JAL-3070 pull up sequence anonymisation hash, presets and params list.

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index a0cd0f4..b1d6452 100644 (file)
--- 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)
         {