X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FJPredClient.java;h=4cb8aeeb348f1c4e28c79b0cc62c732edcddd2f7;hb=a487459285df2b2e06047098ad8cb8e4920b41b8;hp=3711db068cd5fa520cbd036c3010780759404f79;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 3711db0..4cb8aee 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,394 +1,548 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.ws; -import ext.vamsas.*; - -import jalview.analysis.AlignSeq; - -import jalview.datamodel.*; - -import jalview.gui.*; - -import org.apache.axis.client.*; - -import java.awt.*; - import java.util.*; import javax.swing.*; -import javax.xml.namespace.QName; - - -public class JPredClient extends WSClient { - ext.vamsas.JPredWS server; - String altitle = ""; - java.util.Hashtable SequenceInfo = null; +import ext.vamsas.*; +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.gui.*; +import jalview.io.FormatAdapter; + +public class JPredClient + extends WSClient +{ + ext.vamsas.Jpred server; + String altitle = ""; + java.util.Hashtable SequenceInfo = null; + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) { + wsInfo = setWebService(sh); + startJPredClient(title, seq); + } + public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) { + wsInfo = setWebService(sh); + startJPredClient(title, msa); + } + + public JPredClient(String title, SequenceI[] msf) { + startJPredClient(title, msf); + } + + public JPredClient(String title, SequenceI seq) { + startJPredClient(title, seq); + } + + private void startJPredClient(String title, SequenceI[] msf) + { + if (wsInfo==null) + wsInfo = setWebService(); + + SequenceI seq = msf[0]; + altitle = "JNet prediction on " + seq.getName() + + " using alignment from " + title; + + wsInfo.setProgressText("Job details for MSA based prediction (" + + title + ") on sequence :\n>" + seq.getName() + "\n" + + AlignSeq.extractGaps("-. ", seq.getSequence()) + + "\n"); + SequenceI aln[] = new SequenceI[msf.length]; + for (int i=0,j=msf.length; i" + + seq.getName() + "\n" + + AlignSeq.extractGaps("-. ", seq.getSequence()) + + "\n"); + altitle = "JNet prediction for sequence " + seq.getName() + " from " + + title; + + SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + + if (!locateWebService()) + { + return; + } - SequenceI seq = msf[0]; - altitle = "JNet prediction on " + seq.getName() + - " using alignment from " + title; + JPredThread jthread = new JPredThread(seq); + jthread.start(); + } + + private WebserviceInfo setWebService() + { + WebServiceName = "JNetWS"; + WebServiceJobTitle = "JNet secondary structure prediction"; + WebServiceReference = + "\"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\"."; + WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; + + WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle, + WebServiceReference); + + return wsInfo; + } + + private boolean locateWebService() + { + ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default + + try + { + this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties + ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub + } + catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The Secondary Structure Prediction Service named " + + WebServiceName + " at " + WsURL + + " couldn't be located.", + "Internal Jalview Error", + JOptionPane.WARNING_MESSAGE); + wsInfo.setProgressText("Serious! " + WebServiceName + + " Service location failed\nfor URL :" + WsURL + + "\n" + + ex.getMessage()); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + + return false; + } - wsInfo.setProgressText("Job details for MSA based prediction (" + - title + ") on sequence :\n>" + seq.getName() + "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n"); + return true; + } + + class JPredThread + extends Thread + { + String OutputHeader; + vamsas.objects.simple.JpredResult result; + vamsas.objects.simple.Sequence sequence; + vamsas.objects.simple.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 vamsas.objects.simple.Sequence(); + this.sequence.setId(seq.getName()); + this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence())); + } - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + JPredThread(SequenceI[] msf) + { + OutputHeader = wsInfo.getProgressText(); + this.sequence = new vamsas.objects.simple.Sequence(); + this.sequence.setId(msf[0].getName()); + this.sequence.setSeq(AlignSeq.extractGaps("-. ", + msf[0].getSequence())); + + this.msa = new vamsas.objects.simple.Msfalignment(); + jalview.io.PileUpfile pileup = new jalview.io.PileUpfile(); + msa.setMsf(pileup.print(msf)); + } - if (!locateWebService()) { - return; + public void run() + { + StartJob(); + + while (!jobComplete && (allowedServerExceptions > 0)) + { + try + { + if ( (result = server.getresult(jobId)) == null) + { + throw (new Exception( + "Timed out when communicating with server\nTry again later.\n")); + } + if (result.getState()==0) + jalview.bin.Cache.log.debug("Finished "+jobId); + if (result.isRunning()) + { + wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); + } + if (result.isQueued()) + { + wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); + } + + wsInfo.setProgressText(OutputHeader + "\n" + + result.getStatus()); + + if (result.isFinished()) + { + + parseResult(); + jobComplete = true; + jobsRunning--; + } else { + // catch exceptions + if (! (result.isJobFailed() || result.isServerError())) + { + try + { + Thread.sleep(5000); + } + catch (InterruptedException ex1) + { + } + + // System.out.println("I'm alive "+seqid+" "+jobid); + } + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + jobsRunning--; + jobComplete = true; + } + } + } + catch (Exception ex) + { + allowedServerExceptions--; + wsInfo.appendProgressText("\nJPredWS Server exception!\n" + + ex.getMessage()); + + try + { + if (allowedServerExceptions > 0) + { + Thread.sleep(5000); + } + } + catch (InterruptedException ex1) + { + } + } + catch (OutOfMemoryError er) + { + jobComplete = true; + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory handling result!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + JOptionPane.WARNING_MESSAGE); + System.out.println("JPredClient: "+er); + System.gc(); + } + } + if (result!=null) + if (! (result.isJobFailed() || result.isServerError())) + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); + } + else + { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } - - JPredThread jthread = new JPredThread(msf); - jthread.start(); } - public JPredClient(String title, SequenceI seq) { - wsInfo = setWebService(); - wsInfo.setProgressText("Job details for prediction on sequence :\n>" + - seq.getName() + "\n" + - AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n"); - altitle = "JNet prediction for sequence " + seq.getName() + " from " + - title; + void StartJob() + { + try + { + if (msa != null) + { + jobId = server.predictOnMsa(msa); + } + else + { + jobId = server.predict(sequence); + } - SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq); + if (jobId != null) + { + if (jobId.startsWith("Broken")) + { + throw new Exception("Submission " + jobId); + } + else + { + System.out.println(WsURL + " Job Id '" + jobId + "'"); + } + } + else + { + throw new Exception("Server timed out - try again later\n"); + } + } + catch (Exception e) + { + if (e.getMessage().indexOf("Exception")>-1) { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + wsInfo.setProgressText( + "Failed to submit the prediction. (Just close the window)\n" + + + "It is most likely that there is a problem with the server.\n"); + System.err.println( + "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" + + e.getMessage() + "\n"); + + jalview.bin.Cache.log.warn("Server Exception",e); + } else { + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + // JBPNote - this could be a popup informing the user of the problem. + wsInfo.setProgressText("Failed to submit the prediction:\n" + +e.getMessage()+ + wsInfo.getProgressText()); + + jalview.bin.Cache.log.debug("Failed Submission",e); - if (!locateWebService()) { - return; } + allowedServerExceptions = -1; + jobComplete = true; - JPredThread jthread = new JPredThread(seq); - jthread.start(); + } } - private WebserviceInfo setWebService() { - WebServiceName = "JNetWS"; - WebServiceJobTitle = "JNet secondary structure prediction"; - WebServiceReference = "\"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\"."; - WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; - - WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle, - WebServiceReference); - return wsInfo; - } - private boolean locateWebService() { - JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default - - try { - this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties - ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub - } catch (Exception ex) { - JOptionPane.showMessageDialog(Desktop.desktop, - "The Secondary Structure Prediction Service named " + - WebServiceName + " at " + WsURL + " couldn't be located.", - "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); - wsInfo.setProgressText("Serious! " + WebServiceName + - " Service location failed\nfor URL :" + WsURL + "\n" + - ex.getMessage()); - wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR); - - return false; + /* 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+"Parsing..."); + + try + { + jalview.bin.Cache.log.debug("Parsing output from JNet job."); + // 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(); + jalview.bin.Cache.log.debug("Got prediction profile."); + 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)) + { + jalview.bin.Cache.log.debug("Getting associated alignment."); + // 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(new FormatAdapter().readFile( + result.getAligfile(), "Paste", format)); + for (int i=0, j=al.getHeight(); i 0)) { - try { - if ((result = server.getresult(jobId)) == null) { - throw (new Exception( - "Timed out when communicating with server\nTry again later.