JAL-3899 Update usages of uniquify and deuniquify.

[jalview.git] / src / jalview / ws / jws2 / JPredThread.java

diff --git a/src/jalview/ws/jws2/JPredThread.java b/src/jalview/ws/jws2/JPredThread.java
index 67f44fa..f4ad8b2 100644 (file)
--- a/src/jalview/ws/jws2/JPredThread.java
+++ b/src/jalview/ws/jws2/JPredThread.java
@@ -4,8 +4,10 @@ import static java.lang.String.format;
 
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.commands.RemoveGapsCommand;
 import jalview.datamodel.Alignment;
@@ -34,13 +36,13 @@ public class JPredThread extends AWSThread implements WSClientI
 
   private static class JPredJob extends WsJob
   {
-    private final Hashtable<?, ?> sequenceInfo;
+    private final Object sequenceInfo;
     private final List<SequenceI> msf;
     private final int[] delMap;
     private AlignmentI alignment = null;
     private HiddenColumns hiddenCols = null;
 
-    private JPredJob(Hashtable<?, ?> sequenceInfo, SequenceI[] msf, int[] delMap)
+    private JPredJob(Object sequenceInfo, SequenceI[] msf, int[] delMap)
     {
       this.sequenceInfo = sequenceInfo;
       this.msf = List.of(msf);
@@ -68,12 +70,12 @@ public class JPredThread extends AWSThread implements WSClientI
 
   private JPredServiceI server;
   private String title;
-  private Hashtable<?, ?> sequenceInfo;
+  private Object sequenceInfo;
   private SequenceI[] msf;
   private int[] delMap;
 
   public JPredThread(WebserviceInfo wsInfo, String title,
-      JPredServiceI server, Hashtable<?, ?> sequenceInfo,
+      JPredServiceI server, Object sequenceInfo,
       SequenceI[] msf, int[] delMap, AlignmentView view, AlignFrame frame,
       String wsURL)
   {
@@ -261,7 +263,7 @@ public class JPredThread extends AWSThread implements WSClientI
         {
           seqs[i] = alignment.getSequenceAt(i);
         }
-        if (!SeqsetUtils.deuniquify(sequenceInfo, seqs))
+        if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)sequenceInfo, seqs))
         {
           throw (new Exception(MessageManager.getString(
                   "exception.couldnt_recover_sequence_properties_for_alignment")));
@@ -293,7 +295,7 @@ public class JPredThread extends AWSThread implements WSClientI
         profileSeq.setSequence(seqs[msaIndex].getSequenceAsString());
       }
       if (!SeqsetUtils.SeqCharacterUnhash(
-              alignment.getSequenceAt(firstSeq), sequenceInfo))
+              alignment.getSequenceAt(firstSeq), (SequenceInfo)sequenceInfo))
       {
         throw new Exception(MessageManager.getString(
                 "exception.couldnt_recover_sequence_props_for_jnet_query"));