();\r
- j.result.setFinished(true);\r
- j.result.setStatus("Empty Alignment Job");\r
- ((MsaResult) j.result).setMsa(null);\r
- }\r
- try\r
- {\r
- vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);\r
-\r
- if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
- {\r
- j.jobId = jobsubmit.getJobId();\r
- j.submitted = true;\r
- j.subjobComplete = false;\r
- // System.out.println(WsURL + " Job Id '" + jobId + "'");\r
- }\r
- else\r
- {\r
- if (jobsubmit == null)\r
- {\r
- throw new Exception(\r
- "Server at "\r
- + WsUrl\r
- + " returned null object, it probably cannot be contacted. Try again later ?");\r
- }\r
-\r
- throw new Exception(jobsubmit.getJobId());\r
- }\r
- } catch (Exception e)\r
- {\r
- // TODO: JBPNote catch timeout or other fault types explicitly\r
- // For unexpected errors\r
- System.err\r
- .println(WebServiceName\r
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"\r
- + "When contacting Server:" + WsUrl + "\n"\r
- + e.toString() + "\n");\r
- j.allowedServerExceptions = 0;\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo\r
- .appendProgressText(\r
- j.jobnum,\r
- "Failed to submit sequences for alignment.\n"\r
- + "It is most likely that there is a problem with the server.\n"\r
- + "Just close the window\n");\r
-\r
- // e.printStackTrace(); // TODO: JBPNote DEBUG\r
- }\r
- }\r
-\r
- private jalview.datamodel.Sequence[] getVamsasAlignment(\r
- vamsas.objects.simple.Alignment valign)\r
- {\r
- // TODO: refactor to helper class for vamsas.objects.simple objects\r
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
-\r
- for (int i = 0, j = seqs.length; i < j; i++)\r
- {\r
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]\r
- .getSeq());\r
- }\r
-\r
- return msa;\r
- }\r
-\r
- public 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\r
- && jobs[j].hasResults())\r
- {\r
- results++;\r
- vamsas.objects.simple.Alignment valign = ((MsaResult)((MsaWSJob) jobs[j]).result)\r
- .getMsa();\r
- if (valign != null)\r
- {\r
- wsInfo.appendProgressText(jobs[j].jobnum,\r
- "\nAlignment Object Method Notes\n");\r
- String[] lines = valign.getMethod();\r
- for (int line = 0; line < lines.length; line++)\r
- {\r
- wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");\r
- }\r
- // JBPNote The returned files from a webservice could be\r
- // hidden behind icons in the monitor window that,\r
- // when clicked, pop up their corresponding data\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(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(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 newFrame)\r
- {\r
- // view input or result data for each block\r
- Vector alorders = new Vector();\r
- SequenceI[][] results = new SequenceI[jobs.length][];\r
- AlignmentOrder[] orders = new AlignmentOrder[jobs.length];\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
- if (jobs[j].hasResults())\r
- {\r
- Object[] res = ((MsaWSJob) jobs[j]).getAlignment();\r
- alorders.add(res[1]);\r
- results[j] = (SequenceI[]) res[0];\r
- orders[j] = (AlignmentOrder) res[1];\r
-\r
- // SequenceI[] alignment = input.getUpdated\r
- }\r
- else\r
- {\r
- results[j] = null;\r
- }\r
- }\r
- Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
- // trash references to original result data\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
- results[j] = null;\r
- orders[j] = null;\r
- }\r
- SequenceI[] alignment = (SequenceI[]) newview[0];\r
- ColumnSelection columnselection = (ColumnSelection) newview[1];\r
- Alignment al = new Alignment(alignment);\r
- // TODO: add 'provenance' property to alignment from the method notes\r
- // accompanying each subjob\r
- if (dataset != null)\r
- {\r
- al.setDataset(dataset);\r
- }\r
-\r
- propagateDatasetMappings(al);\r
- // JBNote- TODO: warn user if a block is input rather than aligned data ?\r
-\r
- if (newFrame)\r
- {\r
- AlignFrame af = new AlignFrame(al, columnselection,\r
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
-\r
- // initialise with same renderer settings as in parent alignframe.\r
- af.getFeatureRenderer().transferSettings(this.featureSettings);\r
- // update orders\r
- if (alorders.size() > 0)\r
- {\r
- if (alorders.size() == 1)\r
- {\r
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",\r
- (AlignmentOrder) alorders.get(0));\r
- }\r
- else\r
- {\r
- // construct a non-redundant ordering set\r
- Vector names = new Vector();\r
- for (int i = 0, l = alorders.size(); i < l; i++)\r
- {\r
- String orderName = new String(" Region " + i);\r
- int j = i + 1;\r
-\r
- while (j < l)\r
- {\r
- if (((AlignmentOrder) alorders.get(i))\r
- .equals(((AlignmentOrder) alorders.get(j))))\r
- {\r
- alorders.remove(j);\r
- l--;\r
- orderName += "," + j;\r
- }\r
- else\r
- {\r
- j++;\r
- }\r
- }\r
-\r
- if (i == 0 && j == 1)\r
- {\r
- names.add(new String(""));\r
- }\r
- else\r
- {\r
- names.add(orderName);\r
- }\r
- }\r
- for (int i = 0, l = alorders.size(); i < l; i++)\r
- {\r
- af.addSortByOrderMenuItem(WebServiceName\r
- + ((String) names.get(i)) + " Ordering",\r
- (AlignmentOrder) alorders.get(i));\r
- }\r
- }\r
- }\r
-\r
- Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
-\r
- }\r
- else\r
- {\r
- System.out.println("MERGE WITH OLD FRAME");\r
- // TODO: modify alignment in original frame, replacing old for new\r
- // alignment using the commands.EditCommand model to ensure the update can\r
- // be undone\r
- }\r
- }\r
-\r
- public boolean canMergeResults()\r
- {\r
- return false;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.jws1;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import vamsas.objects.simple.MsaResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class MsaWSThread extends JWS1Thread implements WSClientI
+{
+ boolean submitGaps = false; // pass sequences including gaps to alignment
+
+ // service
+
+ boolean preserveOrder = true; // and always store and recover sequence
+
+ // order
+
+ class MsaWSJob extends WSJob
+ {
+ // hold special input for this
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+ /**
+ * MsaWSJob
+ *
+ * @param jobNum
+ * int
+ * @param jobId
+ * String
+ */
+ public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+ {
+ this.jobnum = jobNum;
+ if (!prepareInput(inSeqs, 2))
+ {
+ submitted = true;
+ subjobComplete = true;
+ result = new MsaResult();
+ result.setFinished(true);
+ result.setStatus("Job never ran - input returned to user.");
+ }
+
+ }
+
+ Hashtable SeqNames = new Hashtable();
+
+ Vector emptySeqs = new Vector();
+
+ /**
+ * prepare input sequences for MsaWS service
+ *
+ * @param seqs
+ * jalview sequences to be prepared
+ * @param minlen
+ * minimum number of residues required for this MsaWS service
+ * @return true if seqs contains sequences to be submitted to service.
