JAL-2629 add option to set HMM Logo letter height to info content

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 9a0b33f..05a72e4 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -254,7 +254,7 @@ public class AAFrequencyTest
             "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
     hmm = hmmFile.getHMM();
     int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
-    int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false);
+    int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false, false);
     for (int i = 0; i < actual.length; i++)
     {
       if (i == 2)
@@ -268,7 +268,7 @@ public class AAFrequencyTest
     }
   
     int[] expected2 = { 0, 4, 100, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
-    int[] actual2 = AAFrequency.extractHMMProfile(hmm, 2, true);
+    int[] actual2 = AAFrequency.extractHMMProfile(hmm, 2, true, false);
     for (int i = 0; i < actual2.length; i++)
     {
       if (i == 2)
@@ -281,18 +281,18 @@ public class AAFrequencyTest
       }
     }
 
-    assertNull(AAFrequency.extractHMMProfile(null, 98978867, true));
+    assertNull(AAFrequency.extractHMMProfile(null, 98978867, true, false));
   }
 
   @Test(groups = { "Functional" }, priority = 2)
   public void testGetAnalogueCount()
   {
     int count;
-    count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false);
+    count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, false);
     assertEquals(7859, count);
-    count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false);
+    count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false, false);
     assertEquals(7546, count);
-    count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true);
+    count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true, false);
     assertEquals(0, count);
   }
 
@@ -310,7 +310,7 @@ public class AAFrequencyTest
     seq.setHMM(hmm);
     AlignmentAnnotation annot = new AlignmentAnnotation("", "", annots);
     annot.setSequenceRef(seq);
-    AAFrequency.completeInformation(annot, profs, 0, 1, false, true, 1);
+    AAFrequency.completeInformation(annot, profs, 0, 1, 1, 1f);
     float ic = annot.annotations[0].value;
     assertEquals(0.91532f, ic, 0.0001f);
     ic = annot.annotations[1].value;