X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSThread.java;h=66fddd155f6411ddec93b9bc3e60ea4caf40b779;hb=8dfdafee89d06dd397c392619b4b285f0dc35430;hp=a6e3731bda6fe3aeee874cc9b39408021da402c9;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index a6e3731..66fddd1 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
@@ -34,7 +35,9 @@ import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
 
+import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Map;
 import java.util.Vector;
 
 import vamsas.objects.simple.MsaResult;
@@ -150,6 +153,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete
@@ -168,7 +172,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return null or { Alignment(+features and annotation), NewickFile)}
      */
-    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+    public Object[] getAlignment(Alignment dataset,
+            Map<String, FeatureColourI> featureColours)
     {
 
       if (result != null && result.isFinished())
@@ -285,6 +290,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       if (seqs.getSeqs() != null)
@@ -371,11 +377,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -442,12 +450,14 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
             .getJobId());
   }
 
+  @Override
   public void StartJob(AWsJob job)
   {
     if (!(job instanceof SeqSearchWSJob))
@@ -534,6 +544,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     return msa;
   }
 
+  @Override
   public void parseResult()
   {
     int results = 0; // number of result sets received
@@ -577,6 +588,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -585,6 +597,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -610,7 +623,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     // NewickFile nf[] = new NewickFile[jobs.length];
     for (int j = 0; j < jobs.length; j++)
     {
-      Hashtable featureColours = new Hashtable();
+      Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
       Alignment al = null;
       NewickFile nf = null;
       if (jobs[j].hasResults())
@@ -662,6 +675,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;