JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

[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 69d0ae4..62566cf 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -103,7 +104,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         return null;
       }
-      Alignment al = null;
+      AlignmentI al = null;
       ColumnSelection alcsel = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
@@ -279,7 +280,7 @@ class JPredThread extends JWS1Thread implements WSClientI
      * @param al
      * @param profileseq
      */
-    private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+    private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
     {
       char gc = al.getGapCharacter();
       int[] gapMap = profileseq.gapMap();