From 8590d9e6944ed8d8d624d04eac5e56d0ca97c0ed Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 27 Jul 2018 12:08:13 +0100
Subject: [PATCH] JAL-3070 pull up sequence anonymisation hash, presets and
 params list.

---
 src/jalview/ws/AWsJob.java                 |   24 ++++++++++++++++++++++++
 src/jalview/ws/jws1/MsaWSThread.java       |    3 ---
 src/jalview/ws/jws1/SeqSearchWSThread.java |    3 ---
 src/jalview/ws/jws2/MsaWSThread.java       |   16 ++++------------
 4 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/src/jalview/ws/AWsJob.java b/src/jalview/ws/AWsJob.java
index f5f9377..bb203fc 100644
--- a/src/jalview/ws/AWsJob.java
+++ b/src/jalview/ws/AWsJob.java
@@ -20,6 +20,13 @@
  */
 package jalview.ws;
 
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 /**
  * Generic properties for an individual job within a Web Service Client thread.
  * Derived from jalview web services version 1 statuses, and revised for Jws2.
@@ -145,6 +152,12 @@ public abstract class AWsJob
    */
   protected boolean subjobComplete = false;
 
+  protected WsParamSetI preset = null;
+
+  protected List<ArgumentI> arguments = null;
+
+  protected Hashtable<String, Map> SeqNames = new Hashtable();
+
   public AWsJob()
   {
   }
@@ -227,4 +240,15 @@ public abstract class AWsJob
     String state = "";
     return state;
   }
+
+  public void setPreset(WsParamSetI jobpreset)
+  {
+    preset = jobpreset;
+  }
+
+  public void setArguments(List<ArgumentI> paramset)
+  {
+    arguments = paramset;
+
+  }
 }
diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index 006f014..7b3df82 100644
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -36,7 +36,6 @@ import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
 
-import java.util.Hashtable;
 import java.util.Vector;
 
 import vamsas.objects.simple.MsaResult;
@@ -78,8 +77,6 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
     }
 
-    Hashtable SeqNames = new Hashtable();
-
     Vector emptySeqs = new Vector();
 
     /**
diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 761b758..2f2bf2c 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -37,7 +37,6 @@ import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
 
 import java.util.HashMap;
-import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
 
@@ -77,8 +76,6 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
 
     }
 
-    Hashtable SeqNames = new Hashtable();
-
     Vector emptySeqs = new Vector();
 
     /**
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)
         {
-- 
1.7.10.2