From 928e216d738b36ba7d2cd6b80a65814c82598a42 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 May 2005 16:43:39 +0000
Subject: [PATCH] Semiworking generic MSA client

---
 src/jalview/ws/JPredClient.java |    2 +-
 src/jalview/ws/Jemboss.java     |   33 +--
 src/jalview/ws/MsaWSClient.java |  501 +++++++++++++++++++++------------------
 3 files changed, 271 insertions(+), 265 deletions(-)

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 2eecf46..ba3186c 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -50,7 +50,7 @@ public class JPredClient
 
     wsInfo.setProgressText("Job details for prediction on sequence :\nName : "
                    + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
-
+// TODO: put proper url in
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
     try {
       this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
index 3e01b77..a2e97f6 100755
--- a/src/jalview/ws/Jemboss.java
+++ b/src/jalview/ws/Jemboss.java
@@ -59,30 +59,6 @@ public class Jemboss
       props.getEmbossEnvironmentArray());
   }
   */
-    private Hashtable uniquify(SequenceI[] sequences) {
-        // Generate a safely named sequence set and a hash to recover the sequence names
-        Hashtable map = new Hashtable();
-        for (int i=0; i<sequences.length; i++) {
-            String safename = new String("Sequence"+i);
-            map.put(safename, sequences[i].getName());
-            sequences[i].setName(safename);
-        }
-        return map;
-    }
-
-    private boolean deuniquify(Hashtable map, SequenceI[] sequences) {
-        // recover unsafe sequence names for a sequence set
-        boolean allfound=true;
-        for (int i=0; i<sequences.length; i++) {
-            if (map.containsKey(sequences[i].getName())) {
-                String unsafename = (String) map.get(sequences[i].getName());
-                sequences[i].setName(unsafename);
-            } else {
-                allfound=false;
-            }
-        }
-        return allfound;
-    }
     public SequenceI[] clustalW(SequenceI[] sequences) {
       // Does the same as below but keeps initial sequence order.
       return (this.clustalW(sequences, true));
@@ -138,7 +114,7 @@ public class Jemboss
         myseq[i] = new Sequence(sequences[i]);
     }
     // Uniqueify, and
-    Hashtable namemap = uniquify(myseq);
+    Hashtable namemap = jalview.analysis.SeqsetUtils.uniquify(myseq);
     // Load sequence file into hash
 
     filesToMove.put("jalseqs.fasta",
@@ -176,12 +152,9 @@ public class Jemboss
                                + alfile + "\n---EOF\n");
           else {
             if (PreserveOrder) {
-              float[] ids = new float[alignment.length];
-              for (int i=0; i<alignment.length; i++)
-                ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
-              jalview.util.QuickSort.sort(ids, alignment);
+              jalview.analysis.AlignmentSorter.recoverOrder(alignment);
             }
-            if (!deuniquify(namemap, alignment)) {
+            if (!jalview.analysis.SeqsetUtils.deuniquify(namemap, alignment)) {
                   System.out.println("jalview.Jemboss: Warning: Some of the "
                                      +"original sequence names have not been recovered!\n");
             }
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 91f8ebb..1fa9dac 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,234 +1,267 @@
-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.";
-            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();}
-
-    }
-
-  }
-  }
-
+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();}
+
+    }
+
+  }
+}
+
+
-- 
1.7.10.2