-package jalview.ws;\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
- } else {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\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.getQuerySeqPosition();\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.getScores();\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.*;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public class JPredClient extends WS1Client
+{
+ /**
+ * crate a new GUI JPred Job
+ *
+ * @param sh
+ * ServiceHandle
+ * @param title
+ * String
+ * @param msa
+ * boolean - true - submit alignment as a sequence profile
+ * @param alview
+ * AlignmentView
+ * @param viewonly
+ * TODO
+ */
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ boolean msa, AlignmentView alview, AlignFrame parentFrame,
+ boolean viewonly)
+ {
+ super();
+ wsInfo = setWebService(sh);
+ startJPredClient(title, msa, alview, parentFrame, viewonly);
+
+ }
+
+ /**
+ * startJPredClient TODO: refine submission to cope with local prediction of
+ * visible regions or multiple single sequence jobs TODO: sequence
+ * representative support - could submit alignment of representatives as msa.
+ * TODO: msa hidden region prediction - submit each chunk for prediction.
+ * concatenate results of each. TODO: single seq prediction - submit each
+ * contig of each sequence for prediction (but must cope with flanking regions
+ * and short seqs)
+ *
+ * @param title
+ * String
+ * @param msa
+ * boolean
+ * @param alview
+ * AlignmentView
+ * @param viewonly
+ * if true then the prediction will be made just on the concatenated
+ * visible regions
+ */
+ private void startJPredClient(String title, boolean msa,
+ jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+ boolean viewonly)
+ {
+ AlignmentView input = alview;
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ Jpred server = locateWebService();
+ if (server == null)
+ {
+ Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ return;
+ }
+ SeqCigar[] msf = null;
+ SequenceI seq = null;
+ int[] delMap = null;
+ // original JNetClient behaviour - submit full length of sequence or profile
+ // and mask result.
+ msf = input.getSequences();
+ seq = msf[0].getSeq('-');
+
+ if (viewonly)
+ {
+ int[] viscontigs = alview.getVisibleContigs();
+ int spos = 0;
+ int i = 0;
+ if (viscontigs != null)
+ {
+ // Construct the delMap - mapping from the positions within the input to
+ // Jnet to the contigs in the original sequence
+
+ delMap = new int[seq.getEnd() - seq.getStart() + 1];
+ int gapMap[] = seq.gapMap();
+ for (int contig = 0; contig < viscontigs.length; contig += 2)
+ {
+
+ while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+ {
+ spos++;
+ }
+ while (spos < gapMap.length
+ && gapMap[spos] <= viscontigs[contig + 1])
+ {
+ delMap[i++] = spos++;
+ }
+ }
+ int tmap[] = new int[i];
+ System.arraycopy(delMap, 0, tmap, 0, i);
+ delMap = tmap;
+ }
+ }
+ if (msa && msf.length > 1)
+ {
+
+ String altitle = getPredictionName(WebServiceName) + " on "
+ + (viewonly ? "visible " : "") + seq.getName()
+ + " using alignment from " + title;
+
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = msf[i].getSeq('-');
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ true);
+ if (viewonly)
+ {
+ // Remove hidden regions from sequence objects.
+ String seqs[] = alview.getSequenceStrings('-');
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i].setSequence(seqs[i]);
+ }
+ seq.setSequence(seqs[0]);
+ }
+ wsInfo.setProgressText("Job details for "
+ + (viewonly ? "visible " : "") + "MSA based prediction ("
+ + title + ") on sequence :\n>" + seq.getName() + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ else
+ {
+ if (!msa && msf.length > 1)
+ {
+ throw new Error(
+ "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+ }
+
+ String altitle = getPredictionName(WebServiceName) + " for "
+ + (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ + " from " + title;
+ String seqname = seq.getName();
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seq);
+ if (viewonly)
+ {
+ // Remove hidden regions from input sequence
+ String seqs[] = alview.getSequenceStrings('-');
+ seq.setSequence(seqs[0]);
+ }
+ wsInfo.setProgressText("Job details for prediction on "
+ + (viewonly ? "visible " : "") + "sequence :\n>" + seqname
+ + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+ SequenceInfo, seq, delMap, alview, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ }
+
+ private String getPredictionName(String webServiceName)
+ {
+ if (webServiceName.toLowerCase().indexOf(
+ "secondary structure prediction") > -1)
+ {
+ return webServiceName;
+ }
+ else
+ {
+ return webServiceName + "secondary structure prediction";
+ }
+ }
+
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ SequenceI seq, AlignFrame parentFrame)
+ {
+ super();
+ wsInfo = setWebService(sh);
+ startJPredClient(title, seq, parentFrame);
+ }
+
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ SequenceI[] msa, AlignFrame parentFrame)
+ {
+ wsInfo = setWebService(sh);
+ startJPredClient(title, msa, parentFrame);
+ }
+
+ public JPredClient(String title, SequenceI[] msf)
+ {
+ startJPredClient(title, msf, null);
+ }
+
+ public JPredClient(String title, SequenceI seq)
+ {
+ startJPredClient(title, seq, null);
+ }
+
+ public JPredClient()
+ {
+
+ super();
+ // add a class reference to the list
+ }
+
+ private void startJPredClient(String title, SequenceI[] msf,
+ AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+
+ SequenceI seq = msf[0];
+
+ String 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.getSequenceAsString())
+ + "\n");
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ true);
+
+ Jpred server = locateWebService();
+ if (server == null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, aln, null, null, parentFrame, WsURL);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ public void startJPredClient(String title, SequenceI seq,
+ AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ wsInfo
+ .setProgressText("Job details for prediction on sequence :\n>"
+ + seq.getName()
+ + "\n"
+ + AlignSeq
+ .extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName()
+ + " from " + title;
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seq);
+
+ Jpred server = locateWebService();
+ if (server == null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+ SequenceInfo, seq, null, null, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ private WebserviceInfo setWebService()
+ {
+ WebServiceName = "JNetWS";
+ WebServiceJobTitle = "JNet secondary structure prediction";
+ WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+ + "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 ext.vamsas.Jpred locateWebService()
+ {
+ ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
+ ext.vamsas.Jpred server = null;
+ try
+ {
+ server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set
+ // from properties
+ ((JpredSoapBindingStub) server).setTimeout(60000); // one minute stub
+ // ((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C,
+ // Boolean.TRUE);
+
+ } 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 server;
+ }
+
+ public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+ final AlignFrame af)
+ {
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.setToolTipText(sh.getEndpointURL());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+ if (msa.getSequences().length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af,
+ true);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af,
+ true);
+ }
+ }
+ }
+ });
+ wsmenu.add(method);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff