import jalview.analysis.*;\r
import jalview.datamodel.*;\r
import jalview.gui.*;\r
+import jalview.io.FormatAdapter;\r
+import jalview.io.*;\r
\r
public class JPredClient\r
extends WSClient\r
wsInfo = setWebService();\r
\r
SequenceI seq = msf[0];\r
+\r
altitle = "JNet prediction on " + seq.getName() +\r
" using alignment from " + title;\r
\r
AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
"\n");\r
SequenceI aln[] = new SequenceI[msf.length];\r
- for (int i=0,j=msf.length; i<j;i++)\r
- aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
+ for (int i=0,j=msf.length; i<j;i++) {\r
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
+ }\r
+\r
SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
\r
if (!locateWebService())\r
WebServiceName = "JNetWS";\r
WebServiceJobTitle = "JNet secondary structure prediction";\r
WebServiceReference =\r
- "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
+ "\"Cuff J. A and Barton G.J (2000) Application of " +\r
"multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
"Proteins 40:502-511\".";\r
WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
{\r
this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub\r
+ //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);\r
+\r
}\r
catch (Exception ex)\r
{\r
" Service location failed\nfor URL :" + WsURL +\r
"\n" +\r
ex.getMessage());\r
- wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
\r
return false;\r
}\r
this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
msf[0].getSequence()));\r
\r
- jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
this.msa = new vamsas.objects.simple.Msfalignment();\r
- msa.setMsf(mwrite.print(msf));\r
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
+ msa.setMsf(pileup.print(msf));\r
}\r
\r
public void run()\r
catch (Exception ex)\r
{\r
allowedServerExceptions--;\r
+\r
wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
ex.getMessage());\r
\r
}\r
catch (Exception e)\r
{\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ if (e.getMessage().indexOf("Exception")>-1) {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.setProgressText(\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
+\r
+ jalview.bin.Cache.log.warn("Server Exception",e);\r
+ } else {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ // JBPNote - this could be a popup informing the user of the problem.\r
+ wsInfo.setProgressText("Failed to submit the prediction:\n"\r
+ +e.getMessage()+\r
+ wsInfo.getProgressText());\r
+\r
+ jalview.bin.Cache.log.debug("Failed Submission",e);\r
+\r
+ }\r
allowedServerExceptions = -1;\r
jobComplete = true;\r
\r
- wsInfo.setProgressText("Failed to submit the prediction. (Just close the window)\n"\r
- + ((e.getMessage().indexOf("Exception")>-1) ? (\r
- "It is most likely that there is a problem with the server.\n")\r
- : e.getMessage())\r
- +wsInfo.getProgressText());\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction (Possibly a server error - see below)\n" +\r
- e.getMessage() + "\n");\r
-\r
- jalview.bin.Cache.log.debug("Failed Submission",e);\r
}\r
}\r
\r
\r
\r
- private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+ /* private void addFloatAnnotations(Alignment al, int[] gapmap,\r
Vector values, String Symname,\r
String Visname, float min,\r
float max, int winLength)\r
\r
al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
annotations, min, max, winLength));\r
- }\r
+ }*/\r
\r
void parseResult()\r
{\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 = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
+ String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),\r
"Paste");\r
\r
- if (jalview.io.FormatAdapter.formats.contains(format))\r
+ if (jalview.io.FormatAdapter.isValidFormat(format))\r
{\r
- al = new Alignment(jalview.io.FormatAdapter.readFile(\r
+ al = new Alignment(new FormatAdapter().readFile(\r
result.getAligfile(), "Paste", format));\r
+ SequenceI sqs[] = new SequenceI[al.getHeight()];\r
for (int i=0, j=al.getHeight(); i<j; i++) {\r
- SequenceI sq = al.getSequenceAt(i);\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
- sq, (Hashtable) SequenceInfo.get(sq.getName())))\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 JNet "\r
- +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));\r
+ "Couldn't recover sequence properties for alignment."));\r
}\r
- }\r
+\r
noMsa = false;\r
FirstSeq = 0;\r
}\r
}\r
}\r
\r
+ al.setDataset(null);\r
\r
- AlignmentAnnotation annot;\r
- Annotation[] annotations = null;\r
- int i = 0;\r
- int width = preds[0].getSequence().length();\r
-\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
-\r
- if (gapmap.length != width)\r
- {\r
- throw (new Exception(\r
- "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
- al.getSequenceAt(FirstSeq).getName() + "\n" +\r
- al.getSequenceAt(FirstSeq).getSequence() +\r
- "\nDiffer from number of prediction sites in \n" +\r
- result.getPredfile() + "\n"));\r
+ try {\r
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,\r
+ noMsa);\r
}\r
-\r
- // JBPNote Should also rename the query sequence sometime...\r
- i = 0;\r
-\r
- while (i < preds.length)\r
- {\r
- String id = preds[i].getName().toUpperCase();\r
-\r
- if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
- id.startsWith("JPRED"))\r
- {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
- id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
- id.equals("JNETALIGN") || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation("", "",\r
- preds[i].getCharAt(j), 0);\r
- }\r
- }\r
- else if (id.equals("JNETCONF"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- float value = Float.parseFloat(preds[i].getCharAt(\r
- j) + "");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", preds[i].getCharAt(j),\r
- value);\r
- }\r
- }\r
- else\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", ' ', 0);\r
- }\r
- }\r
-\r
- if (id.equals("JNETCONF"))\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations, 0f,\r
- 10f, 1);\r
- }\r
- else\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations);\r
- }\r
-\r
- al.addAnnotation(annot);\r
-\r
- if (noMsa)\r
- {\r
- al.deleteSequence(preds[i]);\r
- }\r
- }\r
-\r
- i++;\r
+ catch (Exception e) {\r
+ jalview.bin.Cache.log.error("JNet Client: JPred Annotation Parse Error", e);\r
}\r
-\r
- Hashtable scores = prediction.getScores();\r
-\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
-\r
wsInfo.setProgressText(OutputHeader);\r
jalview.bin.Cache.log.debug("Finished parsing output.");\r
AlignFrame af = new AlignFrame(al);\r
}\r
catch (Exception ex)\r
{\r
- jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
- jalview.bin.Cache.log.debug("Exception: ",ex);\r
+ jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff