* <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 SeqSearchWSThread\r
- extends WSThread implements WSClientI\r
+class SeqSearchWSThread extends WSThread implements WSClientI\r
{\r
- String dbs=null;\r
- boolean profile=false;\r
+ String dbs = null;\r
+\r
+ boolean profile = false;\r
\r
- class SeqSearchWSJob\r
- extends WSThread.WSJob\r
+ class SeqSearchWSJob 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 SeqSearchWSJob(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 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
nseqs++;\r
}\r
}\r
- boolean valid = nseqs >= 1; // need at least one sequence for valid input TODO: generalise\r
- vamsas.objects.simple.Sequence[] seqarray =\r
- (valid)\r
- ? new vamsas.objects.simple.Sequence[nseqs]\r
- : null;\r
- boolean submitGaps = (nseqs==1) ? false : true; // profile is submitted with gaps \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
// 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
if (submitGaps)\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
- && ( (SeqSearchResult) result).getAlignment() != null &&\r
- ( (SeqSearchResult) result).getAlignment().getSeqs() != null)\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
\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
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
+ // char alseq_gapchar = '-';\r
+ // int alseq_l = 0;\r
+ if (((SeqSearchResult) result).getAlignment() != null)\r
{\r
- alseqs = getVamsasAlignment( ( (SeqSearchResult) result).getAlignment());\r
- //alseq_gapchar = ( (SeqSearchResult) result).getAlignment().getGapchar().charAt(0);\r
- //alseq_l = alseqs.length;\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 file and sequence features file, and associate any tree-nodes.\r
- * 2. connect alignment back to any associated dataset: 2.a. deuniquify recovers sequence information - but additionally, \r
- * relocations must be made from the returned aligned sequence back to the dataset.\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 applet\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
+ String inFile = null;\r
+ try\r
+ {\r
inFile = ((SeqSearchResult) result).getAnnotation();\r
- if (inFile!=null && inFile.length()>0)\r
+ if (inFile != null && inFile.length() > 0)\r
{\r
- new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, jalview.io.AppletFormatAdapter.PASTE);\r
+ new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,\r
+ jalview.io.AppletFormatAdapter.PASTE);\r
}\r
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
- System.err.println("Failed to parse the annotation file associated with the alignment.");\r
- System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");\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
+ try\r
+ {\r
inFile = ((SeqSearchResult) result).getFeatures();\r
- if (inFile!=null && inFile.length()>0)\r
+ if (inFile != null && inFile.length() > 0)\r
{\r
- jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, jalview.io.AppletFormatAdapter.PASTE);\r
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(\r
+ inFile, jalview.io.AppletFormatAdapter.PASTE);\r
ff.parse(al, featureColours, false);\r
}\r
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
- System.err.println("Failed to parse the Features file associated with the alignment.");\r
- System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");\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
+ jalview.io.NewickFile nf = null;\r
+ try\r
+ {\r
inFile = ((SeqSearchResult) result).getNewickTree();\r
- if (inFile!=null && inFile.length()>0)\r
+ if (inFile != null && inFile.length() > 0)\r
{\r
- nf = new jalview.io.NewickFile(inFile, jalview.io.AppletFormatAdapter.PASTE);\r
- if (!nf.isValid()) {\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
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
- System.err.println("Failed to parse the treeFile associated with the alignment.");\r
- System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");\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
- /* 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\r
- * // finally, attempt to de-uniquify to recover input sequence identity, and try to map back onto dataset\r
- Note: this\r
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);\r
- will NOT WORK - the returned alignment may contain multiple versions of the input sequence, each being a subsequence of the original.\r
- deuniquify also removes existing annotation and features added in the previous step...\r
- al.setDataset(dataset);\r
- // add in new sequences retrieved from sequence search which are not already in dataset.\r
- // trigger a 'fetchDBids' to annotate sequences with database ids...\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
- {\r
- al, nf};\r
+ { al, nf };\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
ext.vamsas.SeqSearchI server = null;\r
\r
private String dbArg;\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
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- AlignmentView alview,\r
- String wsname, String db)\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
\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
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
- String wsname, String title, AlignmentView _msa, String db, Alignment seqset)\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
}\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
- ( (SeqSearchWSJob) jobs[job]).cancel();\r
+ ((SeqSearchWSJob) 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
- ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);\r
+ ((SeqSearchWSJob) job).result = server\r
+ .getResult(((SeqSearchWSJob) job).jobId);\r
}\r
\r
void StartJob(WSJob job)\r
{\r
- if (! (job instanceof SeqSearchWSJob))\r
+ if (!(job instanceof SeqSearchWSJob))\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
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 " + 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.search(j.seqs.getSeqs()[0], dbArg);\r
+ vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs\r
+ .getSeqs()[0], dbArg);\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
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 = ( (SeqSearchResult) jobs[j].result).\r
- getAlignment();\r
+ vamsas.objects.simple.Alignment valign = ((SeqSearchResult) jobs[j].result)\r
+ .getAlignment();\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
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
+ // 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
+ Alignment al = null;\r
NewickFile nf = null;\r
if (jobs[j].hasResults())\r
{\r
- Object[] res = ( (SeqSearchWSJob) jobs[j]).getAlignment(dataset, featureColours);\r
- if (res==null) { continue; };\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
nf = null;\r
continue;\r
}\r
- /*\r
- * We can't map new alignment back with insertions from input's hidden regions until dataset mapping is sorted out...\r
- * but basically it goes like this:\r
- 1. Merge each domain hit back onto the visible segments in 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\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
-\r
- if (dataset != null)\r
- {\r
- al.setDataset(dataset);\r
- }\r
-\r
- propagateDatasetMappings(al);\r
- }\r
- */\r
- \r
- AlignFrame af = new AlignFrame(al,// columnselection,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- if (nf!=null)\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
+ af.ShowNewickTree(nf, "Tree from " + this.alTitle);\r
}\r
// initialise with same renderer settings as in parent alignframe.\r
- af.getFeatureRenderer().transferSettings(\r
- this.featureSettings);\r
- Desktop.addInternalFrame(af, alTitle,\r
- AlignFrame.DEFAULT_WIDTH,\r
+ af.getFeatureRenderer().transferSettings(this.featureSettings);\r
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
AlignFrame.DEFAULT_HEIGHT);\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff