First patch for * JAL-493

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

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 7142e5c..ab3dfbe 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -22,7 +22,6 @@ import java.util.*;
 import jalview.analysis.*;\r
 import jalview.bin.*;\r
 import jalview.datamodel.*;\r
-import jalview.datamodel.Alignment;\r
 import jalview.gui.*;\r
 import vamsas.objects.simple.MsaResult;\r
 \r
@@ -46,7 +45,7 @@ import vamsas.objects.simple.MsaResult;
  * @author not attributable\r
  * @version 1.0\r
  */\r
-class MsaWSThread extends WSThread implements WSClientI\r
+class MsaWSThread extends JWS1Thread implements WSClientI\r
 {\r
   boolean submitGaps = false; // pass sequences including gaps to alignment\r
 \r
@@ -56,7 +55,7 @@ class MsaWSThread extends WSThread implements WSClientI
 \r
   // order\r
 \r
-  class MsaWSJob extends WSThread.WSJob\r
+  class MsaWSJob extends WSJob\r
   {\r
     // hold special input for this\r
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
@@ -280,7 +279,7 @@ class MsaWSThread extends WSThread implements WSClientI
      * \r
      * @return boolean true if job can be submitted.\r
      */\r
-    boolean hasValidInput()\r
+    public boolean hasValidInput()\r
     {\r
       if (seqs.getSeqs() != null)\r
       {\r
@@ -438,12 +437,12 @@ class MsaWSThread extends WSThread implements WSClientI
     }\r
   }\r
 \r
-  void pollJob(WSJob job) throws Exception\r
+  public void pollJob(AWsJob job) throws Exception\r
   {\r
     ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);\r
   }\r
 \r
-  void StartJob(WSJob job)\r
+  public void StartJob(AWsJob job)\r
   {\r
     if (!(job instanceof MsaWSJob))\r
     {\r
@@ -531,7 +530,7 @@ class MsaWSThread extends WSThread implements WSClientI
     return msa;\r
   }\r
 \r
-  void parseResult()\r
+  public void parseResult()\r
   {\r
     int results = 0; // number of result sets received\r
     JobStateSummary finalState = new JobStateSummary();\r
@@ -544,7 +543,7 @@ class MsaWSThread extends WSThread implements WSClientI
                 && jobs[j].hasResults())\r
         {\r
           results++;\r
-          vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result)\r
+          vamsas.objects.simple.Alignment valign =  ((MsaResult)((MsaWSJob) jobs[j]).result)\r
                   .getMsa();\r
           if (valign != null)\r
           {\r