JAL-98 ProfilesI container for profiles for columns

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 1c04b8e..58601a9 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNull;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -41,12 +42,12 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
-
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
+    int width = seq1.getLength();
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
+            false);
 
     // col 0 is 100% C
-    ProfileI col = result[0];
+    ProfileI col = result.get(0);
     assertEquals(100f, col.getPercentageIdentity(false));
     assertEquals(100f, col.getPercentageIdentity(true));
     assertEquals(4, col.getMaxCount());
@@ -54,28 +55,28 @@ public class AAFrequencyTest
     assertNull(col.getCounts());
 
     // col 1 is 75% A
-    col = result[1];
+    col = result.get(1);
     assertEquals(75f, col.getPercentageIdentity(false));
     assertEquals(100f, col.getPercentageIdentity(true));
     assertEquals(3, col.getMaxCount());
     assertEquals("A", col.getModalResidue());
 
     // col 2 is 50% G 50% C or 25/25 counting gaps
-    col = result[2];
+    col = result.get(2);
     assertEquals(25f, col.getPercentageIdentity(false));
     assertEquals(50f, col.getPercentageIdentity(true));
     assertEquals(1, col.getMaxCount());
     assertEquals("CG", col.getModalResidue());
 
     // col 3 is all gaps
-    col = result[3];
+    col = result.get(3);
     assertEquals(0f, col.getPercentageIdentity(false));
     assertEquals(0f, col.getPercentageIdentity(true));
     assertEquals(0, col.getMaxCount());
     assertEquals("", col.getModalResidue());
 
     // col 4 is 75% T 25% G
-    col = result[4];
+    col = result.get(4);
     assertEquals(75f, col.getPercentageIdentity(false));
     assertEquals(75f, col.getPercentageIdentity(true));
     assertEquals(3, col.getMaxCount());
@@ -90,26 +91,27 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
+    int width = seq1.getLength();
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
+            true);
 
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
-    ProfileI profile = result[0];
+    ProfileI profile = result.get(0);
     assertEquals(4, profile.getCounts().getCount('C'));
     assertEquals(4, profile.getHeight());
     assertEquals(4, profile.getNonGapped());
 
-    profile = result[1];
+    profile = result.get(1);
     assertEquals(3, profile.getCounts().getCount('A'));
     assertEquals(4, profile.getHeight());
     assertEquals(3, profile.getNonGapped());
 
-    profile = result[2];
+    profile = result.get(2);
     assertEquals(1, profile.getCounts().getCount('C'));
     assertEquals(1, profile.getCounts().getCount('G'));
     assertEquals(4, profile.getHeight());
     assertEquals(2, profile.getNonGapped());
 
-    profile = result[3];
+    profile = result.get(3);
     assertEquals(3, profile.getCounts().getCount('T'));
     assertEquals(1, profile.getCounts().getCount('G'));
     assertEquals(4, profile.getHeight());
@@ -124,15 +126,16 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
 
-    // ensure class loaded and initialized
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+    // ensure class loaded and initialised
+    int width = seq1.getLength();
+    AAFrequency.calculate(seqs, width, 0, width, true);
+
     int reps = 100000;
     long start = System.currentTimeMillis();
     for (int i = 0; i < reps; i++)
     {
-      AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+      AAFrequency.calculate(seqs, width, 0, width, true);
     }
     System.out.println(System.currentTimeMillis() - start);
   }
@@ -154,11 +157,11 @@ 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 };
-    ProfileI[] profiles = new ProfileI[seq1.getLength()];
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+    int width = seq1.getLength();
+    ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
 
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
-            "PID", new Annotation[seq1.getLength()]);
+            "PID", new Annotation[width]);
     AAFrequency
             .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
 
@@ -195,11 +198,11 @@ 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 };
-    ProfileI[] profiles = new ProfileI[seq1.getLength()];
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+    int width = seq1.getLength();
+    ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
   
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
-            "PID", new Annotation[seq1.getLength()]);
+            "PID", new Annotation[width]);
     AAFrequency
             .completeConsensus(consensus, profiles, 0, 5, true, false, 4);