tidied up system.out messages and moved many to stderr.

[jalview.git] / src / jalview / ws / MsaWSClient.java

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 1fa9dac..4e358a0 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -16,24 +16,17 @@ import vamsas.objects.*;
 
 
 public class MsaWSClient
+    extends WSClient
 {
-  int jobsRunning = 0;
-  ext.vamsas.MuscleWS server;
-  WebserviceInfo wsInfo;
-  /**
-   * MsaWSClient
-   *
-   * @param msa SequenceI[]
-   */
-
-  String WebServiceName;
-  String WebServiceJobTitle;
-  String WebServiceReference;
-  String WsURL;
+    /**
+     * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+     */
+    ext.vamsas.MuscleWS server;
+
   private boolean setWebService(String MsaWSName) {
-    if (MsaWServices.info.contains(MsaWSName.toUpperCase())) {
+    if (MsaWServices.info.containsKey(MsaWSName)) {
       WebServiceName = MsaWSName;
-      String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName.toUpperCase());
+      String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
       WsURL = wsinfo[0];
       WebServiceJobTitle = wsinfo[1];
       WebServiceReference = wsinfo[2];
@@ -43,11 +36,8 @@ public class MsaWSClient
     }
   }
 
-//  public MsaWSClient(String MsaWSName, SequenceI[] msa) {
-//    MsaWSClient(MsaWSName, msa, true);
-//  }
 
-  public MsaWSClient(String MsaWSName, SequenceI[] msa, boolean preserveOrder)
+  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",
@@ -57,13 +47,12 @@ public class MsaWSClient
 
     wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
 
-    wsInfo.setProgressText("Job details\n");
+    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));
+      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
     }
     catch (Exception ex) {
       wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
@@ -72,7 +61,7 @@ public class MsaWSClient
       ex.printStackTrace();
     }
 
-    MsaWSThread musclethread = new MsaWSThread(msa);
+    MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
     wsInfo.setthisService(musclethread);
     musclethread.start();
   }
@@ -89,21 +78,40 @@ public class MsaWSClient
 
     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(SequenceI[] msa)
+    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 = jalview.analysis.SeqsetUtils.unique_name(i);
+        // uniquify as we go
+        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
         seqarray[i] = new vamsas.objects.simple.Sequence();
-        seqarray[i].setId(msa[i].getName());
-        seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));
+        seqarray[i].setId(newname);
+        seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
+                           : AlignSeq.extractGaps("-. ", msa[i].getSequence()));
       }
+
       this.seqs = new vamsas.objects.simple.SequenceSet();
       this.seqs.setSeqs(seqarray);
     }
@@ -194,14 +202,15 @@ public class MsaWSClient
       {
         vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
         if (jobsubmit.getStatus()==1) {
-          System.out.println(jobId=jobsubmit.getJobId());
+          jobId=jobsubmit.getJobId();
+          System.out.println(WsURL+" Job Id '"+jobId+"'");
         } else {
           throw new Exception(jobsubmit.getJobId());
         }
       }
       catch (Exception e)
       {
-        System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
+        System.err.println(ServiceName + " Client: Failed to submit the prediction\n" +
                            e.toString() + "\n");
         e.printStackTrace();
       }
@@ -247,13 +256,22 @@ public class MsaWSClient
 
         wsInfo.setProgressText(OutputHeader);
         if (seqs!=null) {
-          Alignment al;
-          al = new Alignment(seqs);
+          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,
-                                   ServiceName + " Alignment",
+                                   alTitle,
                                    AlignFrame.NEW_WINDOW_WIDTH,
                                    AlignFrame.NEW_WINDOW_HEIGHT);
         }