JAL-98 ProfileI interface for Profile

[jalview.git] / test / jalview / analysis / AAFrequencyTest.java

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index bb3510a..1c04b8e 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -25,7 +25,7 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -41,12 +41,12 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C---G");
     SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Profile[] result = new Profile[seq1.getLength()];
+    ProfileI[] result = new ProfileI[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
 
     // col 0 is 100% C
-    Profile col = result[0];
+    ProfileI col = result[0];
     assertEquals(100f, col.getPercentageIdentity(false));
     assertEquals(100f, col.getPercentageIdentity(true));
     assertEquals(4, col.getMaxCount());
@@ -90,10 +90,10 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Profile[] result = new Profile[seq1.getLength()];
+    ProfileI[] result = new ProfileI[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
-    Profile profile = result[0];
+    ProfileI profile = result[0];
     assertEquals(4, profile.getCounts().getCount('C'));
     assertEquals(4, profile.getHeight());
     assertEquals(4, profile.getNonGapped());
@@ -124,7 +124,7 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Profile[] result = new Profile[seq1.getLength()];
+    ProfileI[] result = new ProfileI[seq1.getLength()];
 
     // ensure class loaded and initialized
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
@@ -154,7 +154,7 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C---G");
     SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Profile[] profiles = new Profile[seq1.getLength()];
+    ProfileI[] profiles = new ProfileI[seq1.getLength()];
     AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
 
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
@@ -195,7 +195,7 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C---G");
     SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Profile[] profiles = new Profile[seq1.getLength()];
+    ProfileI[] profiles = new ProfileI[seq1.getLength()];
     AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
   
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",