From 8e45ad740239d950f7ceb8b322bf30ee307f4e98 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 5 Jan 2016 10:15:22 +0000
Subject: [PATCH] JAL-653 typed map for feature colours in method signature

---
 src/jalview/ws/jws1/SeqSearchWSThread.java |   15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index a28494c..b2e9b35 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -152,6 +152,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete
@@ -170,7 +171,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return null or { Alignment(+features and annotation), NewickFile)}
      */
-    public Object[] getAlignment(Alignment dataset, Map featureColours)
+    public Object[] getAlignment(Alignment dataset,
+            Map<String, Object> featureColours)
     {
 
       if (result != null && result.isFinished())
@@ -287,6 +289,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       if (seqs.getSeqs() != null)
@@ -373,11 +376,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -444,12 +449,14 @@ 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))
@@ -536,6 +543,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     return msa;
   }
 
+  @Override
   public void parseResult()
   {
     int results = 0; // number of result sets received
@@ -579,6 +587,7 @@ 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);
@@ -587,6 +596,7 @@ 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);
@@ -612,7 +622,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     // NewickFile nf[] = new NewickFile[jobs.length];
     for (int j = 0; j < jobs.length; j++)
     {
-      Map featureColours = new HashMap();
+      Map<String, Object> featureColours = new HashMap<String, Object>();
       Alignment al = null;
       NewickFile nf = null;
       if (jobs[j].hasResults())
@@ -664,6 +674,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;
-- 
1.7.10.2