JAL-3899 Update usages of uniquify and deuniquify.

[jalview.git] / src / jalview / ws / jws1 / JPredThread.java

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 23d9eb0..b7b8e5f 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -22,6 +22,7 @@ package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -47,6 +48,7 @@ import jalview.ws.WSClientI;
 
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import vamsas.objects.simple.JpredResult;
 
@@ -66,7 +68,7 @@ class JPredThread extends JWS1Thread implements WSClientI
 
     vamsas.objects.simple.Msfalignment msa;
 
-    java.util.Hashtable SequenceInfo = null;
+    Object SequenceInfo = null;
 
     int msaIndex = 0; // the position of the original sequence in the array of
 
@@ -156,7 +158,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
+            if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)SequenceInfo, sqs))
             {
               throw (new Exception(MessageManager.getString(
                       "exception.couldnt_recover_sequence_properties_for_alignment")));
@@ -211,7 +213,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                al.getSequenceAt(FirstSeq), SequenceInfo))
+                al.getSequenceAt(FirstSeq), (SequenceInfo)SequenceInfo))
         {
           throw (new Exception(MessageManager.getString(
                   "exception.couldnt_recover_sequence_props_for_jnet_query")));
@@ -332,7 +334,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-    public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+    public JPredJob(Object SequenceInfo, SequenceI seq, int[] delMap)
     {
       super();
       this.predMap = delMap;
@@ -351,7 +353,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-    public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
+    public JPredJob(Object SequenceInfo, SequenceI[] msf, int[] delMap)
     {
       this(SequenceInfo, msf[0], delMap);
       if (sequence != null)
@@ -387,7 +389,7 @@ class JPredThread extends JWS1Thread implements WSClientI
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle,
-          ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+          ext.vamsas.Jpred server, String wsurl, SequenceInfo SequenceInfo,
           SequenceI seq, int[] delMap, AlignmentView alview,
           AlignFrame alframe)
   {
@@ -406,9 +408,9 @@ class JPredThread extends JWS1Thread implements WSClientI
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle,
-          ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
-          int[] delMap, AlignmentView alview, AlignFrame alframe,
-          String wsurl)
+          ext.vamsas.Jpred server, Map<String, SequenceInfo> SequenceInfo,
+          SequenceI[] msf, int[] delMap, AlignmentView alview, 
+          AlignFrame alframe, String wsurl)
   {
     this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);