JAL-2629 add basic parameter adjustment to hmmsearch/align

[jalview.git] / test / jalview / hmmer / HMMERTest.java

diff --git a/test/jalview/hmmer/HMMERTest.java b/test/jalview/hmmer/HMMERTest.java
index 17ce2cf..7707dca 100644 (file)
--- a/test/jalview/hmmer/HMMERTest.java
+++ b/test/jalview/hmmer/HMMERTest.java
@@ -14,9 +14,11 @@ import jalview.gui.Desktop;
 import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.ws.params.ArgumentI;
 
 import java.io.IOException;
 import java.net.MalformedURLException;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -60,7 +62,8 @@ public class HMMERTest {
     AlignmentI al = new Alignment(seqs);
     frame = new AlignFrame(al, 150, 20);
 
-    HMMBuildThread thread = new HMMBuildThread(frame);
+    HMMBuildThread thread = new HMMBuildThread(frame,
+            new ArrayList<ArgumentI>());
     thread.hmmbuildWaitTillComplete();
 
     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
@@ -80,7 +83,8 @@ public class HMMERTest {
   @Test(priority = 1)
   public void testHMMAlign() throws MalformedURLException, IOException
   {
-    HMMAlignThread thread = new HMMAlignThread(frame, true);
+    HMMAlignThread thread = new HMMAlignThread(frame, true,
+            new ArrayList<ArgumentI>());
     try
     {
       thread.hmmalignWaitTillComplete();