First patch for * JAL-493

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

diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java
index 2f28d64..550ae43 100644 (file)
--- a/src/jalview/ws/SeqSearchWSThread.java
+++ b/src/jalview/ws/SeqSearchWSThread.java
@@ -47,13 +47,13 @@ import vamsas.objects.simple.SeqSearchResult;
  * @author not attributable\r
  * @version 1.0\r
  */\r
-class SeqSearchWSThread extends WSThread implements WSClientI\r
+class SeqSearchWSThread extends JWS1Thread implements WSClientI\r
 {\r
   String dbs = null;\r
 \r
   boolean profile = false;\r
 \r
-  class SeqSearchWSJob extends WSThread.WSJob\r
+  class SeqSearchWSJob extends WSJob\r
   {\r
     // hold special input for this\r
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
@@ -293,7 +293,7 @@ class SeqSearchWSThread 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
@@ -451,13 +451,13 @@ class SeqSearchWSThread extends WSThread implements WSClientI
     }\r
   }\r
 \r
-  void pollJob(WSJob job) throws Exception\r
+  public void pollJob(AWsJob job) throws Exception\r
   {\r
     ((SeqSearchWSJob) job).result = server\r
             .getResult(((SeqSearchWSJob) job).jobId);\r
   }\r
 \r
-  void StartJob(WSJob job)\r
+  public void StartJob(AWsJob job)\r
   {\r
     if (!(job instanceof SeqSearchWSJob))\r
     {\r
@@ -545,7 +545,7 @@ class SeqSearchWSThread 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
@@ -558,7 +558,7 @@ class SeqSearchWSThread extends WSThread implements WSClientI
                 && jobs[j].hasResults())\r
         {\r
           results++;\r
-          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) jobs[j].result)\r
+          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)\r
                   .getAlignment();\r
           if (valign != null)\r
           {\r