-package jalview.ws;
-
-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.*;
-import vamsas.objects.*;
-
-
-
-
-public class MsaWSClient
-{
- int jobsRunning = 0;
- ext.vamsas.MuscleWS server;
- WebserviceInfo wsInfo;
- /**
- * MsaWSClient
- *
- * @param msa SequenceI[]
- */
-
- String WebServiceName;
- String WebServiceJobTitle;
- String WebServiceReference;
- String WsURL;
- private boolean setWebService(String MsaWSName) {
- if (MsaWServices.info.containsKey(MsaWSName)) {
- WebServiceName = MsaWSName;
- String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
- WsURL = wsinfo[0];
- WebServiceJobTitle = wsinfo[1];
- WebServiceReference = wsinfo[2];
- return true;
- } else {
- return false;
- }
- }
-
-// public MsaWSClient(String MsaWSName, SequenceI[] msa) {
-// MsaWSClient(MsaWSName, msa, true);
-// }
-
- public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
- {
- if (setWebService(MsaWSName)==false) {
- JOptionPane.showMessageDialog(Desktop.desktop, "The Multiple Sequence Alignment Service named "+MsaWSName+" is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
-
- wsInfo.setProgressText("Alignment of "+altitle+"\nJob details\n");
-
- // TODO: MuscleWS transmuted to generic MsaWS client
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
- try {
- this.server = (MuscleWS) loc.getMuscleWS(// JBPNote will be set from properties
- new java.net.URL(WsURL));
- }
- catch (Exception ex) {
- wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
- +WsURL+"\n"+ex.getMessage());
- wsInfo.setStatus(wsInfo.ERROR);
- ex.printStackTrace();
- }
-
- MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
- wsInfo.setthisService(musclethread);
- musclethread.start();
- }
-
-
- protected class MsaWSThread extends Thread implements WSClientI
- {
- String ServiceName = WebServiceName;
-
- public boolean isCancellable()
- {
- return true;
- }
-
- String OutputHeader;
- vamsas.objects.simple.MsaResult result = null;
-
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
- SequenceSet();
-
- Hashtable SeqNames = null;
- boolean submitGaps = false,// default is to strip gaps from sequences
- preserveOrder = true; // and always store and recover sequence order
-
- String jobId;
- String alTitle; // name which will be used to form new alignment window.
- int allowedServerExceptions = 3; // thread dies if too many exceptions.
- MsaWSThread(String title, SequenceI[] msa, boolean subgaps, boolean presorder)
- {
- alTitle = title;
- submitGaps = subgaps;
- preserveOrder = presorder;
-
- OutputHeader = wsInfo.getProgressText();
- SeqNames = new Hashtable();
- vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
- Sequence[msa.length];
-
- for (int i = 0; i < msa.length; i++)
- {
- String newname = new String("Sequence"+i);
- // uniquify as we go - JBPNote: TODO: this is a ubiquitous transformation
- SeqNames.put(newname, msa[i].getName());
- seqarray[i] = new vamsas.objects.simple.Sequence();
- seqarray[i].setId(new String("Sequence"+i));
- seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
- : AlignSeq.extractGaps("-. ", msa[i].getSequence()));
- }
-
- this.seqs = new vamsas.objects.simple.SequenceSet();
- this.seqs.setSeqs(seqarray);
- }
-
- boolean jobComplete = false;
-
- public void cancelJob() {
- if (!jobComplete) {
- String cancelledMessage="";
- try {
- vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
- if (cancelledJob.getStatus() == 2)
- {
- // CANCELLED_JOB
- cancelledMessage = "Job cancelled.";
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
- jobComplete = true;
- jobsRunning--;
- result = null;
- }
- else
- if (cancelledJob.getStatus() == 3)
- {
- // VALID UNSTOPPABLE JOB
- cancelledMessage +=
- "Server cannot cancel this job. just close the window.\n";
- }
- if (cancelledJob.getJobId() != null)
- cancelledMessage += "[" + cancelledJob.getJobId() + "]";
- cancelledMessage +="\n";
- } catch (Exception exc) {
- cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";
- exc.printStackTrace();
- }
- wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
- }
- }
-
- 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("\n"+ServiceName+" Server exception!\n" + ex.getMessage());
- ex.printStackTrace();
- }
- }
-
- if (! (result!=null && (result.isJobFailed() || result.isServerError())))
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- else
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
-
- void StartJob()
- {
- try
- {
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
- if (jobsubmit.getStatus()==1) {
- System.out.println(jobId=jobsubmit.getJobId());
- } else {
- throw new Exception(jobsubmit.getJobId());
- }
- }
- catch (Exception e)
- {
- System.out.println(ServiceName + " 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));
- }
- private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
- for (int i=0, j=seqs.length; i<j;i++)
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
- return msa;
- }
- void parseResult()
- {
- SequenceI[] seqs=null;
- try {
- // OutputHeader = output.getText();
- if (result.isFailed()) {
- OutputHeader +="Job failed.\n";
- }
- if (result.getStatus()!=null) {
- OutputHeader += "\n"+result.getStatus();
- }
- if (result.getMsa()!=null) {
- OutputHeader += "\nAlignment Object Method Notes\n";
- String lines[] = result.getMsa().getMethod();
- for (int line=0;line<lines.length; line++)
- OutputHeader+=lines[line]+"\n";
-
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
- seqs = getVamsasAlignment(result.getMsa());
- }
-
- wsInfo.setProgressText(OutputHeader);
- if (seqs!=null) {
- AlignmentOrder msaorder = new AlignmentOrder(seqs);
-
- if (preserveOrder) {
- jalview.analysis.AlignmentSorter.recoverOrder(seqs);
- }
-
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
-
- Alignment al = new Alignment(seqs);
-
- // TODO: JBPNote Should also rename the query sequence sometime...
- AlignFrame af = new AlignFrame(al);
- af.addSortByOrderMenuItem(ServiceName+" Ordering", msaorder);
-
- Desktop.addInternalFrame(af,
- alTitle,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- }
- }catch(Exception ex){ex.printStackTrace();}
-
- }
-
- }
-}
-
-
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.ws;\r
+\r
+import ext.vamsas.*;\r
+\r
+import jalview.analysis.AlignSeq;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class MsaWSClient\r
+ extends WSClient\r
+{\r
+ /**\r
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
+ */\r
+ ext.vamsas.MuscleWS server;\r
+\r
+\r
+ /**\r
+ * Creates a new MsaWSClient object that uses a service\r
+ * given by an externally retrieved ServiceHandle\r
+ *\r
+ * @param sh service handle of type AbstractName(MsaWS)\r
+ * @param altitle DOCUMENT ME!\r
+ * @param msa DOCUMENT ME!\r
+ * @param submitGaps DOCUMENT ME!\r
+ * @param preserveOrder DOCUMENT ME!\r
+ */\r
+\r
+ public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,\r
+ boolean submitGaps, boolean preserveOrder)\r
+ {\r
+\r
+ if (!sh.getAbstractName().equals("MsaWS"))\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Service called \n" + sh.getName() +\r
+ "\nis not a \nMultiple Sequence Alignment Service !",\r
+ "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ if ((wsInfo = this.setWebService(sh))==null)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Multiple Sequence Alignment Service named " +\r
+ sh.getName() +\r
+ " is unknown", "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ startMsaWSClient(altitle, msa, submitGaps, preserveOrder);\r
+\r
+ }\r
+\r
+\r
+ private void startMsaWSClient(String altitle, SequenceI[] msa,\r
+ boolean submitGaps, boolean preserveOrder)\r
+ {\r
+ if (!locateWebService())\r
+ {\r
+ return;\r
+ }\r
+\r
+ wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +\r
+ " of " + altitle + "\nJob details\n");\r
+\r
+ MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
+ " alignment of " + altitle, msa,\r
+ submitGaps, preserveOrder);\r
+ wsInfo.setthisService(musclethread);\r
+ musclethread.start();\r
+ }\r
+\r
+ /**\r
+ * Initializes the server field with a valid service implementation.\r
+ *\r
+ * @return true if service was located.\r
+ */\r
+ private boolean locateWebService()\r
+ {\r
+ // TODO: MuscleWS transmuted to generic MsaWS client\r
+ MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
+\r
+ try\r
+ {\r
+ this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
+ ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ wsInfo.setProgressText("Serious! " + WebServiceName +\r
+ " Service location failed\nfor URL :" + WsURL +\r
+ "\n" +\r
+ ex.getMessage());\r
+ wsInfo.setStatus(WebserviceInfo.ERROR);\r
+ ex.printStackTrace();\r
+\r
+ return false;\r
+ }\r
+\r
+ loc.getEngine().setOption("axis", "1");\r
+\r
+ return true;\r
+ }\r
+\r
+ protected class MsaWSThread\r
+ extends Thread implements WSClientI\r
+ {\r
+ String ServiceName = WebServiceName;\r
+ String OutputHeader;\r
+ vamsas.objects.simple.MsaResult result = null;\r
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.\r
+ SequenceSet();\r
+ Hashtable SeqNames = null;\r
+ boolean submitGaps = false; // and always store and recover sequence order\r
+ boolean preserveOrder = true; // and always store and recover sequence order\r
+ String jobId;\r
+ String alTitle; // name which will be used to form new alignment window.\r
+ int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
+ boolean jobComplete = false;\r
+\r
+ MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
+ boolean presorder)\r
+ {\r
+ alTitle = title;\r
+ submitGaps = subgaps;\r
+ preserveOrder = presorder;\r
+\r
+ OutputHeader = wsInfo.getProgressText();\r
+ SeqNames = new Hashtable();\r
+\r
+ vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.\r
+ Sequence[msa.length];\r
+\r
+ for (int i = 0; i < msa.length; i++)\r
+ {\r
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i);\r
+\r
+ // uniquify as we go\r
+ // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation\r
+ SeqNames.put(newname,\r
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));\r
+ seqarray[i] = new vamsas.objects.simple.Sequence();\r
+ seqarray[i].setId(newname);\r
+ seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()\r
+ : AlignSeq.extractGaps(\r
+ jalview.util.Comparison.GapChars,\r
+ msa[i].getSequence()));\r
+ }\r
+\r
+ this.seqs = new vamsas.objects.simple.SequenceSet();\r
+ this.seqs.setSeqs(seqarray);\r
+ }\r
+\r
+ public boolean isCancellable()\r
+ {\r
+ return true;\r
+ }\r
+\r
+ public void cancelJob()\r
+ {\r
+ if ( (jobId != null) && !jobId.equals("") && !jobComplete)\r
+ {\r
+ String cancelledMessage = "";\r
+\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
+\r
+ if (cancelledJob.getStatus() == 2)\r
+ {\r
+ // CANCELLED_JOB\r
+ cancelledMessage = "Job cancelled.";\r
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ result = null;\r
+ }\r
+ else if (cancelledJob.getStatus() == 3)\r
+ {\r
+ // VALID UNSTOPPABLE JOB\r
+ cancelledMessage +=\r
+ "Server cannot cancel this job. just close the window.\n";\r
+ }\r
+\r
+ if (cancelledJob.getJobId() != null)\r
+ {\r
+ cancelledMessage += ("[" + cancelledJob.getJobId() +\r
+ "]");\r
+ }\r
+\r
+ cancelledMessage += "\n";\r
+ }\r
+ catch (Exception exc)\r
+ {\r
+ cancelledMessage +=\r
+ ("\nProblems cancelling the job : Exception received...\n" +\r
+ exc + "\n");\r
+ exc.printStackTrace();\r
+ }\r
+\r
+ wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");\r
+ }\r
+ else\r
+ {\r
+ if (!jobComplete)\r
+ {\r
+ wsInfo.setProgressText(OutputHeader +\r
+ "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ StartJob();\r
+\r
+ while (!jobComplete && (allowedServerExceptions > 0))\r
+ {\r
+ try\r
+ {\r
+ if ( (result = server.getResult(jobId)) == null)\r
+ {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+ jalview.bin.Cache.log.debug("Result state " + result.getState() +\r
+ "(ServerError=" + result.isServerError() +\r
+ ")");\r
+ if (result.isRunning())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ }\r
+ else if (result.isQueued())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
+\r
+ if (result.isFinished())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ parseResult();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ }\r
+ else\r
+ {\r
+ if (result.getStatus() != null)\r
+ {\r
+ wsInfo.setProgressText(OutputHeader + "\n"+ result.getStatus());\r
+ }\r
+ if (result.isServerError())\r
+ {\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+\r
+ break;\r
+ }\r
+ if (! (result.isJobFailed() || result.isServerError() ||\r
