X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=03a801effca126e07a36adc80db6a33eb08f599f;hb=300c01c1363c3d0d0f92df3750a07314479ed7ca;hp=44ffa113e73171c3491e94b263663d64d07a9e36;hpb=895aec0787b4b2104c1a78d98fab530d586693ac;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 44ffa11..03a801e 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,233 +1,170 @@
-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[]
-   */
-  public MsaWSClient(SequenceI[] msa)
-  {
-    wsInfo = new jalview.gui.WebserviceInfo("Muscle Alignment job",
-                                "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.");
-
-
-    wsInfo.setProgressText("Job details\n");
-
-
-    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
-    try {
-      this.server = (MuscleWS) loc.getMuscleWS(); // JBPNote will be set from properties
-    }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! MuscleWS Service location failed\nfor URL :"
-                     +loc.getMuscleWSAddress()+"\n"+ex.getMessage());
-      ex.printStackTrace();
-    }
-
-    MsaWSThread musclethread = new MsaWSThread(msa);
-    wsInfo.setthisService(musclethread);
-    musclethread.start();
-  }
-
-
-  protected class MsaWSThread extends Thread implements WSClientI
-  {
-    String ServiceName = "MuscleWS";
-    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.";
-            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();}
-
-    }
-
-  }
-  }
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MsaWSClient
+    extends WSClient
+{
+  /**
+   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+   */
+  ext.vamsas.MuscleWS server;
+  AlignFrame alignFrame;
+
+  /**
+   * Creates a new MsaWSClient object that uses a service
+   * given by an externally retrieved ServiceHandle
+   *
+   * @param sh service handle of type AbstractName(MsaWS)
+   * @param altitle DOCUMENT ME!
+   * @param msa DOCUMENT ME!
+   * @param submitGaps DOCUMENT ME!
+   * @param preserveOrder DOCUMENT ME!
+   */
+
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     jalview.datamodel.AlignmentView msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
+  {
+    super();
+    alignFrame = _alignFrame;
+    if (!sh.getAbstractName().equals("MsaWS"))
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Service called \n" + sh.getName() +
+                                    "\nis not a \nMultiple Sequence Alignment Service !",
+                                    "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+
+    if ( (wsInfo = setWebService(sh)) == null)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Multiple Sequence Alignment Service named " +
+                                    sh.getName() +
+                                    " is unknown", "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
+
+  }
+
+  private void startMsaWSClient(String altitle, AlignmentView msa,
+                                boolean submitGaps, boolean preserveOrder,
+                                Alignment seqdataset)
+  {
+    if (!locateWebService())
+    {
+      return;
+    }
+
+    wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
+                           " of " + altitle + "\nJob details\n");
+    String jobtitle = WebServiceName.toLowerCase();
+    if (jobtitle.endsWith("alignment"))
+    {
+      if (submitGaps
+          && (!jobtitle.endsWith("realignment")
+              || jobtitle.indexOf("profile") == -1))
+      {
+        int pos = jobtitle.indexOf("alignment");
+        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " +
+            altitle;
+      }
+      else
+      {
+        jobtitle = WebServiceName + " of " + altitle;
+      }
+    }
+    else
+    {
+      jobtitle = WebServiceName + (submitGaps ? " re" : " ") + "alignment of " +
+          altitle;
+    }
+
+    MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
+                                            WebServiceName,
+                                            jobtitle,
+                                            msa,
+                                            submitGaps, preserveOrder,
+                                            seqdataset);
+    wsInfo.setthisService(msathread);
+    msathread.start();
+  }
+
+  /**
+   * Initializes the server field with a valid service implementation.
+   *
+   * @return true if service was located.
+   */
+  private boolean locateWebService()
+  {
+    // TODO: MuscleWS transmuted to generic MsaWS client
+    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+
+    try
+    {
+      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
+    }
+    catch (Exception ex)
+    {
+      wsInfo.setProgressText("Serious! " + WebServiceName +
+                             " Service location failed\nfor URL :" + WsURL +
+                             "\n" +
+                             ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.ERROR);
+      ex.printStackTrace();
+
+      return false;
+    }
+
+    loc.getEngine().setOption("axis", "1");
+
+    return true;
+  }
+
+  protected String getServiceActionKey()
+  {
+    return "MsaWS";
+  }
+
+  protected String getServiceActionDescription()
+  {
+    return "Multiple Sequence Alignment";
+  }
+}