+ */
+ private boolean prepareInput(SequenceI[] seqs, int minlen)
+ {
+ int nseqs = 0;
+ if (minlen < 0)
+ {
+ throw new Error(
+ "Implementation error: minlen must be zero or more.");
+ }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ nseqs++;
+ }
+ }
+ boolean valid = nseqs > 1; // need at least two seqs
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ : null;
+ for (int i = 0, n = 0; i < seqs.length; i++)
+ {
+
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+ // for
+ // any
+ // subjob
+ SeqNames.put(newname, jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seqs[i]));
+ if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ seqarray[n] = new vamsas.objects.simple.Sequence();
+ seqarray[n].setId(newname);
+ seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString()));
+ }
+ else
+ {
+ String empty = null;
+ if (seqs[i].getEnd() >= seqs[i].getStart())
+ {
+ empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+ .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+ .getSequenceAsString());
+ }
+ emptySeqs.add(new String[]
+ { newname, empty });
+ }
+ }
+ this.seqs = new vamsas.objects.simple.SequenceSet();
+ this.seqs.setSeqs(seqarray);
+ return valid;
+ }
+
+ /**
+ *
+ * @return true if getAlignment will return a valid alignment result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete && result != null && result.isFinished()
+ && ((MsaResult) result).getMsa() != null
+ && ((MsaResult) result).getMsa().getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public Object[] getAlignment()
+ {
+
+ if (result != null && result.isFinished())
+ {
+ SequenceI[] alseqs = null;
+ char alseq_gapchar = '-';
+ int alseq_l = 0;
+ if (((MsaResult) result).getMsa() != null)
+ {
+ alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
+ alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()
+ .charAt(0);
+ alseq_l = alseqs.length;
+ }
+ if (emptySeqs.size() > 0)
+ {
+ SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
+ // get width
+ int i, w = 0;
+ if (alseq_l > 0)
+ {
+ for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
+ {
+ if (w < alseqs[i].getLength())
+ {
+ w = alseqs[i].getLength();
+ }
+ t_alseqs[i] = alseqs[i];
+ alseqs[i] = null;
+ }
+ }
+ // check that aligned width is at least as wide as emptySeqs width.
+ int ow = w, nw = w;
+ for (i = 0, w = emptySeqs.size(); i < w; i++)
+ {
+ String[] es = (String[]) emptySeqs.get(i);
+ if (es != null && es[1] != null)
+ {
+ int sw = es[1].length();
+ if (nw < sw)
+ {
+ nw = sw;
+ }
+ }
+ }
+ // make a gapped string.
+ StringBuffer insbuff = new StringBuffer(w);
+ for (i = 0; i < nw; i++)
+ {
+ insbuff.append(alseq_gapchar);
+ }
+ if (ow < nw)
+ {
+ for (i = 0; i < alseq_l; i++)
+ {
+ int sw = t_alseqs[i].getLength();
+ if (nw > sw)
+ {
+ // pad at end
+ alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
+ + insbuff.substring(0, sw - nw));
+ }
+ }
+ }
+ for (i = 0, w = emptySeqs.size(); i < w; i++)
+ {
+ String[] es = (String[]) emptySeqs.get(i);
+ if (es[1] == null)
+ {
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
+ insbuff.toString(), 1, 0);
+ }
+ else
+ {
+ if (es[1].length() < nw)
+ {
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+ es[0],
+ es[1] + insbuff.substring(0, nw - es[1].length()),
+ 1, 1 + es[1].length());
+ }
+ else
+ {
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+ es[0], es[1]);
+ }
+ }
+ }
+ alseqs = t_alseqs;
+ }
+ AlignmentOrder msaorder = new AlignmentOrder(alseqs);
+ // always recover the order - makes parseResult()'s life easier.
+ jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+ // account for any missing sequences
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+ return new Object[]
+ { alseqs, msaorder };
+ }
+ return null;
+ }
+
+ /**
+ * mark subjob as cancelled and set result object appropriatly
+ */
+ void cancel()
+ {
+ cancelled = true;
+ subjobComplete = true;
+ result = null;
+ }
+
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ public boolean hasValidInput()
+ {
+ if (seqs.getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+ }
+
+ String alTitle; // name which will be used to form new alignment window.
+
+ Alignment dataset; // dataset to which the new alignment will be
+
+ // associated.
+
+ ext.vamsas.MuscleWS server = null;
+
+ /**
+ * set basic options for this (group) of Msa jobs
+ *
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ */
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ AlignmentView alview, String wsname, boolean subgaps,
+ boolean presorder)
+ {
+ super(alFrame, wsinfo, alview, wsname, wsUrl);
+ this.server = server;
+ this.submitGaps = subgaps;
+ this.preserveOrder = presorder;
+ }
+
+ /**
+ * create one or more Msa jobs to align visible seuqences in _msa
+ *
+ * @param title
+ * String
+ * @param _msa
+ * AlignmentView
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ * @param seqset
+ * Alignment
+ */
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ String wsname, String title, AlignmentView _msa, boolean subgaps,
+ boolean presorder, Alignment seqset)
+ {
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
+ OutputHeader = wsInfo.getProgressText();
+ alTitle = title;
+ dataset = seqset;
+
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+ if (conmsa != null)
+ {
+ int njobs = conmsa.length;
+ jobs = new MsaWSJob[njobs];
+ for (int j = 0; j < njobs; j++)
+ {
+ if (j != 0)
+ {
+ jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
+ }
+ else
+ {
+ jobs[j] = new MsaWSJob(0, conmsa[j]);
+ }
+ if (njobs > 0)
+ {
+ wsinfo
+ .setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
+ }
+ wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
+ }
+ }
+ }
+
+ public boolean isCancellable()
+ {
+ return true;
+ }
+
+ public void cancelJob()
+ {
+ if (!jobComplete && jobs != null)
+ {
+ boolean cancelled = true;
+ for (int job = 0; job < jobs.length; job++)
+ {
+ if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete())
+ {
+ String cancelledMessage = "";
+ try
+ {
+ vamsas.objects.simple.WsJobId cancelledJob = server
+ .cancel(jobs[job].getJobId());
+ if (cancelledJob.getStatus() == 2)
+ {
+ // CANCELLED_JOB
+ cancelledMessage = "Job cancelled.";
+ ((MsaWSJob) jobs[job]).cancel();
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+ }
+ else if (cancelledJob.getStatus() == 3)
+ {
+ // VALID UNSTOPPABLE JOB
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+ cancelled = false;
+ // wsInfo.setStatus(jobs[job].jobnum,
+ // WebserviceInfo.STATE_RUNNING);
+ }
+
+ if (cancelledJob.getJobId() != null)
+ {
+ cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+ }
+
+ cancelledMessage += "\n";
+ } catch (Exception exc)
+ {
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ + exc + "\n");
+ Cache.log.warn(
+ "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ }
+ wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ + cancelledMessage + "\n");
+ }
+ }
+ if (cancelled)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+ jobComplete = true;
+ }
+ this.interrupt(); // kick thread to update job states.
+ }
+ else
+ {
+ if (!jobComplete)
+ {
+ wsInfo
+ .setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ }
+ }
+ }
+
+ public void pollJob(AWsJob job) throws Exception
+ {
+ ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId());
+ }
+
+ public void StartJob(AWsJob job)
+ {
+ if (!(job instanceof MsaWSJob))
+ {
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+ + job.getClass());
+ }
+ MsaWSJob j = (MsaWSJob) job;
+ if (j.isSubmitted())
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Tried to submit an already submitted job "
+ + j.getJobId());
+ }
+ return;
+ }
+ if (j.seqs.getSeqs() == null)
+ {
+ // special case - selection consisted entirely of empty sequences...
