\r
import java.util.*;\r
\r
-import javax.swing.*;\r
-\r
-import vamsas.objects.simple.JpredResult;\r
-\r
import jalview.analysis.*;\r
import jalview.bin.*;\r
import jalview.datamodel.*;\r
+import jalview.datamodel.Alignment;\r
import jalview.gui.*;\r
import jalview.io.*;\r
import jalview.util.*;\r
+import vamsas.objects.simple.JpredResult;\r
\r
class JPredThread\r
-extends WSThread\r
-implements WSClientI\r
+ 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
+ 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
+ int[] predMap = null; // mapping from sequence(i) to the original sequence(predMap[i]) being predicted on\r
vamsas.objects.simple.Sequence sequence;\r
vamsas.objects.simple.Msfalignment msa;\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
+ 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
*\r
* @return true if getResultSet will return a valid alignment and prediction result.\r
}\r
return false;\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
* @throws Exception\r
*/\r
public Object[] getResultSet()\r
- throws Exception\r
+ throws Exception\r
{\r
if (result == null || !result.isFinished())\r
{\r
return null;\r
}\r
Alignment al = null;\r
- ColumnSelection alcsel=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
// 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
+ "Paste");\r
SequenceI[] preds = prediction.getSeqsAsArray();\r
jalview.bin.Cache.log.debug("Got prediction profile.");\r
\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
+ "Paste");\r
\r
if (jalview.io.FormatAdapter.isValidFormat(format))\r
{\r
SequenceI sqs[];\r
- if (predMap!=null) {\r
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
+ if (predMap != null)\r
+ {\r
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(\r
+ alignFrame.getViewport().getGapCharacter());\r
sqs = (SequenceI[]) alandcolsel[0];\r
al = new Alignment(sqs);\r
- alcsel=(ColumnSelection) alandcolsel[1];\r
- } else {\r
+ alcsel = (ColumnSelection) alandcolsel[1];\r
+ }\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
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, FirstSeq,\r
- false,predMap);\r
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
+ FirstSeq,\r
+ false, predMap);\r
\r
}\r
else\r
{\r
throw (new Exception(\r
- "Unknown format "+format+" for file : \n" +\r
+ "Unknown format " + format + " for file : \n" +\r
result.getAligfile()));\r
}\r
}\r
{\r
al = new Alignment(preds);\r
FirstSeq = prediction.getQuerySeqPosition();\r
- if (predMap!=null) {\r
+ if (predMap != null)\r
+ {\r
char gc = alignFrame.getViewport().getGapCharacter();\r
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];\r
- if (this.msaIndex>=sqs.length)\r
+ SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.\r
+ getAlignmentAndColumnSelection(gc))[\r
+ 0];\r
+ if (this.msaIndex >= sqs.length)\r
+ {\r
throw new Error("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[] {sqs[msaIndex]},\r
- alignFrame.getCurrentView().getAlignment());\r
+ new SequenceI[]\r
+ {sqs[msaIndex]},\r
+ alignFrame.getCurrentView().\r
+ getAlignment());\r
\r
- SequenceI profileseq=al.getSequenceAt(FirstSeq);\r
+ SequenceI profileseq = al.getSequenceAt(FirstSeq);\r
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r
}\r
\r
al.getSequenceAt(FirstSeq), SequenceInfo))\r
{\r
throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- } else {\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, FirstSeq,\r
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
+ FirstSeq,\r
true, predMap);\r
- SequenceI profileseq=al.getSequenceAt(0); // this includes any gaps.\r
+ SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.\r
alignToProfileSeq(al, profileseq);\r
- if (predMap!=null) {\r
+ if (predMap != null)\r
+ {\r
// Adjust input view for gaps\r
// propagate insertions into profile\r
- alcsel=propagateInsertions(profileseq, al, input);\r
+ alcsel = propagateInsertions(profileseq, al, input);\r
}\r
}\r
}\r
- return new Object[] { al, alcsel}; // , FirstSeq, noMsa};\r
+ return new Object[]\r
+ {\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
* @param al\r
* @param profileseq\r
*/\r
- private void alignToProfileSeq(Alignment al, SequenceI profileseq) {\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
- if (gapMap[r]-lp>1) {\r
- StringBuffer sb=new StringBuffer();\r
- for (int s=0, ns=gapMap[r]-lp; s<ns; s++) {\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
+ 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
+ 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
- sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
+ sq = sq + sb;\r
+ while ( (diff = gapMap[r] - sq.length()) > 0)\r
+ {\r
+ sq = sq +\r
+ ( (diff >= sb.length()) ? sb.toString() :\r
+ sb.substring(0, diff));\r
}\r
al.getSequenceAt(s).setSequence(sq);\r
- } else {\r
- al.getSequenceAt(s).setSequence(sq.substring(0,gapMap[r])+sb.toString()+sq.substring(gapMap[r]));\r
+ }\r
+ else\r
+ {\r
+ al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) +\r
+ sb.toString() +\r
+ sq.substring(gapMap[r]));\r
}\r
}\r
}\r
- lp=gapMap[r];\r
+ lp = gapMap[r];\r
}\r
}\r
\r
* @param al\r
* @param input\r
*/\r
- private ColumnSelection propagateInsertions(SequenceI profileseq, Alignment al, AlignmentView input) {\r
+ private ColumnSelection propagateInsertions(SequenceI profileseq,\r
+ Alignment al,\r
+ 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[]) alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's mapping to view.\r
- int[] viscontigs=nview.getVisibleContigs(0, profileseq.getLength());\r
- int spos=0;\r
- int offset=0;\r
+ nview.pruneDeletions(ShiftList.parseMap( (origseq = ( (SequenceI[])\r
+ alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's 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
// add profile to visible contigs\r
- for (int v=0; v<viscontigs.length; v+=2) {\r
- if (viscontigs[v]>spos) {\r
- StringBuffer sb=new StringBuffer();\r
- for (int s=0, ns=viscontigs[v]-spos; s<ns; s++) {\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
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
+ {\r
SequenceI sqobj = al.getSequenceAt(s);\r
- if (sqobj!=profileseq) {\r
+ if (sqobj != profileseq)\r
+ {\r
String sq = al.getSequenceAt(s).getSequenceAsString();\r
- if (sq.length()<=spos+offset) {\r
+ if (sq.length() <= spos + offset)\r
+ {\r
// pad sequence\r
- int diff=spos+offset-sq.length()-1;\r
- if (diff>0) {\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
- sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
+ sq = sq + sb;\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
}\r
}\r
- sq+=sb.toString();\r
- } else {\r
- al.getSequenceAt(s).setSequence(sq.substring(0,spos+offset)+sb.toString()+sq.substring(spos+offset));\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
}\r
}\r
}\r
//offset+=sb.length();\r
}\r
- spos = viscontigs[v+1]+1;\r
+ spos = viscontigs[v + 1] + 1;\r
}\r
- if ((offset+spos)<profileseq.getLength()) {\r
- StringBuffer sb=new StringBuffer();\r
- for (int s=0, ns=profileseq.getLength()-spos-offset; s<ns; s++) {\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
+ 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
- sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
- diff=origseq.getLength()-sq.length();\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
+ diff = origseq.getLength() - sq.length();\r
}\r
}\r
}\r
}\r
}\r
}\r
+\r
ext.vamsas.Jpred server;\r
String altitle = "";\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, String wsurl, AlignmentView alview, AlignFrame alframe) {\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
+ String wsurl, AlignmentView alview, AlignFrame alframe)\r
+ {\r
super();\r
this.altitle = altitle;\r
this.server = server;\r
WsUrl = wsurl;\r
}\r
\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,SequenceI seq, int[] delMap, AlignmentView alview, AlignFrame alframe)\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
{\r
- this(wsinfo, altitle, server,wsurl, alview, alframe);\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
- {\r
+ {\r
job};\r
job.jobnum = 0;\r
}\r
}\r
\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf, int[] delMap, AlignmentView alview, AlignFrame alframe, String wsurl)\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
{\r
- this(wsinfo, altitle, server,wsurl, alview, alframe);\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
+ {\r
job};\r
OutputHeader = wsInfo.getProgressText();\r
job.jobnum = 0;\r
}\r
}\r
+\r
void StartJob(WSJob j)\r
{\r
if (! (j instanceof JPredJob))\r
{\r
throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
- j.getClass());\r
+ j.getClass());\r
}\r
try\r
{\r
job.jobId = server.predictOnMsa(job.msa);\r
}\r
else\r
- if (job.sequence!=null)\r
- {\r
- job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//\r
- }\r
+ if (job.sequence != null)\r
+ {\r
+ job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//\r
+ }\r
\r
if (job.jobId != null)\r
{\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
+ "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.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"\r
+ + e.getMessage() +\r
+ wsInfo.getProgressText());\r
\r
jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
\r
{\r
\r
Cache.log.error("Unexpected exception when processing results for " +\r
- altitle, ex);\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
+ .addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(\r
java.awt.event.ActionEvent evt)\r
}\r
});\r
wsInfo.mergeResults\r
- .addActionListener(new java.awt.event.ActionListener()\r
+ .addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(\r
java.awt.event.ActionEvent evt)\r
if (jobs != null)\r
{\r
Object[] res = null;\r
- boolean msa=false;\r
+ boolean msa = false;\r
for (int jn = 0; jn < jobs.length; jn++)\r
{\r
Object[] jobres = null;\r
if (j.hasResults())\r
{\r
// hack - we only deal with all single seuqence predictions or all profile predictions\r
- msa = (j.msa!=null) ? true : msa;\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
+ if (jobs.length == 1)\r
+ {\r
res = jobres;\r
- else {\r
+ }\r
+ else\r
+ {\r
// do merge with other job results\r
- throw new Error("Multiple JNet subjob merging not yet implemented.");\r
+ throw new Error(\r
+ "Multiple JNet subjob merging not yet implemented.");\r
}\r
}\r
catch (Exception e)\r
e);\r
wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
wsInfo.appendProgressText(j.jobnum,\r
- OutputHeader + "\n" +\r
- j.result.getStatus() +\r
- "\nInvalid JNet job result data!\n" +\r
- e.getMessage());\r
+ OutputHeader + "\n" +\r
+ j.result.getStatus() +\r
+ "\nInvalid JNet job result data!\n" +\r
+ e.getMessage());\r
j.result.setBroken(true);\r
}\r
}\r
if (newWindow)\r
{\r
AlignFrame af;\r
- if (input==null) {\r
- if (res[1]!=null) {\r
- af = new AlignFrame((Alignment)res[0], (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
- } else {\r
- af = new AlignFrame((Alignment)res[0], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ if (input == null)\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
+ }\r
+ else\r
+ {\r
+ af = new AlignFrame( (Alignment) res[0], AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
/*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
-\r
- if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\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
+ }\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
\r
- af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
}\r
Desktop.addInternalFrame(af, altitle,\r
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
}\r
else\r
{\r
}\r
}\r
}\r
+\r
void pollJob(WSJob job)\r
- throws Exception\r
+ throws Exception\r
{\r
job.result = server.getresult(job.jobId);\r
}\r
+\r
public boolean isCancellable()\r
{\r
return false;\r
}\r
\r
}\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff