JAL-2110 JAL-2131 JAL-1765 remove reference to jalview.datamodel.Alignment from Align...

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

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index b2e9b35..86c2b9f 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -23,6 +23,7 @@ package jalview.ws.jws1;
 import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -171,7 +172,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return null or { Alignment(+features and annotation), NewickFile)}
      */
-    public Object[] getAlignment(Alignment dataset,
+    public Object[] getAlignment(AlignmentI dataset,
             Map<String, Object> featureColours)
     {
 
@@ -302,7 +303,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -344,7 +345,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, String db,
-          Alignment seqset)
+          AlignmentI seqset)
   {
     this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
     OutputHeader = wsInfo.getProgressText();