+ j.setSubmitted(true);
+ j.result = new MsaResult();
+ j.result.setFinished(true);
+ j.result.setStatus("Empty Alignment Job");
+ ((MsaResult) j.result).setMsa(null);
+ }
+ try
+ {
+ vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
+
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+ {
+ j.setJobId(jobsubmit.getJobId());
+ j.setSubmitted(true);
+ j.setSubjobComplete(false);
+ // 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)
+ {
+ // TODO: JBPNote catch timeout or other fault types explicitly
+ // For unexpected errors
+ System.err
+ .println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n"
+ + e.toString() + "\n");
+ j.setAllowedServerExceptions(0);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo
+ .appendProgressText(
+ j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "It is most likely that there is a problem with the server.\n"
+ + "Just close the window\n");
+
+ // e.printStackTrace(); // TODO: JBPNote DEBUG
+ }
+ }
+
+ private jalview.datamodel.Sequence[] getVamsasAlignment(
+ vamsas.objects.simple.Alignment valign)
+ {
+ // TODO: refactor to helper class for vamsas.objects.simple objects
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+ for (int i = 0, j = seqs.length; i < j; i++)
+ {
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+ .getSeq());
+ }
+
+ return msa;
+ }
+
+ public 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].isSubmitted() && jobs[j].isSubjobComplete()
+ && jobs[j].hasResults())
+ {
+ results++;
+ vamsas.objects.simple.Alignment valign = ((MsaResult)((MsaWSJob) jobs[j]).result)
+ .getMsa();
+ if (valign != null)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(),
+ "\nAlignment Object Method Notes\n");
+ String[] lines = valign.getMethod();
+ for (int line = 0; line < lines.length; line++)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+ }
+ // JBPNote The returned files from a webservice could be
+ // hidden behind icons in the monitor window that,
+ // when clicked, pop up their corresponding data
+ }
+ }
+ }
+ } 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 newFrame)
+ {
+ // view input or result data for each block
+ Vector alorders = new Vector();
+ SequenceI[][] results = new SequenceI[jobs.length][];
+ AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+ for (int j = 0; j < jobs.length; j++)
+ {
+ if (jobs[j].hasResults())
+ {
+ Object[] res = ((MsaWSJob) jobs[j]).getAlignment();
+ alorders.add(res[1]);
+ results[j] = (SequenceI[]) res[0];
+ orders[j] = (AlignmentOrder) res[1];
+
+ // SequenceI[] alignment = input.getUpdated
+ }
+ else
+ {
+ results[j] = null;
+ }
+ }
+ Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+ // trash references to original result data
+ for (int j = 0; j < jobs.length; j++)
+ {
+ results[j] = null;
+ orders[j] = null;
+ }
+ SequenceI[] alignment = (SequenceI[]) newview[0];
+ ColumnSelection columnselection = (ColumnSelection) newview[1];
+ Alignment al = new Alignment(alignment);
+ // TODO: add 'provenance' property to alignment from the method notes
+ // accompanying each subjob
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ propagateDatasetMappings(al);
+ // JBNote- TODO: warn user if a block is input rather than aligned data ?
+
+ if (newFrame)
+ {
+ AlignFrame af = new AlignFrame(al, columnselection,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+ // update orders
+ if (alorders.size() > 0)
+ {
+ if (alorders.size() == 1)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+ (AlignmentOrder) alorders.get(0));
+ }
+ else
+ {
+ // construct a non-redundant ordering set
+ Vector names = new Vector();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = new String(" Region " + i);
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (((AlignmentOrder) alorders.get(i))
+ .equals(((AlignmentOrder) alorders.get(j))))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add(new String(""));
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem(WebServiceName
+ + ((String) names.get(i)) + " Ordering",
+ (AlignmentOrder) alorders.get(i));
+ }
+ }
+ }
+
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ }
+ else
+ {
+ System.out.println("MERGE WITH OLD FRAME");
+ // TODO: modify alignment in original frame, replacing old for new
+ // alignment using the commands.EditCommand model to ensure the update can
+ // be undone
+ }
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import java.awt.Component;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.ActionListener;\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.StringTokenizer;\r
-import java.util.Vector;\r
-\r
-import javax.swing.*;\r
-\r
-import ext.vamsas.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SeqSearchWSClient extends WS1Client\r
-{\r
- /**\r
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
- */\r
- ext.vamsas.SeqSearchI server;\r
-\r
- AlignFrame alignFrame;\r
-\r
- /**\r
- * Creates a new MsaWSClient object that uses a service given by an externally\r
- * retrieved ServiceHandle\r
- * \r
- * @param sh\r
- * service handle of type AbstractName(MsaWS)\r
- * @param altitle\r
- * DOCUMENT ME!\r
- * @param msa\r
- * DOCUMENT ME!\r
- * @param submitGaps\r
- * DOCUMENT ME!\r
- * @param preserveOrder\r
- * DOCUMENT ME!\r
- */\r
-\r
- public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,\r
- jalview.datamodel.AlignmentView msa, String db,\r
- Alignment seqdataset, AlignFrame _alignFrame)\r
- {\r
- super();\r
- alignFrame = _alignFrame;\r
- // can generalise the two errors below for metadata mapping from interface\r
- // name to service client name\r
- if (!sh.getAbstractName().equals(this.getServiceActionKey()))\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Service called \n" + sh.getName()\r
- + "\nis not a \nSequence Search Service !",\r
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- if ((wsInfo = setWebService(sh)) == null)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Sequence Search Service named " + sh.getName()\r
- + " is unknown", "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
- startSeqSearchClient(altitle, msa, db, seqdataset);\r
-\r
- }\r
-\r
- /**\r
- * non-process web service interaction - use this for calling HEADLESS\r
- * synchronous service methods\r
- * \r
- * @param sh\r
- */\r
- public SeqSearchWSClient(ServiceHandle sh)\r
- {\r
- setWebService(sh, true);\r
- }\r
-\r
- public SeqSearchWSClient()\r
- {\r
-\r
- super();\r
- // add a class reference to the list\r
- }\r
-\r
- private void startSeqSearchClient(String altitle, AlignmentView msa,\r
- String db, Alignment seqdataset)\r
- {\r
- if (!locateWebService())\r
- {\r
- return;\r
- }\r
- String visdb = (db == null || db == "") ? "default" : db; // need a visible\r
- // name for a\r
- // sequence db\r
- boolean profileSearch = msa.getSequences().length > 2 ? true : false;\r
- // single sequence or profile from alignment view\r
- wsInfo.setProgressText("Searching "\r
- + visdb\r
- + (!profileSearch ? " with sequence "\r
- + msa.getSequences()[0].getRefSeq().getName()\r
- : " with profile") + " from " + altitle\r
- + "\nJob details\n");\r
-\r
- String jobtitle = WebServiceName\r
- + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")\r
- + " of "\r
- + visdb\r
- + (!profileSearch ? " with sequence "\r
- + msa.getSequences()[0].getRefSeq().getName()\r
- : " with profile") + " from " + altitle;\r
- SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,\r
- wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,\r
- seqdataset);\r
- wsInfo.setthisService(ssthread);\r
- ssthread.start();\r
- }\r
-\r
- /**\r
- * Initializes the server field with a valid service implementation.\r
- * \r
- * @return true if service was located.\r
- */\r
- private boolean locateWebService()\r
- {\r
- // this can be abstracted using reflection\r
- // TODO: MuscleWS transmuted to generic MsaWS client\r
- SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default\r
-\r
- try\r
- {\r
- this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(\r
- WsURL));\r
- ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One\r
- // minute\r
- // timeout\r
- } catch (Exception ex)\r
- {\r
- wsInfo.setProgressText("Serious! " + WebServiceName\r
- + " Service location failed\nfor URL :" + WsURL + "\n"\r
- + ex.getMessage());\r
- wsInfo.setStatus(WebserviceInfo.ERROR);\r
- ex.printStackTrace();\r
-\r
- return false;\r
- }\r
-\r
- loc.getEngine().setOption("axis", "1");\r
-\r
- return true;\r
- }\r
-\r
- protected String getServiceActionKey()\r
- {\r
- return "SeqSearch";\r
- }\r
-\r
- protected String getServiceActionDescription()\r
- {\r
- return "Sequence Database Search";\r
- }\r
-\r
- // simple caching of db parameters for each service endpoint\r
- private static Hashtable dbParamsForEndpoint;\r
- static\r
- {\r
- dbParamsForEndpoint = new Hashtable();\r
- }\r
-\r
- public String[] getSupportedDatabases() throws Exception\r
- {\r
-\r
- // check that we haven't already been to this service endpoint\r
- if (dbParamsForEndpoint.containsKey(WsURL))\r
- {\r
