import jalview.analysis.AlignSeq;\r
import ext.vamsas.*;\r
\r
+\r
public class JPredClient\r
{\r
-\r
- JInternalFrame outputFrame = new JInternalFrame();\r
- CutAndPasteTransfer output = new CutAndPasteTransfer(false);\r
int jobsRunning = 0;\r
ext.vamsas.JpredSoapBindingStub server;\r
+ WebserviceInfo wsInfo;\r
\r
- public JPredClient(SequenceI seq)\r
+ public JPredClient(SequenceI[] msf)\r
{\r
- output.formatForOutput();\r
- outputFrame.setContentPane(output);\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
- output.setText("Job details for prediction on sequence :\nName : "\r
- + seq.getName() + "\nSequence : " + seq.getSequence() + "\n");\r
- Desktop.addInternalFrame(outputFrame,\r
- "JNet secondary structure prediction job", 800,\r
- 300);\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
- output.setText("Serious! JPred Service location failed\nfor URL :"\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
+ JPredThread jthread = new JPredThread(msf);\r
jthread.start();\r
- ImageTwirler thread = new ImageTwirler();\r
- thread.start();\r
}\r
\r
- class ImageTwirler\r
- extends Thread\r
+ public JPredClient(SequenceI seq)\r
{\r
- ImageIcon[] imageIcon;\r
- int imageIndex = 0;\r
- public ImageTwirler()\r
- {\r
- imageIcon = new ImageIcon[9];\r
- for (int i = 0; i < 9; i++)\r
- {\r
- java.net.URL url = getClass().getResource("/images/dna" + (i + 1) +\r
- ".gif");\r
- if (url != null)\r
- imageIcon[i] = new ImageIcon(url);\r
- }\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
- public void run()\r
- {\r
- while (jobsRunning > 0)\r
- {\r
- try\r
- {\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %= 9;\r
- outputFrame.setFrameIcon(imageIcon[imageIndex]);\r
- outputFrame.setTitle("JNet Secondary Structure Prediction : " +\r
- jobsRunning + " jobs running.");\r
\r
- }\r
- catch (Exception ex)\r
- {}\r
+ wsInfo.setProgressText("Job details for prediction on sequence :\nName : "\r
+ + seq.getName() + "\nSequence : " + 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(seq);\r
+ jthread.start();\r
}\r
\r
+\r
class JPredThread\r
extends Thread\r
{\r
String OutputHeader;\r
- ext.vamsas.Secstructpred result;\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 = output.getText();\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\r
- && (allowedServerExceptions > 0))\r
+ while (!jobComplete && (allowedServerExceptions > 0))\r
{\r
try\r
{\r
- result = server.getpredict(jobId);\r
+ result = server.getresult(jobId);\r
\r
- if (result.getOutput().indexOf("Job") != 0)\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
}\r
else\r
{\r
- output.setText(OutputHeader + "\n" + result.getOutput());\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
- Thread.sleep(5000);\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
-\r
}\r
catch (Exception ex)\r
{\r
allowedServerExceptions--;\r
- String msg = output.getText();\r
- output.setText(msg + "\nJPredWS Server exception!\n" + ex.getMessage());\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
- jobId = server.predict(sequence);\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
}\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
- output.setText(OutputHeader + result.getOutput());\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
- JPredFile prediction=new JPredFile(result.getOutput(), "Paste");\r
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");\r
SequenceI[] preds = prediction.getSeqsAsArray();\r
- Alignment al = new Alignment(preds);\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
- // Rename the query sequence\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"))\r
+ if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))\r
{\r
annotations = new Annotation[al.getWidth()];\r
\r
|| id.equals("JNETPSSM")\r
|| id.equals("JNETFREQ")\r
|| id.equals("JNETHMM")\r
- || id.equals("JNETALIGN"))\r
+ || id.equals("JNETALIGN")\r
+ || id.equals("JPRED"))\r
{\r
- for (int j = 0; j < al.getWidth(); j++)\r
- annotations[j] = new Annotation("", "", preds[i].getCharAt(j), 0);\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 < al.getWidth(); j++)\r
+ for (int j = 0; j < width; j++)\r
{\r
float value = Float.parseFloat(preds[i].getCharAt(j)+"");\r
- annotations[j] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);\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 < al.getWidth(); j++)\r
- annotations[j] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);\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
- "Jpred Output",\r
+ "JNet Output",\r
annotations,0f,10f,1);\r
\r
else annot = new AlignmentAnnotation(preds[i].getName(),\r
- "Jpred Output",\r
+ "JNet Output",\r
annotations);\r
al.addAnnotation(annot);\r
- al.deleteSequence(preds[i]);\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
- Vector values = (Vector)scores.get("JNETPROPH");\r
- annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < al.getWidth(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[j] = new Annotation("", value+"",' ',value);\r
- }\r
- annot = new AlignmentAnnotation("Jnetproph", "Jpred Output", annotations, 0f,1f,1);\r
- al.addAnnotation(annot);\r
-\r
- values = (Vector)scores.get("JNETPROPB");\r
- annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < al.getWidth(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[j] = new Annotation("", value+"",' ',value);\r
- }\r
- annot = new AlignmentAnnotation("JnetpropB", "Jpred Output", annotations, 0f,1f,1);\r
- al.addAnnotation(annot);\r
-\r
- values = (Vector)scores.get("JNETPROPC");\r
- annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < al.getWidth(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[j] = new Annotation("", value+"",' ',value);\r
- }\r
- annot = new AlignmentAnnotation("JnetpropC", "Jpred Output", annotations, 0f,1f,1);\r
- al.addAnnotation(annot);\r
-\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
- /* JBPNote - need to set correct style of display for the secstrpred alignment object.\r
- af.clustalColour.setSelected(true);\r
- af.clustalColour_actionPerformed(null);\r
- */\r
Desktop.addInternalFrame(af,\r
"JNet Prediction for sequence ",\r
- 700, 500);\r
+ AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
}catch(Exception ex){ex.printStackTrace();}\r
\r
}\r