* <p>\r
* Title:\r
* </p>\r
- *\r
+ * \r
* <p>\r
* Description:\r
* </p>\r
- *\r
+ * \r
* <p>\r
* Copyright: Copyright (c) 2004\r
* </p>\r
- *\r
+ * \r
* <p>\r
* Company: Dundee University\r
* </p>\r
- *\r
+ * \r
* @author not attributable\r
* @version 1.0\r
*/\r
-class MsaWSThread\r
- extends WSThread implements WSClientI\r
+class MsaWSThread extends WSThread implements WSClientI\r
{\r
boolean submitGaps = false; // pass sequences including gaps to alignment\r
\r
\r
// order\r
\r
- class MsaWSJob\r
- extends WSThread.WSJob\r
+ class MsaWSJob extends WSThread.WSJob\r
{\r
// hold special input for this\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.\r
- SequenceSet();\r
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
\r
/**\r
* MsaWSJob\r
- *\r
+ * \r
* @param jobNum\r
- * int\r
+ * int\r
* @param jobId\r
- * String\r
+ * String\r
*/\r
public MsaWSJob(int jobNum, SequenceI[] inSeqs)\r
{\r
}\r
\r
Hashtable SeqNames = new Hashtable();\r
+\r
Vector emptySeqs = new Vector();\r
+\r
/**\r
* prepare input sequences for MsaWS service\r
- * @param seqs jalview sequences to be prepared\r
- * @param minlen minimum number of residues required for this 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
int nseqs = 0;\r
if (minlen < 0)\r
{\r
- throw new Error("Implementation error: minlen must be zero or more.");\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
}\r
}\r
boolean valid = nseqs > 1; // need at least two seqs\r
- vamsas.objects.simple.Sequence[] seqarray =\r
- (valid)\r
- ? new vamsas.objects.simple.Sequence[nseqs]\r
- : null;\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
// any\r
// subjob\r
SeqNames.put(newname, jalview.analysis.SeqsetUtils\r
- .SeqCharacterHash(seqs[i]));\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(\r
- jalview.util.Comparison.GapChars, seqs[i]\r
- .getSequenceAsString()));\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()\r
- : AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars, seqs[i]\r
- .getSequenceAsString());\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
+ { newname, empty });\r
}\r
}\r
this.seqs = new vamsas.objects.simple.SequenceSet();\r
}\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
+ && ((MsaResult) result).getMsa() != null\r
+ && ((MsaResult) result).getMsa().getSeqs() != null)\r
{\r
return true;\r
}\r
SequenceI[] alseqs = null;\r
char alseq_gapchar = '-';\r
int alseq_l = 0;\r
- if ( ( (MsaResult) result).getMsa() != null)\r
+ if (((MsaResult) result).getMsa() != null)\r
{\r
- alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());\r
- alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);\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
if (nw > sw)\r
{\r
// pad at end\r
- alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +\r
- insbuff.substring(0, sw - nw));\r
+ alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()\r
+ + insbuff.substring(0, sw - nw));\r
}\r
}\r
}\r
String[] es = (String[]) emptySeqs.get(i);\r
if (es[1] == null)\r
{\r
- t_alseqs[i +\r
- alseq_l] = new jalview.datamodel.Sequence(es[0],\r
- insbuff.toString(), 1, 0);\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 +\r
- alseq_l] = new jalview.datamodel.Sequence(es[0],\r
- es[1] + insbuff.substring(0, nw - es[1].length()), 1,\r
- 1 + es[1].length());\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 +\r
- alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
+ es[0], es[1]);\r
}\r
}\r
}\r
// account for any missing sequences\r
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);\r
return new Object[]\r
- {\r
- alseqs, msaorder};\r
+ { alseqs, msaorder };\r
}\r
return null;\r
}\r
}\r
\r
/**\r
- *\r
+ * \r
* @return boolean true if job can be submitted.\r
*/\r
boolean hasValidInput()\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
+ * \r
* @param subgaps\r
- * boolean\r
+ * boolean\r
* @param presorder\r
- * boolean\r
+ * boolean\r
*/\r
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- AlignmentView alview,\r
- String wsname, boolean subgaps, boolean presorder)\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
\r
/**\r
* create one or more Msa jobs to align visible seuqences in _msa\r
- *\r
+ * \r
* @param title\r
- * String\r
+ * String\r
* @param _msa\r
- * AlignmentView\r
+ * AlignmentView\r
* @param subgaps\r
- * boolean\r
+ * boolean\r
* @param presorder\r
- * boolean\r
+ * boolean\r
* @param seqset\r
- * Alignment\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
+ 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
}\r
if (njobs > 0)\r
{\r
- wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);\r
+ wsinfo\r
+ .setProgressName("region " + jobs[j].jobnum,\r
+ jobs[j].jobnum);\r
}\r
wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);\r
}\r
try\r
{\r
vamsas.objects.simple.WsJobId cancelledJob = server\r
- .cancel(jobs[job].jobId);\r
+ .cancel(jobs[job].jobId);\r
if (cancelledJob.getStatus() == 2)\r
{\r
// CANCELLED_JOB\r
cancelledMessage = "Job cancelled.";\r
- ( (MsaWSJob) jobs[job]).cancel();\r
+ ((MsaWSJob) jobs[job]).cancel();\r
wsInfo.setStatus(jobs[job].jobnum,\r
- WebserviceInfo.STATE_CANCELLED_OK);\r
+ WebserviceInfo.STATE_CANCELLED_OK);\r
}\r
else if (cancelledJob.getStatus() == 3)\r
{\r
// VALID UNSTOPPABLE JOB\r
- cancelledMessage +=\r
- "Server cannot cancel this job. just close the window.\n";\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
+ // WebserviceInfo.STATE_RUNNING);\r
}\r
\r
if (cancelledJob.getJobId() != null)\r
}\r
\r
cancelledMessage += "\n";\r
- }\r
- catch (Exception exc)\r
+ } catch (Exception exc)\r
{\r
- cancelledMessage +=\r
- ("\nProblems cancelling the job : Exception received...\n"\r
- + exc + "\n");\r
- Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,\r
- exc);\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
+ + cancelledMessage + "\n");\r
}\r
}\r
if (cancelled)\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
+ .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
- void pollJob(WSJob job)\r
- throws Exception\r
+ void pollJob(WSJob job) throws Exception\r
{\r
- ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);\r
+ ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);\r
}\r
\r
void StartJob(WSJob job)\r
{\r
- if (! (job instanceof MsaWSJob))\r
+ if (!(job instanceof MsaWSJob))\r
{\r
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +\r
- job.getClass());\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 " + j.jobId);\r
+ Cache.log.debug("Tried to submit an already submitted job "\r
+ + j.jobId);\r
}\r
return;\r
}\r
j.result = new MsaResult();\r
j.result.setFinished(true);\r
j.result.setStatus("Empty Alignment Job");\r
- ( (MsaResult) j.result).setMsa(null);\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
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
{\r
j.jobId = jobsubmit.getJobId();\r
j.submitted = true;\r
if (jobsubmit == null)\r
{\r
throw new Exception(\r
- "Server at "\r
- + WsUrl\r
- +\r
- " returned null object, it probably cannot be contacted. Try again later ?");\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
- }\r
- catch (Exception e)\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
+ .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
+ .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
+ 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.\r
- length];\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
+ .getSeq());\r
}\r
\r
return msa;\r
for (int j = 0; j < jobs.length; j++)\r
{\r
finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
- if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())\r
+ if (jobs[j].submitted && jobs[j].subjobComplete\r
+ && jobs[j].hasResults())\r
{\r
results++;\r
- vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).\r
- getMsa();\r
+ vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result)\r
+ .getMsa();\r
if (valign != null)\r
{\r
wsInfo.appendProgressText(jobs[j].jobnum,\r
- "\nAlignment Object Method Notes\n");\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
+ // hidden behind icons in the monitor window that,\r
// when clicked, pop up their corresponding data\r
}\r
}\r
}\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
\r
- Cache.log.error("Unexpected exception when processing results for " +\r
- alTitle, ex);\r
+ Cache.log.error("Unexpected exception when processing results for "\r
+ + alTitle, ex);\r
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
}\r
if (results > 0)\r
{\r
wsInfo.showResultsNewFrame\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(true);\r
- }\r
- });\r
+ .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(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(false);\r
- }\r
- });\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
if (jobs[j].hasResults())\r
{\r
- Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();\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
+ // SequenceI[] alignment = input.getUpdated\r
}\r
else\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 accompanying each subjob\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
if (newFrame)\r
{\r
AlignFrame af = new AlignFrame(al, columnselection,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
\r
// initialise with same renderer settings as in parent alignframe.\r
- af.getFeatureRenderer().transferSettings(\r
- this.featureSettings);\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
+ (AlignmentOrder) alorders.get(0));\r
}\r
else\r
{\r
\r
while (j < l)\r
{\r
- if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (\r
- AlignmentOrder) alorders.get(j))))\r
+ if (((AlignmentOrder) alorders.get(i))\r
+ .equals(((AlignmentOrder) alorders.get(j))))\r
{\r
alorders.remove(j);\r
l--;\r
for (int i = 0, l = alorders.size(); i < l; i++)\r
{\r
af.addSortByOrderMenuItem(WebServiceName\r
- + ( (String) names.get(i)) +\r
- " Ordering",\r
- (AlignmentOrder) alorders.get(i));\r
+ + ((String) names.get(i)) + " Ordering",\r
+ (AlignmentOrder) alorders.get(i));\r
}\r
}\r
}\r
\r
- Desktop.addInternalFrame(af, alTitle,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\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 alignment using the commands.EditCommand model to ensure the update can be undone\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
git://source.jalview.org / jalview.git / blobdiff