- return (String[]) dbParamsForEndpoint.get(WsURL);\r
- }\r
- if (!locateWebService())\r
- {\r
- throw new Exception("Cannot contact service endpoint at " + WsURL);\r
- }\r
- String database = server.getDatabase();\r
- if (database == null)\r
- {\r
- dbParamsForEndpoint.put(WsURL, new String[]\r
- {});\r
- return null;\r
- }\r
- StringTokenizer en = new StringTokenizer(database.trim(), ",| ");\r
- String[] dbs = new String[en.countTokens()];\r
- for (int i = 0; i < dbs.length; i++)\r
- {\r
- dbs[i++] = en.nextToken().trim();\r
- }\r
- dbParamsForEndpoint.put(WsURL, dbs);\r
- return dbs;\r
- }\r
-\r
- public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,\r
- final AlignFrame af)\r
- {\r
- // look for existing database service submenus on wsmenu\r
- Hashtable dbsrchs = new Hashtable();\r
- Vector newdbsrch = new Vector();\r
- Component entries[] = wsmenu.getComponents();\r
- for (int i = 0; entries != null && i < entries.length; i++)\r
- {\r
- if (entries[i] instanceof JMenu)\r
- {\r
- dbsrchs.put(entries[i].getName(), entries[i]);\r
- }\r
- }\r
- JMenu defmenu = (JMenu) dbsrchs.get("Default Database");\r
- if (defmenu == null)\r
- {\r
- dbsrchs.put("Default Database", defmenu = new JMenu(\r
- "Default Database"));\r
- newdbsrch.addElement(defmenu);\r
- }\r
-\r
- String dbs[] = null;\r
- try\r
- {\r
- dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();\r
- } catch (Exception e)\r
- {\r
- jalview.bin.Cache.log.warn(\r
- "Database list request failed, so disabling SeqSearch Service client "\r
- + sh.getName() + " at " + sh.getEndpointURL(), e);\r
- return;\r
- }\r
- JMenuItem method;\r
- // do default entry\r
- defmenu.add(method = new JMenuItem(sh.getName()));\r
- method.setToolTipText(sh.getEndpointURL());\r
- method.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- // use same input gatherer as for secondary structure prediction\r
- // we could actually parameterise the gatherer method here...\r
- AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();\r
- new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, af\r
- .getViewport().getAlignment().getDataset(), af);\r
- }\r
- });\r
- // add entry for each database the service supports\r
- for (int db = 0; dbs != null && db < dbs.length; db++)\r
- {\r
- JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);\r
- if (dbmenu == null)\r
- {\r
- dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));\r
- newdbsrch.addElement(dbmenu);\r
- }\r
- // add the client handler code for this service\r
- dbmenu.add(method = new JMenuItem(sh.getName()));\r
- method.setToolTipText(sh.getEndpointURL());\r
- final String searchdb = dbs[db];\r
- method.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();\r
- new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa,\r
- searchdb, af.getViewport().getAlignment().getDataset(),\r
- af);\r
- }\r
- });\r
- }\r
- // add the databases onto the seqsearch menu\r
- Enumeration e = newdbsrch.elements();\r
- while (e.hasMoreElements())\r
- {\r
- Object el = e.nextElement();\r
- if (el instanceof JMenu)\r
- {\r
- wsmenu.add((JMenu) el);\r
- }\r
- else\r
- {\r
- wsmenu.add((JMenuItem) el);\r
- }\r
- }\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.jws1;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqSearchWSClient extends WS1Client
+{
+ /**
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */
+ ext.vamsas.SeqSearchI server;
+
+ AlignFrame alignFrame;
+
+ /**
+ * Creates a new MsaWSClient object that uses a service given by an externally
+ * retrieved ServiceHandle
+ *
+ * @param sh
+ * service handle of type AbstractName(MsaWS)
+ * @param altitle
+ * DOCUMENT ME!
+ * @param msa
+ * DOCUMENT ME!
+ * @param submitGaps
+ * DOCUMENT ME!
+ * @param preserveOrder
+ * DOCUMENT ME!
+ */
+
+ public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+ jalview.datamodel.AlignmentView msa, String db,
+ Alignment seqdataset, AlignFrame _alignFrame)
+ {
+ super();
+ alignFrame = _alignFrame;
+ // can generalise the two errors below for metadata mapping from interface
+ // name to service client name
+ if (!sh.getAbstractName().equals(this.getServiceActionKey()))
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The Service called \n" + sh.getName()
+ + "\nis not a \nSequence Search Service !",
+ "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if ((wsInfo = setWebService(sh)) == null)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The Sequence Search Service named " + sh.getName()
+ + " is unknown", "Internal Jalview Error",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ startSeqSearchClient(altitle, msa, db, seqdataset);
+
+ }
+
+ /**
+ * non-process web service interaction - use this for calling HEADLESS
+ * synchronous service methods
+ *
+ * @param sh
+ */
+ public SeqSearchWSClient(ServiceHandle sh)
+ {
+ setWebService(sh, true);
+ }
+
+ public SeqSearchWSClient()
+ {
+
+ super();
+ // add a class reference to the list
+ }
+
+ private void startSeqSearchClient(String altitle, AlignmentView msa,
+ String db, Alignment seqdataset)
+ {
+ if (!locateWebService())
+ {
+ return;
+ }
+ String visdb = (db == null || db == "") ? "default" : db; // need a visible
+ // name for a
+ // sequence db
+ boolean profileSearch = msa.getSequences().length > 2 ? true : false;
+ // single sequence or profile from alignment view
+ wsInfo.setProgressText("Searching "
+ + visdb
+ + (!profileSearch ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile") + " from " + altitle
+ + "\nJob details\n");
+
+ String jobtitle = WebServiceName
+ + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
+ + " of "
+ + visdb
+ + (!profileSearch ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile") + " from " + altitle;
+ SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
+ wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
+ seqdataset);
+ wsInfo.setthisService(ssthread);
+ ssthread.start();
+ }
+
+ /**
+ * Initializes the server field with a valid service implementation.
+ *
+ * @return true if service was located.
+ */
+ private boolean locateWebService()
+ {
+ // this can be abstracted using reflection
+ // TODO: MuscleWS transmuted to generic MsaWS client
+ SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
+
+ try
+ {
+ this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(
+ WsURL));
+ ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
+ // minute
+ // timeout
+ } catch (Exception ex)
+ {
+ wsInfo.setProgressText("Serious! " + WebServiceName
+ + " Service location failed\nfor URL :" + WsURL + "\n"
+ + ex.getMessage());
+ wsInfo.setStatus(WebserviceInfo.ERROR);
+ ex.printStackTrace();
+
+ return false;
+ }
+
+ loc.getEngine().setOption("axis", "1");
+
+ return true;
+ }
+
+ protected String getServiceActionKey()
+ {
+ return "SeqSearch";
+ }
+
+ protected String getServiceActionDescription()
+ {
+ return "Sequence Database Search";
+ }
+
+ // simple caching of db parameters for each service endpoint
+ private static Hashtable dbParamsForEndpoint;
+ static
+ {
+ dbParamsForEndpoint = new Hashtable();
+ }
+
+ public String[] getSupportedDatabases() throws Exception
+ {
+
+ // check that we haven't already been to this service endpoint
+ if (dbParamsForEndpoint.containsKey(WsURL))
+ {
+ return (String[]) dbParamsForEndpoint.get(WsURL);
+ }
+ if (!locateWebService())
+ {
+ throw new Exception("Cannot contact service endpoint at " + WsURL);
+ }
+ String database = server.getDatabase();
+ if (database == null)
+ {
+ dbParamsForEndpoint.put(WsURL, new String[]
+ {});
+ return null;
+ }
+ StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
+ String[] dbs = new String[en.countTokens()];
+ for (int i = 0; i < dbs.length; i++)
+ {
+ dbs[i++] = en.nextToken().trim();
+ }
+ dbParamsForEndpoint.put(WsURL, dbs);
+ return dbs;
+ }
+
+ public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+ final AlignFrame af)
+ {
+ // look for existing database service submenus on wsmenu
+ Hashtable dbsrchs = new Hashtable();
+ Vector newdbsrch = new Vector();
+ Component entries[] = wsmenu.getComponents();
+ for (int i = 0; entries != null && i < entries.length; i++)
+ {
+ if (entries[i] instanceof JMenu)
+ {
+ dbsrchs.put(entries[i].getName(), entries[i]);
+ }
+ }
+ JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
+ if (defmenu == null)
+ {
+ dbsrchs.put("Default Database", defmenu = new JMenu(
+ "Default Database"));
+ newdbsrch.addElement(defmenu);
+ }
+
+ String dbs[] = null;
+ try
+ {
+ dbs = new jalview.ws.jws1.SeqSearchWSClient(sh).getSupportedDatabases();
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn(
+ "Database list request failed, so disabling SeqSearch Service client "
+ + sh.getName() + " at " + sh.getEndpointURL(), e);
+ return;
+ }
+ JMenuItem method;
+ // do default entry
+ defmenu.add(method = new JMenuItem(sh.getName()));
+ method.setToolTipText(sh.getEndpointURL());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // use same input gatherer as for secondary structure prediction
+ // we could actually parameterise the gatherer method here...
+ AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+ new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa, null, af
+ .getViewport().getAlignment().getDataset(), af);
+ }
+ });
+ // add entry for each database the service supports
+ for (int db = 0; dbs != null && db < dbs.length; db++)
+ {
+ JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
+ if (dbmenu == null)
+ {
+ dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
+ newdbsrch.addElement(dbmenu);
+ }
+ // add the client handler code for this service
+ dbmenu.add(method = new JMenuItem(sh.getName()));
+ method.setToolTipText(sh.getEndpointURL());
+ final String searchdb = dbs[db];
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+ new jalview.ws.jws1.SeqSearchWSClient(sh, af.getTitle(), msa,
+ searchdb, af.getViewport().getAlignment().getDataset(),
+ af);
+ }
+ });
+ }
+ // add the databases onto the seqsearch menu
+ Enumeration e = newdbsrch.elements();
+ while (e.hasMoreElements())
+ {
+ Object el = e.nextElement();
+ if (el instanceof JMenu)
+ {
+ wsmenu.add((JMenu) el);
+ }
+ else
+ {
+ wsmenu.add((JMenuItem) el);
+ }
+ }
+
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import jalview.io.NewickFile;\r
-import vamsas.objects.simple.MsaResult;\r
-import vamsas.objects.simple.SeqSearchResult;\r
-\r
-/**\r
- * <p>\r
- * Title:\r
- * </p>\r
- * \r
- * <p>\r
- * Description:\r
- * </p>\r
- * \r
- * <p>\r
- * Copyright: Copyright (c) 2004\r
- * </p>\r
- * \r
- * <p>\r
- * Company: Dundee University\r
- * </p>\r
- * \r
- * @author not attributable\r
- * @version 1.0\r
- */\r
-class SeqSearchWSThread extends JWS1Thread implements WSClientI\r
-{\r
- String dbs = null;\r
-\r
- boolean profile = false;\r
-\r
- class SeqSearchWSJob extends WSJob\r
- {\r
- // hold special input for this\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
-\r
- /**\r
- * MsaWSJob\r
- * \r
- * @param jobNum\r
- * int\r
- * @param jobId\r
- * String\r
- */\r
- public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)\r
- {\r
- this.jobnum = jobNum;\r
- if (!prepareInput(inSeqs, 2))\r
- {\r
- submitted = true;\r
- subjobComplete = true;\r
- result = new MsaResult();\r
- result.setFinished(true);\r
- result.setStatus("Job never ran - input returned to user.");\r
- }\r
-\r
- }\r
-\r
- Hashtable SeqNames = new Hashtable();\r
-\r
- Vector emptySeqs = new Vector();\r
-\r
- /**\r
- * prepare input sequences for service\r
- * \r
- * @param seqs\r
- * jalview sequences to be prepared\r
- * @param minlen\r
- * minimum number of residues required for this MsaWS service\r
- * @return true if seqs contains sequences to be submitted to service.\r
- */\r
- private boolean prepareInput(SequenceI[] seqs, int minlen)\r
- {\r
- int nseqs = 0;\r
- if (minlen < 0)\r
- {\r
- throw new Error(\r
- "Implementation error: minlen must be zero or more.");\r
- }\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
- {\r
- nseqs++;\r
- }\r
- }\r
- boolean valid = nseqs >= 1; // need at least one sequence for valid input\r
- // TODO: generalise\r
- vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
- : null;\r
- boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted\r
- // with gaps\r
- for (int i = 0, n = 0; i < seqs.length; i++)\r
- {\r
-\r
- String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same\r
- // for\r
- // any\r
- // subjob\r
- SeqNames.put(newname, jalview.analysis.SeqsetUtils\r
- .SeqCharacterHash(seqs[i]));\r
- if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
- {\r
- seqarray[n] = new vamsas.objects.simple.Sequence();\r
- seqarray[n].setId(newname);\r
- seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()\r
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,\r
- seqs[i].getSequenceAsString()));\r
- }\r
- else\r
- {\r
- String empty = null;\r
- if (seqs[i].getEnd() >= seqs[i].getStart())\r
- {\r
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq\r
- .extractGaps(jalview.util.Comparison.GapChars, seqs[i]\r
- .getSequenceAsString());\r
- }\r
- emptySeqs.add(new String[]\r
- { newname, empty });\r
- }\r
- }\r
- if (submitGaps)\r
- {\r
- // almost certainly have to remove gapped columns here\r
- }\r
- this.seqs = new vamsas.objects.simple.SequenceSet();\r
- this.seqs.setSeqs(seqarray);\r
- return valid;\r
- }\r
-\r
- /**\r
- * \r
- * @return true if getAlignment will return a valid alignment result.\r
- */\r
- public boolean hasResults()\r
- {\r
- if (subjobComplete\r
- && result != null\r
- && result.isFinished()\r
- && ((SeqSearchResult) result).getAlignment() != null\r
- && ((SeqSearchResult) result).getAlignment().getSeqs() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- /**\r
- * return sequence search results for display\r
- * \r
- * @return null or { Alignment(+features and annotation), NewickFile)}\r
- */\r
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)\r
- {\r
-\r
- if (result != null && result.isFinished())\r
- {\r
- SequenceI[] alseqs = null;\r
- // char alseq_gapchar = '-';\r
- // int alseq_l = 0;\r
- if (((SeqSearchResult) result).getAlignment() != null)\r
- {\r
- alseqs = getVamsasAlignment(((SeqSearchResult) result)\r
- .getAlignment());\r
- // alseq_gapchar = ( (SeqSearchResult)\r
- // result).getAlignment().getGapchar().charAt(0);\r
- // alseq_l = alseqs.length;\r
- }\r
- /**\r
- * what has to be done. 1 - annotate returned alignment with annotation\r
- * file and sequence features file, and associate any tree-nodes. 2.\r
- * connect alignment back to any associated dataset: 2.a. deuniquify\r
- * recovers sequence information - but additionally, relocations must be\r
- * made from the returned aligned sequence back to the dataset.\r
- */\r
- // construct annotated alignment as it would be done by the jalview\r
- // applet\r
- jalview.datamodel.Alignment al = new Alignment(alseqs);\r
- // al.setDataset(dataset);\r
- // make dataset\r
- String inFile = null;\r
- try\r
- {\r
- inFile = ((SeqSearchResult) result).getAnnotation();\r
- if (inFile != null && inFile.length() > 0)\r
- {\r
- new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,\r
- jalview.io.AppletFormatAdapter.PASTE);\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Failed to parse the annotation file associated with the alignment.");\r
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
- e.printStackTrace(System.err);\r
- }\r
-\r
- try\r
- {\r
- inFile = ((SeqSearchResult) result).getFeatures();\r
- if (inFile != null && inFile.length() > 0)\r
- {\r
- jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(\r
- inFile, jalview.io.AppletFormatAdapter.PASTE);\r
- ff.parse(al, featureColours, false);\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Failed to parse the Features file associated with the alignment.");\r
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
- e.printStackTrace(System.err);\r
- }\r
- jalview.io.NewickFile nf = null;\r
- try\r
- {\r
- inFile = ((SeqSearchResult) result).getNewickTree();\r
- if (inFile != null && inFile.length() > 0)\r
- {\r
- nf = new jalview.io.NewickFile(inFile,\r
- jalview.io.AppletFormatAdapter.PASTE);\r
- if (!nf.isValid())\r
- {\r
- nf.close();\r
- nf = null;\r
- }\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Failed to parse the treeFile associated with the alignment.");\r
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
- e.printStackTrace(System.err);\r
- }\r
-\r
- /*\r
- * TODO: housekeeping w.r.t. recovery of dataset and annotation\r
- * references for input sequences, and then dataset sequence creation\r
- * for new sequences retrieved from service // finally, attempt to\r
- * de-uniquify to recover input sequence identity, and try to map back\r
- * onto dataset Note: this\r
- * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will\r
- * NOT WORK - the returned alignment may contain multiple versions of\r
- * the input sequence, each being a subsequence of the original.\r
- * deuniquify also removes existing annotation and features added in the\r
- * previous step... al.setDataset(dataset); // add in new sequences\r
- * retrieved from sequence search which are not already in dataset. //\r
- * trigger a 'fetchDBids' to annotate sequences with database ids...\r
- */\r
-\r
- return new Object[]\r
- { al, nf };\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * mark subjob as cancelled and set result object appropriatly\r
- */\r
- void cancel()\r
- {\r
- cancelled = true;\r
- subjobComplete = true;\r
- result = null;\r
- }\r
-\r
- /**\r
- * \r
- * @return boolean true if job can be submitted.\r
- */\r
- public boolean hasValidInput()\r
- {\r
- if (seqs.getSeqs() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
- }\r
-\r
- String alTitle; // name which will be used to form new alignment window.\r
-\r
- Alignment dataset; // dataset to which the new alignment will be\r
-\r
- // associated.\r
-\r
- ext.vamsas.SeqSearchI server = null;\r
-\r
- private String dbArg;\r
-\r
- /**\r
- * set basic options for this (group) of Msa jobs\r
- * \r
- * @param subgaps\r
- * boolean\r
- * @param presorder\r
- * boolean\r
- */\r
- SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- AlignmentView alview, String wsname, String db)\r
- {\r
- super(alFrame, wsinfo, alview, wsname, wsUrl);\r
- this.server = server;\r
- this.dbArg = db;\r
- }\r
-\r
- /**\r
- * create one or more Msa jobs to align visible seuqences in _msa\r
- * \r
- * @param title\r
- * String\r
- * @param _msa\r
- * AlignmentView\r
- * @param subgaps\r
- * boolean\r
- * @param presorder\r
- * boolean\r
- * @param seqset\r
- * Alignment\r
- */\r
- SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- String wsname, String title, AlignmentView _msa, String db,\r
- Alignment seqset)\r
- {\r
- this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);\r
- OutputHeader = wsInfo.getProgressText();\r
- alTitle = title;\r
- dataset = seqset;\r
-\r
- SequenceI[][] conmsa = _msa.getVisibleContigs('-');\r
- if (conmsa != null)\r
- {\r
- int njobs = conmsa.length;\r
- jobs = new SeqSearchWSJob[njobs];\r
- for (int j = 0; j < njobs; j++)\r
- {\r
- if (j != 0)\r
- {\r
- jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);\r
- }\r
- else\r
- {\r
- jobs[j] = new SeqSearchWSJob(0, conmsa[j]);\r
- }\r
- if (njobs > 0)\r
- {\r
- wsinfo\r
- .setProgressName("region " + jobs[j].jobnum,\r
- jobs[j].jobnum);\r
- }\r
- wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);\r
- }\r
- }\r
- }\r
-\r
- public boolean isCancellable()\r
- {\r
- return true;\r
- }\r
-\r
- public void cancelJob()\r
- {\r
- if (!jobComplete && jobs != null)\r
- {\r
- boolean cancelled = true;\r
- for (int job = 0; job < jobs.length; job++)\r
- {\r
- if (jobs[job].submitted && !jobs[job].subjobComplete)\r
- {\r
- String cancelledMessage = "";\r
- try\r
- {\r
- vamsas.objects.simple.WsJobId cancelledJob = server\r
- .cancel(jobs[job].jobId);\r
- if (cancelledJob.getStatus() == 2)\r
- {\r
- // CANCELLED_JOB\r
- cancelledMessage = "Job cancelled.";\r
- ((SeqSearchWSJob) jobs[job]).cancel();\r
- wsInfo.setStatus(jobs[job].jobnum,\r
- WebserviceInfo.STATE_CANCELLED_OK);\r
- }\r
- else if (cancelledJob.getStatus() == 3)\r
- {\r
- // VALID UNSTOPPABLE JOB\r
- cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
- cancelled = false;\r
- // wsInfo.setStatus(jobs[job].jobnum,\r
- // WebserviceInfo.STATE_RUNNING);\r
- }\r
-\r
- if (cancelledJob.getJobId() != null)\r
- {\r
- cancelledMessage += ("[" + cancelledJob.getJobId() + "]");\r
- }\r
-\r
- cancelledMessage += "\n";\r
- } catch (Exception exc)\r
- {\r
- cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"\r
- + exc + "\n");\r
- Cache.log.warn(\r
- "Exception whilst cancelling " + jobs[job].jobId, exc);\r
- }\r
- wsInfo.setProgressText(jobs[job].jobnum, OutputHeader\r
- + cancelledMessage + "\n");\r
- }\r
- }\r
- if (cancelled)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
- jobComplete = true;\r
- }\r
- this.interrupt(); // kick thread to update job states.\r
- }\r
- else\r
- {\r
- if (!jobComplete)\r
- {\r
- wsInfo\r
- .setProgressText(OutputHeader\r
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
- }\r
- }\r
- }\r
-\r
- public void pollJob(AWsJob job) throws Exception\r
- {\r
- ((SeqSearchWSJob) job).result = server\r
- .getResult(((SeqSearchWSJob) job).jobId);\r
- }\r
-\r
- public void StartJob(AWsJob job)\r
- {\r
- if (!(job instanceof SeqSearchWSJob))\r
- {\r
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "\r
- + job.getClass());\r
- }\r
- SeqSearchWSJob j = (SeqSearchWSJob) job;\r
- if (j.submitted)\r
- {\r
- if (Cache.log.isDebugEnabled())\r
- {\r
- Cache.log.debug("Tried to submit an already submitted job "\r
- + j.jobId);\r
- }\r
- return;\r
- }\r
- if (j.seqs.getSeqs() == null)\r
- {\r
- // special case - selection consisted entirely of empty sequences...\r
- j.submitted = true;\r
- j.result = new MsaResult();\r
- j.result.setFinished(true);\r
- j.result.setStatus("Empty Alignment Job");\r
- ((MsaResult) j.result).setMsa(null);\r
- }\r
- try\r
- {\r
- vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs\r
- .getSeqs()[0], dbArg);\r
-\r
- if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
- {\r
- j.jobId = jobsubmit.getJobId();\r
- j.submitted = true;\r
- j.subjobComplete = false;\r
- // System.out.println(WsURL + " Job Id '" + jobId + "'");\r
- }\r
- else\r
- {\r
- if (jobsubmit == null)\r
- {\r
- throw new Exception(\r
- "Server at "\r
- + WsUrl\r
- + " returned null object, it probably cannot be contacted. Try again later ?");\r
- }\r
-\r
- throw new Exception(jobsubmit.getJobId());\r
- }\r
- } catch (Exception e)\r
- {\r
- // TODO: JBPNote catch timeout or other fault types explicitly\r
- // For unexpected errors\r
- System.err\r
- .println(WebServiceName\r
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"\r
- + "When contacting Server:" + WsUrl + "\n"\r
- + e.toString() + "\n");\r
- j.allowedServerExceptions = 0;\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo\r
- .appendProgressText(\r
- j.jobnum,\r
- "Failed to submit sequences for alignment.\n"\r
- + "It is most likely that there is a problem with the server.\n"\r
- + "Just close the window\n");\r
-\r
- // e.printStackTrace(); // TODO: JBPNote DEBUG\r
- }\r
- }\r
-\r
- private jalview.datamodel.Sequence[] getVamsasAlignment(\r
- vamsas.objects.simple.Alignment valign)\r
- {\r
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
-\r
- for (int i = 0, j = seqs.length; i < j; i++)\r
- {\r
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]\r
- .getSeq());\r
- }\r
-\r
- return msa;\r
- }\r
-\r
- public 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\r
- && jobs[j].hasResults())\r
- {\r
- results++;\r
- vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)\r
- .getAlignment();\r
- if (valign != null)\r
- {\r
- wsInfo.appendProgressText(jobs[j].jobnum,\r
- "\nAlignment Object Method Notes\n");\r
- String[] lines = valign.getMethod();\r
- for (int line = 0; line < lines.length; line++)\r
- {\r
- wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");\r
- }\r
- // JBPNote The returned files from a webservice could be\r
- // hidden behind icons in the monitor window that,\r
- // when clicked, pop up their corresponding data\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(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(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 newFrame)\r
- {\r
- if (!newFrame)\r
- {\r
- System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");\r
- return;\r
- }\r
- // each subjob is an independent alignment for the moment\r
- // Alignment al[] = new Alignment[jobs.length];\r
- // NewickFile nf[] = new NewickFile[jobs.length];\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
- Hashtable featureColours = new Hashtable();\r
- Alignment al = null;\r
- NewickFile nf = null;\r
- if (jobs[j].hasResults())\r
- {\r
- Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,\r
- featureColours);\r
- if (res == null)\r
- {\r
- continue;\r
- }\r
- ;\r
- al = (Alignment) res[0];\r
- nf = (NewickFile) res[1];\r
- }\r
- else\r
- {\r
- al = null;\r
- nf = null;\r
- continue;\r
- }\r
- /*\r
- * We can't map new alignment back with insertions from input's hidden\r
- * regions until dataset mapping is sorted out... but basically it goes\r
- * like this: 1. Merge each domain hit back onto the visible segments in\r
- * the same way as a Jnet prediction is mapped back\r
- * \r
- * Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
- * // trash references to original result data for (int j = 0; j <\r
- * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]\r
- * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =\r
- * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);\r
- * \r
- * if (dataset != null) { al.setDataset(dataset); }\r
- * \r
- * propagateDatasetMappings(al); }\r
- */\r
-\r
- AlignFrame af = new AlignFrame(al,// columnselection,\r
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
- if (nf != null)\r
- {\r
- af.ShowNewickTree(nf, "Tree from " + this.alTitle);\r
- }\r
- // initialise with same renderer settings as in parent alignframe.\r
- af.getFeatureRenderer().transferSettings(this.featureSettings);\r
- Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
-\r
- public boolean canMergeResults()\r
- {\r
- return false;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.jws1;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.NewickFile;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SeqSearchResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class SeqSearchWSThread extends JWS1Thread implements WSClientI
+{
+ String dbs = null;
+
+ boolean profile = false;
+
+ class SeqSearchWSJob extends WSJob
+ {
+ // hold special input for this
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+ /**
+ * MsaWSJob
+ *
+ * @param jobNum
+ * int
+ * @param jobId
+ * String
+ */
+ public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
+ {
+ this.jobnum = jobNum;
+ if (!prepareInput(inSeqs, 2))
+ {
+ submitted = true;
+ subjobComplete = true;
+ result = new MsaResult();
+ result.setFinished(true);
+ result.setStatus("Job never ran - input returned to user.");
+ }
+
+ }
+
+ Hashtable SeqNames = new Hashtable();
+
+ Vector emptySeqs = new Vector();
+
+ /**
+ * prepare input sequences for service
+ *
+ * @param seqs
+ * jalview sequences to be prepared
+ * @param minlen
+ * minimum number of residues required for this MsaWS service
+ * @return true if seqs contains sequences to be submitted to service.
+ */
+ private boolean prepareInput(SequenceI[] seqs, int minlen)
+ {
+ int nseqs = 0;
+ if (minlen < 0)
+ {
+ throw new Error(
+ "Implementation error: minlen must be zero or more.");
+ }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ nseqs++;
+ }
+ }
+ boolean valid = nseqs >= 1; // need at least one sequence for valid input
+ // TODO: generalise
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ : null;
+ boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
+ // with gaps
+ for (int i = 0, n = 0; i < seqs.length; i++)
+ {
+
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+ // for
+ // any
+ // subjob
+ SeqNames.put(newname, jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seqs[i]));
+ if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ seqarray[n] = new vamsas.objects.simple.Sequence();
+ seqarray[n].setId(newname);
+ seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString()));
+ }
+ else
+ {
+ String empty = null;
+ if (seqs[i].getEnd() >= seqs[i].getStart())
+ {
+ empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+ .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+ .getSequenceAsString());
+ }
+ emptySeqs.add(new String[]
+ { newname, empty });
+ }
+ }
+ if (submitGaps)
+ {
+ // almost certainly have to remove gapped columns here
+ }
+ this.seqs = new vamsas.objects.simple.SequenceSet();
+ this.seqs.setSeqs(seqarray);
+ return valid;
+ }
+
+ /**
+ *
+ * @return true if getAlignment will return a valid alignment result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete
+ && result != null
+ && result.isFinished()
+ && ((SeqSearchResult) result).getAlignment() != null
+ && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * return sequence search results for display
+ *
+ * @return null or { Alignment(+features and annotation), NewickFile)}
+ */
+ public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ {
+
+ if (result != null && result.isFinished())
+ {
+ SequenceI[] alseqs = null;
+ // char alseq_gapchar = '-';
+ // int alseq_l = 0;
+ if (((SeqSearchResult) result).getAlignment() != null)
+ {
+ alseqs = getVamsasAlignment(((SeqSearchResult) result)
+ .getAlignment());
+ // alseq_gapchar = ( (SeqSearchResult)
+ // result).getAlignment().getGapchar().charAt(0);
+ // alseq_l = alseqs.length;
+ }
+ /**
+ * what has to be done. 1 - annotate returned alignment with annotation
+ * file and sequence features file, and associate any tree-nodes. 2.
+ * connect alignment back to any associated dataset: 2.a. deuniquify
+ * recovers sequence information - but additionally, relocations must be
+ * made from the returned aligned sequence back to the dataset.
+ */
+ // construct annotated alignment as it would be done by the jalview
+ // applet
+ jalview.datamodel.Alignment al = new Alignment(alseqs);
+ // al.setDataset(dataset);
+ // make dataset
+ String inFile = null;
+ try
+ {
+ inFile = ((SeqSearchResult) result).getAnnotation();
+ if (inFile != null && inFile.length() > 0)
+ {
+ new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
+ jalview.io.AppletFormatAdapter.PASTE);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the annotation file associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+
+ try
+ {
+ inFile = ((SeqSearchResult) result).getFeatures();
+ if (inFile != null && inFile.length() > 0)
+ {
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
+ inFile, jalview.io.AppletFormatAdapter.PASTE);
+ ff.parse(al, featureColours, false);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the Features file associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+ jalview.io.NewickFile nf = null;
+ try
+ {
+ inFile = ((SeqSearchResult) result).getNewickTree();
+ if (inFile != null && inFile.length() > 0)
+ {
+ nf = new jalview.io.NewickFile(inFile,
+ jalview.io.AppletFormatAdapter.PASTE);
+ if (!nf.isValid())
+ {
+ nf.close();
+ nf = null;
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the treeFile associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+
+ /*
+ * TODO: housekeeping w.r.t. recovery of dataset and annotation
+ * references for input sequences, and then dataset sequence creation
+ * for new sequences retrieved from service // finally, attempt to
+ * de-uniquify to recover input sequence identity, and try to map back
+ * onto dataset Note: this
+ * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
+ * NOT WORK - the returned alignment may contain multiple versions of
+ * the input sequence, each being a subsequence of the original.
+ * deuniquify also removes existing annotation and features added in the
+ * previous step... al.setDataset(dataset); // add in new sequences
+ * retrieved from sequence search which are not already in dataset. //
+ * trigger a 'fetchDBids' to annotate sequences with database ids...
+ */
+
+ return new Object[]
+ { al, nf };
+ }
+ return null;
+ }
+
+ /**
+ * mark subjob as cancelled and set result object appropriatly
+ */
+ void cancel()
+ {
+ cancelled = true;
+ subjobComplete = true;
+ result = null;
+ }
+
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ public boolean hasValidInput()
+ {
+ if (seqs.getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+ }
+
+ String alTitle; // name which will be used to form new alignment window.
+
+ Alignment dataset; // dataset to which the new alignment will be
+
+ // associated.
+
+ ext.vamsas.SeqSearchI server = null;
+
+ private String dbArg;
+
+ /**
+ * set basic options for this (group) of Msa jobs
+ *
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ */
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ AlignmentView alview, String wsname, String db)
+ {
+ super(alFrame, wsinfo, alview, wsname, wsUrl);
+ this.server = server;
+ this.dbArg = db;
+ }
+
+ /**
+ * create one or more Msa jobs to align visible seuqences in _msa
+ *
+ * @param title
+ * String
+ * @param _msa
+ * AlignmentView
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ * @param seqset
+ * Alignment
+ */
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ String wsname, String title, AlignmentView _msa, String db,
+ Alignment seqset)
+ {
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
+ OutputHeader = wsInfo.getProgressText();
+ alTitle = title;
+ dataset = seqset;
+
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+ if (conmsa != null)
+ {
+ int njobs = conmsa.length;
+ jobs = new SeqSearchWSJob[njobs];
+ for (int j = 0; j < njobs; j++)
+ {
+ if (j != 0)
+ {
+ jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
+ }
+ else
+ {
+ jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
+ }
+ if (njobs > 0)
+ {
+ wsinfo
+ .setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
+ }
+ wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
+ }
+ }
+ }
+
+ public boolean isCancellable()
+ {
+ return true;
+ }
+
+ public void cancelJob()
+ {
+ if (!jobComplete && jobs != null)
+ {
+ boolean cancelled = true;
+ for (int job = 0; job < jobs.length; job++)
+ {
+ if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete())
+ {
+ String cancelledMessage = "";
+ try
+ {
+ vamsas.objects.simple.WsJobId cancelledJob = server
+ .cancel(jobs[job].getJobId());
+ if (cancelledJob.getStatus() == 2)
+ {
+ // CANCELLED_JOB
+ cancelledMessage = "Job cancelled.";
+ ((SeqSearchWSJob) jobs[job]).cancel();
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+ }
+ else if (cancelledJob.getStatus() == 3)
+ {
+ // VALID UNSTOPPABLE JOB
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+ cancelled = false;
+ // wsInfo.setStatus(jobs[job].jobnum,
+ // WebserviceInfo.STATE_RUNNING);
+ }
+
+ if (cancelledJob.getJobId() != null)
+ {
+ cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+ }
+
+ cancelledMessage += "\n";
+ } catch (Exception exc)
+ {
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ + exc + "\n");
+ Cache.log.warn(
+ "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ }
+ wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ + cancelledMessage + "\n");
+ }
+ }
+ if (cancelled)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+ jobComplete = true;
+ }
+ this.interrupt(); // kick thread to update job states.
+ }
+ else
+ {
+ if (!jobComplete)
+ {
+ wsInfo
+ .setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ }
+ }
+ }
+
+ public void pollJob(AWsJob job) throws Exception
+ {
+ ((SeqSearchWSJob) job).result = server
+ .getResult(((SeqSearchWSJob) job).getJobId());
+ }
+
+ public void StartJob(AWsJob job)
+ {
+ if (!(job instanceof SeqSearchWSJob))
+ {
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+ + job.getClass());
+ }
+ SeqSearchWSJob j = (SeqSearchWSJob) job;
+ if (j.isSubmitted())
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Tried to submit an already submitted job "
+ + j.getJobId());
+ }
+ return;
+ }
+ if (j.seqs.getSeqs() == null)
+ {
+ // special case - selection consisted entirely of empty sequences...
+ j.setSubmitted(true);
+ j.result = new MsaResult();
+ j.result.setFinished(true);
+ j.result.setStatus("Empty Alignment Job");
+ ((MsaResult) j.result).setMsa(null);
+ }
+ try
+ {
+ vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
+ .getSeqs()[0], dbArg);
+
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+ {
+ j.setJobId(jobsubmit.getJobId());
+ j.setSubmitted(true);
+ j.setSubjobComplete(false);
+ // 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)
+ {
+ // TODO: JBPNote catch timeout or other fault types explicitly
+ // For unexpected errors
+ System.err
+ .println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n"
+ + e.toString() + "\n");
+ j.setAllowedServerExceptions(0);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo
+ .appendProgressText(
+ j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "It is most likely that there is a problem with the server.\n"
+ + "Just close the window\n");
+
+ // e.printStackTrace(); // TODO: JBPNote DEBUG
+ }
+ }
+
+ private jalview.datamodel.Sequence[] getVamsasAlignment(
+ vamsas.objects.simple.Alignment valign)
+ {
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+ for (int i = 0, j = seqs.length; i < j; i++)
+ {
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+ .getSeq());
+ }
+
+ return msa;
+ }
+
+ public 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].isSubmitted() && jobs[j].isSubjobComplete()
+ && jobs[j].hasResults())
+ {
+ results++;
+ vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)
+ .getAlignment();
+ if (valign != null)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(),
+ "\nAlignment Object Method Notes\n");
+ String[] lines = valign.getMethod();
+ for (int line = 0; line < lines.length; line++)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+ }
+ // JBPNote The returned files from a webservice could be
+ // hidden behind icons in the monitor window that,
+ // when clicked, pop up their corresponding data
+ }
+ }
+ }
+ } 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 newFrame)
+ {
+ if (!newFrame)
+ {
+ System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+ return;
+ }
+ // each subjob is an independent alignment for the moment
+ // Alignment al[] = new Alignment[jobs.length];
+ // NewickFile nf[] = new NewickFile[jobs.length];
+ for (int j = 0; j < jobs.length; j++)
+ {
+ Hashtable featureColours = new Hashtable();
+ Alignment al = null;
+ NewickFile nf = null;
+ if (jobs[j].hasResults())
+ {
+ Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,
+ featureColours);
+ if (res == null)
+ {
+ continue;
+ }
+ ;
+ al = (Alignment) res[0];
+ nf = (NewickFile) res[1];
+ }
+ else
+ {
+ al = null;
+ nf = null;
+ continue;
+ }
+ /*
+ * We can't map new alignment back with insertions from input's hidden
+ * regions until dataset mapping is sorted out... but basically it goes
+ * like this: 1. Merge each domain hit back onto the visible segments in
+ * the same way as a Jnet prediction is mapped back
+ *
+ * Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+ * // trash references to original result data for (int j = 0; j <
+ * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]
+ * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =
+ * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);
+ *
+ * if (dataset != null) { al.setDataset(dataset); }
+ *
+ * propagateDatasetMappings(al); }
+ */
+
+ AlignFrame af = new AlignFrame(al,// columnselection,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ if (nf != null)
+ {
+ af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+ }
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+}
/**
*
*/
-package jalview.ws;
+package jalview.ws.jws1;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
+import jalview.ws.WSClient;
+import jalview.ws.WSMenuEntryProviderI;
import javax.swing.JMenu;
/**
*
*/
-package jalview.ws;
+package jalview.ws.jws1;
+
+import jalview.ws.AWsJob;
abstract class WSJob extends AWsJob
{
git://source.jalview.org / jalview.git / commitdiff