+++ /dev/null
-package jalview.io;\r
-\r
-import org.apache.axis.client.*;\r
-import javax.xml.namespace.QName;\r
-import java.util.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-import jalview.analysis.AlignSeq;\r
-import ext.vamsas.*;\r
-\r
-\r
-public class JPredClient\r
-{\r
- int jobsRunning = 0;\r
- ext.vamsas.JpredSoapBindingStub server;\r
- WebserviceInfo wsInfo;\r
-\r
- public JPredClient(SequenceI[] msf)\r
- {\r
- wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
- "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
-\r
- SequenceI seq = msf[0];\r
- wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "\r
- + seq.getName() + "\nSequence : "\r
- + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
-\r
-\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
- try {\r
- this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
- }\r
- catch (Exception ex) {\r
- wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
- +loc.getjpredAddress()+"\n"+ex.getMessage());\r
- }\r
-\r
- JPredThread jthread = new JPredThread(msf);\r
- jthread.start();\r
- }\r
-\r
- public JPredClient(SequenceI seq)\r
- {\r
- wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
- "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
-\r
-\r
- wsInfo.setProgressText("Job details for prediction on sequence :\nName : "\r
- + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
-\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
- try {\r
- this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
- }\r
- catch (Exception ex) {\r
- wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
- +loc.getjpredAddress()+"\n"+ex.getMessage());\r
- }\r
-\r
- JPredThread jthread = new JPredThread(seq);\r
- jthread.start();\r
- }\r
-\r
-\r
- class JPredThread\r
- extends Thread\r
- {\r
- String OutputHeader;\r
- ext.vamsas.JpredResult result;\r
- ext.vamsas.Sequence sequence;\r
- ext.vamsas.Msfalignment msa;\r
- String jobId;\r
- boolean jobComplete = false;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- JPredThread(SequenceI seq)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(seq.getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));\r
- }\r
-\r
- JPredThread(SequenceI[] msf)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(msf[0].getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));\r
- jalview.io.MSFfile mwrite = new jalview.io.MSFfile();\r
- this.msa = new ext.vamsas.Msfalignment();\r
- msa.setMsf(mwrite.print(msf));\r
- }\r
-\r
-\r
- public void run()\r
- {\r
-\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0))\r
- {\r
- try\r
- {\r
- result = server.getresult(jobId);\r
-\r
- if( result.isRunning() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- else if( result.isQueued() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
-\r
- if (result.isFinished())\r
- {\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- }\r
- else\r
- {\r
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- Thread.sleep(5000);\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\r
- }\r
- }\r
-\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- else\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
-\r
- void StartJob()\r
- {\r
- try\r
- {\r
- if (msa!=null) {\r
- jobId = server.predictOnMsa(msa);\r
- } else {\r
- jobId = server.predict(sequence);\r
- }\r
- System.out.println(jobId);\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("JPredWS Client: Failed to submit the prediction\n" +\r
- e.toString() + "\n");\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {\r
-\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < values.size(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value+"",' ',value);\r
- }\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));\r
- }\r
-\r
- void parseResult()\r
- {\r
- // OutputHeader = output.getText();\r
- if (result.isFailed()) {\r
- OutputHeader +="Job failed.\n";\r
- }\r
- if (result.getStatus()!=null) {\r
- OutputHeader += "\n"+result.getStatus();\r
- }\r
- if (result.getPredfile()!=null) {\r
- OutputHeader += "\n"+result.getPredfile();\r
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
- }\r
- if (result.getAligfile()!=null) {\r
- OutputHeader += "\n"+result.getAligfile();\r
- }\r
- wsInfo.setProgressText(OutputHeader);\r
- try {\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- Alignment al;\r
- int FirstSeq; // the position of the query sequence in Alignment al\r
- boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
- if (this.msa!=null && result.getAligfile()!=null) {\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");\r
- if (jalview.io.FormatAdapter.formats.contains(format))\r
- {\r
- al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));\r
- noMsa = false;\r
- FirstSeq = 0;\r
- }\r
- else\r
- {\r
- throw (new Exception("Unknown format 'format' for file : \n" +\r
- result.getAligfile()));\r
- }\r
-\r
- } else {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.QuerySeqPosition;\r
- }\r
-\r
- AlignmentAnnotation annot;\r
- Annotation [] annotations = null;\r
- int i = 0;\r
- int width = preds[0].getSequence().length();\r
-\r
-\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
- if (gapmap.length!=width) {\r
- throw (new Exception("Jpred 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"+result.getPredfile()+"\n"));\r
- }\r
- // JBPNote Should also rename the query sequence sometime...\r
- i=0;\r
- while (i < preds.length)\r
- {\r
- String id = preds[i].getName().toUpperCase();\r
- if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))\r
- {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if(id.equals("JNETPRED")\r
- || id.equals("JNETPSSM")\r
- || id.equals("JNETFREQ")\r
- || id.equals("JNETHMM")\r
- || id.equals("JNETALIGN")\r
- || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0);\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(j)+"");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);\r
- }\r
- }\r
- else\r
- {\r
- for (int j = 0; j < width; j++) {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);\r
- }\r
- }\r
-\r
- if(id.equals("JNETCONF"))\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations,0f,10f,1);\r
-\r
- else annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output",\r
- annotations);\r
- al.addAnnotation(annot);\r
- if (noMsa)\r
- al.deleteSequence(preds[i]);\r
- }\r
- i++;\r
- }\r
-\r
- Hashtable scores = prediction.Scores;\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
- AlignFrame af = new AlignFrame(al);\r
-\r
-\r
- Desktop.addInternalFrame(af,\r
- "JNet Prediction for sequence ",\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
- }\r
-}\r
-\r