+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.ws;\r
\r
import java.util.*;\r
import jalview.util.*;\r
import vamsas.objects.simple.JpredResult;\r
\r
-class JPredThread\r
- extends WSThread implements WSClientI\r
+class JPredThread extends WSThread implements WSClientI\r
{\r
- // TODO: put mapping between JPredJob input and input data here - JNetAnnotation adding is done after result parsing.\r
- class JPredJob\r
- extends WSThread.WSJob\r
+ // TODO: put mapping between JPredJob input and input data here -\r
+ // JNetAnnotation adding is done after result parsing.\r
+ class JPredJob extends WSThread.WSJob\r
{\r
- // TODO: make JPredJob deal only with what was sent to and received from a JNet service\r
- int[] predMap = null; // mapping from sequence(i) to the original sequence(predMap[i]) being predicted on\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
+ // 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
- 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\r
+\r
+ int msaIndex = 0; // the position of the original sequence in the array of\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 result.\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
+ && ((JpredResult) result).getPredfile() != null\r
+ && ((JpredResult) result).getAligfile() != null)\r
{\r
return true;\r
}\r
}\r
\r
/**\r
- *\r
- * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.\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()\r
- throws Exception\r
+ public Object[] getResultSet() throws Exception\r
{\r
if (result == null || !result.isFinished())\r
{\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
+ JpredResult result = (JpredResult) this.result;\r
\r
jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
- getPredfile(),\r
- "Paste");\r
+ // 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
+ if ((this.msa != null) && (result.getAligfile() != null))\r
{\r
jalview.bin.Cache.log.debug("Getting associated alignment.");\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result.\r
- getAligfile(),\r
- "Paste");\r
+ // 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.getAlignmentAndColumnSelection(\r
- getGapChar());\r
+ Object[] alandcolsel = input\r
+ .getAlignmentAndColumnSelection(getGapChar());\r
sqs = (SequenceI[]) alandcolsel[0];\r
al = new Alignment(sqs);\r
alcsel = (ColumnSelection) alandcolsel[1];\r
else\r
{\r
al = new FormatAdapter().readFile(result.getAligfile(),\r
- "Paste", format);\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( (Hashtable)\r
- SequenceInfo, sqs))\r
+ if (!jalview.analysis.SeqsetUtils.deuniquify(\r
+ (Hashtable) SequenceInfo, sqs))\r
{\r
throw (new Exception(\r
- "Couldn't recover sequence properties for alignment."));\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,\r
- false, predMap);\r
+ FirstSeq, false, predMap);\r
\r
}\r
else\r
{\r
- throw (new Exception(\r
- "Unknown format " + format + " for file : \n" +\r
- result.getAligfile()));\r
+ throw (new Exception("Unknown format " + format\r
+ + " for file : \n" + result.getAligfile()));\r
}\r
}\r
else\r
if (predMap != null)\r
{\r
char gc = getGapChar();\r
- SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.\r
- getAlignmentAndColumnSelection(gc))[\r
- 0];\r
+ SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input\r
+ .getAlignmentAndColumnSelection(gc))[0];\r
if (this.msaIndex >= sqs.length)\r
{\r
- throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
+ throw new Error(\r
+ "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
}\r
\r
- /////\r
- //Uses RemoveGapsCommand\r
- /////\r
+ // ///\r
+ // Uses RemoveGapsCommand\r
+ // ///\r
new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
- new SequenceI[]\r
- {sqs[msaIndex]},\r
- currentView);\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(\r
- al.getSequenceAt(FirstSeq), SequenceInfo))\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
+ "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,\r
- true, predMap);\r
+ FirstSeq, true, predMap);\r
SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.\r
alignToProfileSeq(al, profileseq);\r
if (predMap != null)\r
}\r
}\r
return new Object[]\r
- {\r
- al, alcsel}; // , FirstSeq, noMsa};\r
+ { al, alcsel }; // , FirstSeq, noMsa};\r
}\r
\r
/**\r
- * 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\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
{\r
// pad gaps\r
sq = sq + sb;\r
- while ( (diff = gapMap[r] - sq.length()) > 0)\r
+ while ((diff = gapMap[r] - sq.length()) > 0)\r
{\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() :\r
- sb.substring(0, diff));\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(sq.substring(0, gapMap[r]) +\r
- sb.toString() +\r
- sq.substring(gapMap[r]));\r
+ al.getSequenceAt(s).setSequence(\r
+ sq.substring(0, gapMap[r]) + sb.toString()\r
+ + sq.substring(gapMap[r]));\r
}\r
}\r
}\r
}\r
\r
/**\r
- * Add gaps into the sequences aligned to profileseq under the given AlignmentView\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,\r
- AlignmentView input)\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.parseMap( (origseq = ( (SequenceI[])\r
- alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's mapping to view.\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[]) alandcolsel[0])[0].gapMap()))\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
{\r
// pad gaps\r
sq = sq + sb;\r
- while ( (diff = spos + offset - sq.length() - 1) > 0)\r
+ while ((diff = spos + offset - sq.length() - 1) > 0)\r
{\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() :\r
- sb.substring(0, diff));\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(sq.substring(0, spos + offset) +\r
- sb.toString() +\r
- sq.substring(spos + offset));\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
+ // offset+=sb.length();\r
}\r
spos = viscontigs[v + 1] + 1;\r
}\r
- if ( (offset + spos) < profileseq.getLength())\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
int diff = origseq.getLength() - sq.length();\r
while (diff > 0)\r
{\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() : sb.substring(0, diff));\r
+ sq = sq\r
+ + ((diff >= sb.length()) ? sb.toString() : sb\r
+ .substring(0, diff));\r
diff = origseq.getLength() - sq.length();\r
}\r
}\r
{\r
super();\r
this.predMap = delMap;\r
- String sq = AlignSeq.extractGaps(Comparison.GapChars,\r
- seq.getSequenceAsString());\r
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq\r
+ .getSequenceAsString());\r
if (sq.length() >= 20)\r
{\r
this.SequenceInfo = SequenceInfo;\r
}\r
\r
ext.vamsas.Jpred server;\r
+\r
String altitle = "";\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
- String wsurl, AlignmentView alview, AlignFrame alframe)\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, ext.vamsas.Jpred server,\r
- String wsurl, Hashtable SequenceInfo, SequenceI seq, int[] delMap,\r
- AlignmentView alview, AlignFrame alframe)\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
{\r
OutputHeader = wsInfo.getProgressText();\r
jobs = new WSJob[]\r
- {\r
- job};\r
+ { job };\r
job.jobnum = 0;\r
}\r
}\r
\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
- Hashtable SequenceInfo, SequenceI[] msf, int[] delMap,\r
- AlignmentView alview, AlignFrame alframe, String wsurl)\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
- {\r
- job};\r
+ { job };\r
OutputHeader = wsInfo.getProgressText();\r
job.jobnum = 0;\r
}\r
\r
void StartJob(WSJob j)\r
{\r
- if (! (j instanceof JPredJob))\r
+ if (!(j instanceof JPredJob))\r
{\r
- throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
- j.getClass());\r
+ throw new Error(\r
+ "Implementation error - StartJob(JpredJob) called on "\r
+ + j.getClass());\r
}\r
try\r
{\r
{\r
job.jobId = server.predictOnMsa(job.msa);\r
}\r
- else\r
- if (job.sequence != null)\r
+ else if (job.sequence != null)\r
{\r
- job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//\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 = (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
+ throw new Exception(job.jobId);\r
}\r
else\r
{\r
{\r
throw new Exception("Server timed out - try again later\n");\r
}\r
- }\r
- catch (Exception e)\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.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setProgressText(j.jobnum,\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- +\r
- "It is most likely that there is a problem with the server.\n");\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +\r
- e.getMessage() + "\n");\r
+ 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
wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
// JBPNote - this could be a popup informing the user of the problem.\r
wsInfo.appendProgressText(j.jobnum,\r
- "Failed to submit the prediction:\n"\r
- + e.getMessage() +\r
- wsInfo.getProgressText());\r
+ "Failed to submit the prediction:\n" + e.getMessage()\r
+ + wsInfo.getProgressText());\r
\r
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum,\r
+ e);\r
\r
}\r
j.allowedServerExceptions = -1;\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
}\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 (j.hasResults())\r
{\r
- // hack - we only deal with all single seuqence predictions or all profile predictions\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
{\r
// do merge with other job results\r
throw new Error(\r
- "Multiple JNet subjob merging not yet implemented.");\r
+ "Multiple JNet subjob merging not yet implemented.");\r
}\r
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
jalview.bin.Cache.log.error(\r
- "JNet Client: JPred Annotation Parse Error",\r
- e);\r
+ "JNet Client: JPred Annotation Parse Error", e);\r
wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- wsInfo.appendProgressText(j.jobnum,\r
- OutputHeader + "\n" +\r
- j.result.getStatus() +\r
- "\nInvalid JNet job result data!\n" +\r
- e.getMessage());\r
+ 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
if (res[1] != null)\r
{\r
- af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\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], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
+ af = new AlignFrame((Alignment) res[0],\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
}\r
}\r
else\r
{\r
- /*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
- if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
- if (msa) {\r
- throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");\r
- }\r
- }\r
- if (!msa) {\r
- // update hidden regions to account for loss of gaps in profile. - if any\r
- // gapMap returns insert list, interpreted as delete list by pruneDeletions\r
- //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));\r
- }*/\r
-\r
- af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
+ /*\r
+ * java.lang.Object[] alandcolsel =\r
+ * input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
+ * if (((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,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
+ Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
}\r
else\r
{\r
}\r
}\r
\r
- void pollJob(WSJob job)\r
- throws Exception\r
+ void pollJob(WSJob job) throws Exception\r
{\r
job.result = server.getresult(job.jobId);\r
}\r
git://source.jalview.org / jalview.git / blobdiff