From b8682cd59130357f2b81c768461273f7d68bc81c Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 5 May 2005 11:40:24 +0000 Subject: [PATCH] --- src/jalview/io/JPredClient.java | 302 --------------------------------------- 1 file changed, 302 deletions(-) delete mode 100755 src/jalview/io/JPredClient.java diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java deleted file mode 100755 index c463c51..0000000 --- a/src/jalview/io/JPredClient.java +++ /dev/null @@ -1,302 +0,0 @@ -package jalview.io; - -import org.apache.axis.client.*; -import javax.xml.namespace.QName; -import java.util.*; -import jalview.datamodel.*; -import jalview.gui.*; -import javax.swing.*; -import java.util.*; -import java.awt.*; -import jalview.analysis.AlignSeq; -import ext.vamsas.*; - - -public class JPredClient -{ - int jobsRunning = 0; - ext.vamsas.JpredSoapBindingStub server; - WebserviceInfo wsInfo; - - public JPredClient(SequenceI[] msf) - { - wsInfo = new WebserviceInfo("JNet secondary structure prediction job", - "\"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\"."); - - SequenceI seq = msf[0]; - wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : " - + seq.getName() + "\nSequence : " - + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); - - - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - try { - this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); - } - - JPredThread jthread = new JPredThread(msf); - jthread.start(); - } - - public JPredClient(SequenceI seq) - { - wsInfo = new WebserviceInfo("JNet secondary structure prediction job", - "\"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\"."); - - - wsInfo.setProgressText("Job details for prediction on sequence :\nName : " - + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n"); - - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - try { - this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties - } - catch (Exception ex) { - wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :" - +loc.getjpredAddress()+"\n"+ex.getMessage()); - } - - JPredThread jthread = new JPredThread(seq); - jthread.start(); - } - - - class JPredThread - extends Thread - { - String OutputHeader; - ext.vamsas.JpredResult result; - ext.vamsas.Sequence sequence; - ext.vamsas.Msfalignment msa; - String jobId; - boolean jobComplete = false; - int allowedServerExceptions = 3; // thread dies if too many exceptions. - JPredThread(SequenceI seq) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new ext.vamsas.Sequence(); - this.sequence.setId(seq.getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence())); - } - - JPredThread(SequenceI[] msf) - { - OutputHeader = wsInfo.getProgressText(); - this.sequence = new ext.vamsas.Sequence(); - this.sequence.setId(msf[0].getName()); - this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence())); - jalview.io.MSFfile mwrite = new jalview.io.MSFfile(); - this.msa = new ext.vamsas.Msfalignment(); - msa.setMsf(mwrite.print(msf)); - } - - - public void run() - { - - StartJob(); - - while (!jobComplete && (allowedServerExceptions > 0)) - { - try - { - result = server.getresult(jobId); - - if( result.isRunning() ) - wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); - else if( result.isQueued() ) - wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); - - if (result.isFinished()) - { - parseResult(); - jobComplete = true; - jobsRunning--; - } - else - { - wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus()); - if (! (result.isJobFailed() || result.isServerError())) - { - Thread.sleep(5000); - // System.out.println("I'm alive "+seqid+" "+jobid); - } - } - } - catch (Exception ex) - { - allowedServerExceptions--; - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage()); - } - } - - if (! (result.isJobFailed() || result.isServerError())) - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); - else - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - } - - void StartJob() - { - try - { - if (msa!=null) { - jobId = server.predictOnMsa(msa); - } else { - jobId = server.predict(sequence); - } - System.out.println(jobId); - } - catch (Exception e) - { - System.out.println("JPredWS Client: Failed to submit the prediction\n" + - e.toString() + "\n"); - e.printStackTrace(); - } - } - - private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) { - - Annotation[] annotations = new Annotation[al.getWidth()]; - for (int j = 0; j < values.size(); j++) - { - float value = Float.parseFloat(values.get(j).toString()); - annotations[gapmap[j]] = new Annotation("", value+"",' ',value); - } - al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength)); - } - - void parseResult() - { - // OutputHeader = output.getText(); - if (result.isFailed()) { - OutputHeader +="Job failed.\n"; - } - if (result.getStatus()!=null) { - OutputHeader += "\n"+result.getStatus(); - } - if (result.getPredfile()!=null) { - OutputHeader += "\n"+result.getPredfile(); - // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data - } - if (result.getAligfile()!=null) { - OutputHeader += "\n"+result.getAligfile(); - } - wsInfo.setProgressText(OutputHeader); - try { - // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File"); - jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste"); - SequenceI[] preds = prediction.getSeqsAsArray(); - Alignment al; - int FirstSeq; // the position of the query sequence in Alignment al - boolean noMsa = true; // set if no MSA has been returned by JPred - - if (this.msa!=null && result.getAligfile()!=null) { - // we ignore the returned alignment if we only predicted on a single sequence - String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste"); - if (jalview.io.FormatAdapter.formats.contains(format)) - { - al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format)); - noMsa = false; - FirstSeq = 0; - } - else - { - throw (new Exception("Unknown format 'format' for file : \n" + - result.getAligfile())); - } - - } else { - al = new Alignment(preds); - FirstSeq = prediction.QuerySeqPosition; - } - - AlignmentAnnotation annot; - Annotation [] annotations = null; - int i = 0; - int width = preds[0].getSequence().length(); - - - int[] gapmap = al.getSequenceAt(FirstSeq).gapMap(); - if (gapmap.length!=width) { - throw (new Exception("Jpred Client Error\nNumber of residues in supposed query sequence :\n" - +al.getSequenceAt(FirstSeq).getName()+"\n" - +al.getSequenceAt(FirstSeq).getSequence() - +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n")); - } - // JBPNote Should also rename the query sequence sometime... - i=0; - while (i < preds.length) - { - String id = preds[i].getName().toUpperCase(); - if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) - { - annotations = new Annotation[al.getWidth()]; - - if(id.equals("JNETPRED") - || id.equals("JNETPSSM") - || id.equals("JNETFREQ") - || id.equals("JNETHMM") - || id.equals("JNETALIGN") - || id.equals("JPRED")) - { - for (int j = 0; j < width; j++) - annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0); - } - else if(id.equals("JNETCONF")) - { - for (int j = 0; j < width; j++) - { - float value = Float.parseFloat(preds[i].getCharAt(j)+""); - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value); - } - } - else - { - for (int j = 0; j < width; j++) { - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0); - } - } - - if(id.equals("JNETCONF")) - annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", - annotations,0f,10f,1); - - else annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", - annotations); - al.addAnnotation(annot); - if (noMsa) - al.deleteSequence(preds[i]); - } - i++; - } - - Hashtable scores = prediction.Scores; - /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), - "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); - - addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"), - "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1); - - addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"), - "JnetpropC", "Jnet Coil Propensity", 0f,1f,1); - */ - AlignFrame af = new AlignFrame(al); - - - Desktop.addInternalFrame(af, - "JNet Prediction for sequence ", - AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); - }catch(Exception ex){ex.printStackTrace();} - - } - - } -} - -- 1.7.10.2