+ result.isBroken() || result.isFailed()))\r
+ {\r
+ Thread.sleep(5000);\r
+\r
+ // System.out.println("I'm alive "+seqid+" "+jobid);\r
+ }\r
+ else\r
+ {\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ allowedServerExceptions--;\r
+ wsInfo.appendProgressText("\n" + ServiceName +\r
+ " Server exception!\n" + ex.getMessage());\r
+ System.err.println(ServiceName + " Server exception: " +\r
+ ex.getMessage());\r
+\r
+ // ex.printStackTrace(); JBPNote Debug\r
+ try\r
+ {\r
+ if (allowedServerExceptions > 0)\r
+ {\r
+ Thread.sleep(5000);\r
+ }\r
+ }\r
+ catch (InterruptedException ex1)\r
+ {\r
+ }\r
+ }\r
+ catch(OutOfMemoryError er)\r
+ {\r
+ jobComplete = true;\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory handling result!!"\r
+ +"\nSee help files for increasing Java Virtual Machine memory."\r
+ ,"Out of memory", JOptionPane.WARNING_MESSAGE );\r
+ System.out.println("MsaWSClient: "+er);\r
+ System.gc();\r
+ }\r
+ }\r
+\r
+ if (allowedServerExceptions == 0)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ else\r
+ {\r
+ if (result != null)\r
+ {\r
+ if ( !(result.isJobFailed() || result.isServerError()))\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+\r
+ if (result.isBroken() || result.isFailed())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+\r
+ if (result.isServerError())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void StartJob()\r
+ {\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
+\r
+ if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
+ {\r
+ jobId = jobsubmit.getJobId();\r
+ System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ }\r
+ else\r
+ {\r
+ if (jobsubmit == null)\r
+ {\r
+ throw new Exception("Server at " + WsURL +\r
+ " returned null object, it probably cannot be contacted. Try again later ?");\r
+ }\r
+\r
+ throw new Exception(jobsubmit.getJobId());\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ // TODO: JBPNote catch timeout or other fault types explicitly\r
+ // For unexpected errors\r
+ System.err.println(WebServiceName +\r
+ "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +\r
+ "When contacting Server:" + WsURL + "\n" +\r
+ e.toString() +\r
+ "\n");\r
+ this.allowedServerExceptions = 0;\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.appendProgressText(\r
+ "Failed to submit sequences for alignment.\n" +\r
+ "It is most likely that there is a problem with the server.\n" +\r
+ "Just close the window\n");\r
+\r
+ // e.printStackTrace(); // TODO: JBPNote DEBUG\r
+ }\r
+ }\r
+\r
+ private jalview.datamodel.Sequence[] getVamsasAlignment(\r
+ vamsas.objects.simple.Alignment valign)\r
+ {\r
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.\r
+ length];\r
+\r
+ for (int i = 0, j = seqs.length; i < j; i++)\r
+ {\r
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),\r
+ seqs[i].getSeq());\r
+ }\r
+\r
+ return msa;\r
+ }\r
+\r
+ void parseResult()\r
+ {\r
+ SequenceI[] seqs = null;\r
+\r
+ try\r
+ {\r
+ // OutputHeader = output.getText();\r
+ if (result.isFailed())\r
+ {\r
+ OutputHeader += "Job failed.\n";\r
+ }\r
+\r
+ if (result.getStatus() != null)\r
+ {\r
+ OutputHeader += ("\n" + result.getStatus());\r
+ }\r
+\r
+ if (result.getMsa() != null)\r
+ {\r
+ OutputHeader += "\nAlignment Object Method Notes\n";\r
+\r
+ String[] lines = result.getMsa().getMethod();\r
+\r
+ for (int line = 0; line < lines.length; line++)\r
+ {\r
+ OutputHeader += (lines[line] + "\n");\r
+ }\r
+\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
+ seqs = getVamsasAlignment(result.getMsa());\r
+ }\r
+\r
+ wsInfo.setProgressText(OutputHeader);\r
+\r
+ if (seqs != null)\r
+ {\r
+ AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
+\r
+ if (preserveOrder)\r
+ {\r
+ jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
+ }\r
+\r
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
+\r
+ Alignment al = new Alignment(seqs);\r
+\r
+ // TODO: JBPNote Should also rename the query sequence sometime...\r
+ AlignFrame af = new AlignFrame(al);\r
+ af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ msaorder);\r
+\r
+ Desktop.addInternalFrame(af, alTitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff