X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=b1d6452712e6a542d70256bf2171b7d0668e95b0;hb=8590d9e6944ed8d8d624d04eac5e56d0ca97c0ed;hp=a0cd0f4c4f41a9e0c4e180a563612cbfaeb9d7d9;hpb=686783e6402dd664d29a0ebd01a8b9149f134cfa;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index a0cd0f4..b1d6452 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -42,9 +42,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -69,10 +67,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     long lastChunk = 0;
 
-    WsParamSetI preset = null;
-
-    List<ArgumentI> arguments = null;
-
     /**
      * input
      */
@@ -107,8 +101,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     }
 
-    Hashtable<String, Map> SeqNames = new Hashtable();
-
     Vector<String[]> emptySeqs = new Vector();
 
     /**
@@ -490,7 +482,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     if (conmsa != null)
     {
       int nvalid = 0, njobs = conmsa.length;
-      jobs = new MsaWSJob[njobs];
+      jobs = new AWsJob[njobs];
       for (int j = 0; j < njobs; j++)
       {
         if (j != 0)
@@ -501,12 +493,12 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         {
           jobs[j] = new MsaWSJob(0, conmsa[j]);
         }
-        if (((MsaWSJob) jobs[j]).hasValidInput())
+        if (jobs[j].hasValidInput())
         {
           nvalid++;
         }
-        ((MsaWSJob) jobs[j]).preset = preset;
-        ((MsaWSJob) jobs[j]).arguments = paramset;
+        jobs[j].setPreset(preset);
+        jobs[j].setArguments(paramset);
         ((MsaWSJob) jobs[j]).alignmentProgram = wsname;
         if (njobs > 0)
         {