-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
-import vamsas.objects.*;\r
-\r
-public class MsaWSClient\r
-{\r
- int jobsRunning = 0;\r
- ext.vamsas.MuscleWS server;\r
- WebserviceInfo wsInfo;\r
- /**\r
- * MsaWSClient\r
- *\r
- * @param msa SequenceI[]\r
- */\r
- public MsaWSClient(SequenceI[] msa)\r
- {\r
- wsInfo = new jalview.gui.WebserviceInfo("Muscle Alignment job",\r
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.");\r
-\r
-\r
- wsInfo.setProgressText("Job details\n");\r
-\r
-\r
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
- try {\r
- this.server = (MuscleWS) loc.getMuscleWS(); // JBPNote will be set from properties\r
- }\r
- catch (Exception ex) {\r
- wsInfo.setProgressText("Serious! MuscleWS Service location failed\nfor URL :"\r
- +loc.getMuscleWSAddress()+"\n"+ex.getMessage());\r
- ex.printStackTrace();\r
- }\r
-\r
- MsaWSThread musclethread = new MsaWSThread(msa);\r
- wsInfo.setthisService(musclethread);\r
- musclethread.start();\r
- }\r
-\r
-\r
- protected class MsaWSThread extends Thread implements WSClientI\r
- {\r
- String ServiceName = "MuscleWS";\r
- public boolean isCancellable()\r
- {\r
- return true;\r
- }\r
-\r
- String OutputHeader;\r
- vamsas.objects.simple.MsaResult result = null;\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.\r
- SequenceSet();\r
- String jobId;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- MsaWSThread(SequenceI[] msa)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.\r
- Sequence[msa.length];\r
- for (int i = 0; i < msa.length; i++)\r
- {\r
- seqarray[i] = new vamsas.objects.simple.Sequence();\r
- seqarray[i].setId(msa[i].getName());\r
- seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));\r
- }\r
- this.seqs = new vamsas.objects.simple.SequenceSet();\r
- this.seqs.setSeqs(seqarray);\r
- }\r
-\r
- boolean jobComplete = false;\r
-\r
- public void cancelJob() {\r
- if (!jobComplete) {\r
- String cancelledMessage="";\r
- try {\r
- vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\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\r
- if (cancelledJob.getStatus() == 3)\r
- {\r
- // VALID UNSTOPPABLE JOB\r
- cancelledMessage +=\r
- "Server cannot cancel this job. just close the window.\n";\r
- }\r
- if (cancelledJob.getJobId() != null)\r
- cancelledMessage += "[" + cancelledJob.getJobId() + "]";\r
- cancelledMessage +="\n";\r
- } catch (Exception exc) {\r
- cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";\r
- exc.printStackTrace();\r
- }\r
- wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");\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
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\n"+ServiceName+" Server exception!\n" + ex.getMessage());\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- if (! (result!=null && (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
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
- if (jobsubmit.getStatus()==1) {\r
- System.out.println(jobId=jobsubmit.getJobId());\r
- } else {\r
- throw new Exception(jobsubmit.getJobId());\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println(ServiceName + " 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
- private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {\r
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
- for (int i=0, j=seqs.length; i<j;i++)\r
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());\r
- return msa;\r
- }\r
- void parseResult()\r
- {\r
- SequenceI[] seqs=null;\r
- try {\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.getMsa()!=null) {\r
- OutputHeader += "\nAlignment Object Method Notes\n";\r
- String lines[] = result.getMsa().getMethod();\r
- for (int line=0;line<lines.length; line++)\r
- OutputHeader+=lines[line]+"\n";\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
- if (seqs!=null) {\r
- Alignment al;\r
- al = new Alignment(seqs);\r
-\r
- // TODO: JBPNote Should also rename the query sequence sometime...\r
- AlignFrame af = new AlignFrame(al);\r
- Desktop.addInternalFrame(af,\r
- ServiceName + " Alignment",\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
- }\r
- }\r
-\r
+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.contains(MsaWSName.toUpperCase())) {
+ WebServiceName = MsaWSName;
+ String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName.toUpperCase());
+ 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, SequenceI[] msa, 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("Job 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(msa);
+ 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();
+ String jobId;
+ int allowedServerExceptions = 3; // thread dies if too many exceptions.
+ MsaWSThread(SequenceI[] msa)
+ {
+ OutputHeader = wsInfo.getProgressText();
+ vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
+ Sequence[msa.length];
+ for (int i = 0; i < msa.length; i++)
+ {
+ seqarray[i] = new vamsas.objects.simple.Sequence();
+ seqarray[i].setId(msa[i].getName());
+ seqarray[i].setSeq(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) {
+ Alignment al;
+ al = new Alignment(seqs);
+
+ // TODO: JBPNote Should also rename the query sequence sometime...
+ AlignFrame af = new AlignFrame(al);
+ Desktop.addInternalFrame(af,
+ ServiceName + " Alignment",
+ AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+ }
+ }catch(Exception ex){ex.printStackTrace();}
+
+ }
+
+ }
+}
+
+
git://source.jalview.org / jalview.git / commitdiff