Updated with latest from mchmmer branch

[jalview.git] / test / jalview / datamodel / ResidueCountTest.java

diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java
index 4eb6dbf..9a8f93d 100644 (file)
--- a/test/jalview/datamodel/ResidueCountTest.java
+++ b/test/jalview/datamodel/ResidueCountTest.java
@@ -27,6 +27,8 @@ import static org.testng.Assert.assertTrue;
 import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.gui.JvOptionPane;
 
+import java.util.Arrays;
+
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -69,6 +71,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount('N'), 1);
     assertEquals(rc.getCount('?'), 0);
     assertEquals(rc.getCount('-'), 0);
+    assertEquals(rc.getTotalResidueCount(), 11);
 
     assertFalse(rc.isCountingInts());
     assertFalse(rc.isUsingOtherData());
@@ -90,6 +93,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount(' '), 4);
     assertEquals(rc.getCount('-'), 4);
     assertEquals(rc.getCount('.'), 4);
+    assertEquals(rc.getTotalResidueCount(), 0);
     assertFalse(rc.isUsingOtherData());
     assertFalse(rc.isCountingInts());
   }
@@ -158,6 +162,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount('m'), 13);
     assertEquals(rc.getCount('G'), 0);
     assertEquals(rc.getCount('-'), 0);
+    assertEquals(rc.getTotalResidueCount(), 27);
 
     assertFalse(rc.isCountingInts());
     assertFalse(rc.isUsingOtherData());
@@ -439,4 +444,23 @@ public class ResidueCountTest
     assertEquals(rc.getCount('?'), 6);
     assertEquals(rc.getCount('!'), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testConstructor_forSequences()
+  {
+    SequenceI seq1 = new Sequence("seq1", "abcde--. FCD");
+    SequenceI seq2 = new Sequence("seq2", "ab.kKqBd-.");
+    ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2));
+
+    assertEquals(rc.getGapCount(), 7);
+    assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps
+    assertEquals(rc.getCount('a'), 2);
+    assertEquals(rc.getCount('A'), 2);
+    assertEquals(rc.getCount('B'), 3);
+    assertEquals(rc.getCount('c'), 2);
+    assertEquals(rc.getCount('D'), 3);
+    assertEquals(rc.getCount('f'), 1);
+    assertEquals(rc.getCount('K'), 2);
+    assertEquals(rc.getCount('Q'), 1);
+  }
 }