X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=7d65cebb08cfd5f3b3476a2ea288fb3b0968fc95;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=0d4b2c13b27e20676ff02d323cfb1a9519987264;hpb=e5c2e37b24f09c90f2f7c748f6be10ce025da261;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 0d4b2c1..7d65ceb 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -43,6 +43,7 @@ public class MsaWSClient
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   ext.vamsas.MuscleWS server;
+  AlignFrame alignFrame;
 
 
   /**
@@ -56,10 +57,14 @@ public class MsaWSClient
    * @param preserveOrder DOCUMENT ME!
    */
 
-  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder)
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     SequenceI[] msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
   {
 
+    alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -81,13 +86,13 @@ public class MsaWSClient
 
        return;
      }
-    startMsaWSClient(altitle, msa, submitGaps, preserveOrder);
+    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
   }
 
 
   private void startMsaWSClient(String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder)
+                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
     if (!locateWebService())
     {
@@ -99,7 +104,7 @@ public class MsaWSClient
 
     MsaWSThread musclethread = new MsaWSThread(WebServiceName +
                                                " alignment of " + altitle, msa,
-                                               submitGaps, preserveOrder);
+                                               submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(musclethread);
     musclethread.start();
   }
@@ -125,7 +130,7 @@ public class MsaWSClient
                              " Service location failed\nfor URL :" + WsURL +
                              "\n" +
                              ex.getMessage());
-      wsInfo.setStatus(wsInfo.ERROR);
+      wsInfo.setStatus(WebserviceInfo.ERROR);
       ex.printStackTrace();
 
       return false;
@@ -145,20 +150,22 @@ public class MsaWSClient
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
         SequenceSet();
     Hashtable SeqNames = null;
-    boolean submitGaps = false; // and always store and recover sequence order
+    boolean submitGaps = false; // pass sequences including gaps to alignment service
     boolean 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.
     boolean jobComplete = false;
 
+    Alignment dataset; // dataset to which the new alignment will be associated.
+
     MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
-                boolean presorder)
+                boolean presorder, Alignment seqset)
     {
       alTitle = title;
       submitGaps = subgaps;
       preserveOrder = presorder;
-
+      dataset = seqset;
       OutputHeader = wsInfo.getProgressText();
       SeqNames = new Hashtable();
 
@@ -257,7 +264,7 @@ public class MsaWSClient
             throw (new Exception(
                 "Timed out when communicating with server\nTry again later.\n"));
           }
-          jalview.bin.Jalview.log.debug("Result state " + result.getState() +
+          jalview.bin.Cache.log.debug("Result state " + result.getState() +
                                         "(ServerError=" + result.isServerError() +
                                         ")");
           if (result.isRunning())
@@ -280,9 +287,7 @@ public class MsaWSClient
           {
             if (result.getStatus() != null)
             {
-              System.out.println("result "+result.getStatus().length());
-              wsInfo.setProgressText(OutputHeader + "\n" );
-                                //     result.getStatus());
+              wsInfo.setProgressText(OutputHeader + "\n"+   result.getStatus());
             }
             if (result.isServerError())
             {
@@ -335,6 +340,7 @@ public class MsaWSClient
              +"\nSee help files for increasing Java Virtual Machine memory."
              ,"Out of memory", JOptionPane.WARNING_MESSAGE );
           System.out.println("MsaWSClient: "+er);
+          System.gc();
         }
       }
 
@@ -396,7 +402,7 @@ public class MsaWSClient
                            e.toString() +
                            "\n");
         this.allowedServerExceptions = 0;
-        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
         wsInfo.appendProgressText(
             "Failed to submit sequences for alignment.\n" +
             "It is most likely that there is a problem with the server.\n" +
@@ -436,21 +442,18 @@ public class MsaWSClient
 
         if (result.getStatus() != null)
         {
-          System.out.println("get status  " +result.getStatus().length());
-         // OutputHeader += ("\n" + result.getStatus());
+          OutputHeader += ("\n" + result.getStatus());
         }
 
         if (result.getMsa() != null)
         {
-          System.out.println("get msa");
-       //   OutputHeader += "\nAlignment Object Method Notes\n";
+          OutputHeader += "\nAlignment Object Method Notes\n";
 
           String[] lines = result.getMsa().getMethod();
 
-System.out.println("lines "+lines.length);
           for (int line = 0; line < lines.length; line++)
           {
-           // OutputHeader += (lines[line] + "\n");
+            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
@@ -471,9 +474,15 @@ System.out.println("lines "+lines.length);
           jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
 
           Alignment al = new Alignment(seqs);
-
+          if (dataset!=null) {
+            al.setDataset(dataset);
+          }
           // TODO: JBPNote Should also rename the query sequence sometime...
           AlignFrame af = new AlignFrame(al);
+
+          //>>>This is a fix for the moment, until a better solution is found!!<<<
+          af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
           af.addSortByOrderMenuItem(ServiceName + " Ordering",
                                     msaorder);