\n")); - } - - 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())) { - try { - Thread.sleep(5000); - } catch (InterruptedException ex1) { - } - - // System.out.println("I'm alive "+seqid+" "+jobid); - } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - } - } - } catch (Exception ex) { - allowedServerExceptions--; - wsInfo.appendProgressText("\nJPredWS Server exception!\n" + - ex.getMessage()); - - try { - if (allowedServerExceptions > 0) { - Thread.sleep(5000); - } - } catch (InterruptedException ex1) { - } - } + // 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); + } } - - if (!(result.isJobFailed() || result.isServerError())) { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); - } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + 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); + } } - } - void StartJob() { - try { - if (msa != null) { - jobId = server.predictOnMsa(msa); - } else { - jobId = server.predict(sequence); - } - - if (jobId != null) { - if (jobId.startsWith("Broken")) { - throw new Exception("Submission " + jobId); - } else { - System.out.println(WsURL + " Job Id '" + jobId + "'"); - } - } else { - throw new Exception("Server timed out - try again later\n"); - } - } catch (Exception e) { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - allowedServerExceptions = 0; - jobComplete = false; - wsInfo.appendProgressText("Failed to submit the prediction: " + - e.toString() + "\nJust close the window\n"); - System.err.println( - "JPredWS Client: Failed to submit the prediction\n" + - e.toString() + "\n"); - - // e.printStackTrace(); TODO: JBPNote DEBUG + 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); } - } - 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()]; + al.addAnnotation(annot); - for (int j = 0; j < values.size(); j++) { - float value = Float.parseFloat(values.get(j).toString()); - annotations[gapmap[j]] = new Annotation("", value + "", ' ', - value); + if (noMsa) + { + al.deleteSequence(preds[i]); } + } - al.addAnnotation(new AlignmentAnnotation(Symname, Visname, - annotations, min, max, winLength)); + i++; } - void parseResult() { - // OutputHeader = output.getText(); - if (result.isFailed()) { - OutputHeader += "Job failed.\n"; - } + //Hashtable scores = prediction.getScores(); - if (result.getStatus() != null) { - OutputHeader += ("\n" + result.getStatus()); - } + /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), + "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); - if (result.getPredfile() != null) { - OutputHeader += ("\n" + result.getPredfile()); + addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"), + "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1); - // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data - } + addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"), + "JnetpropC", "Jnet Coil Propensity", 0f,1f,1); + */ - if (result.getAligfile() != null) { - OutputHeader += ("\n" + result.getAligfile()); - } + wsInfo.setProgressText(OutputHeader); + jalview.bin.Cache.log.debug("Finished parsing output."); + AlignFrame af = new AlignFrame(al); - 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.getQuerySeqPosition(); - } - - if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( - al.getSequenceAt(FirstSeq), SequenceInfo)) { - throw (new Exception( - "Couldn't recover sequence properties for JNet Query sequence!")); - } - - 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( - "Jnet 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.getScores(); - - /* 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, altitle, - AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); - } catch (Exception ex) { - ex.printStackTrace(); - } - } + Desktop.addInternalFrame(af, altitle, + AlignFrame.NEW_WINDOW_WIDTH, + AlignFrame.NEW_WINDOW_HEIGHT); + } + catch (Exception ex) + { + jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction."); + jalview.bin.Cache.log.debug("Exception: ",ex); + } } + } }