JAL-4019 Added tests for new Nucleotide sequence detection

[jalview.git] / test / jalview / util / ComparisonTest.java

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index cef9ffc..99c097f 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -24,13 +24,15 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class ComparisonTest
 {
 
@@ -41,6 +43,12 @@ public class ComparisonTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+  }
+
   @Test(groups = { "Functional" })
   public void testIsGap()
   {
@@ -60,24 +68,41 @@ public class ComparisonTest
   @Test(groups = { "Functional" })
   public void testIsNucleotide_sequences()
   {
-    SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
+    SequenceI seq = new Sequence("eightypercent+fivepercent", "agctuagcPV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
     assertFalse(
             Comparison.isNucleotide(new SequenceI[][]
             { new SequenceI[] { seq } }));
 
-    seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
+    seq = new Sequence("eightyfivepercent+tenpercent",
+            "agctuagcgVagctuagcuVE");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence(">nineyfivepercent+0percent",
+            "aagctuagcgEagctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
-    seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
+    seq = new Sequence("nineyfivepercent+fivepercent",
+            "agctuagcgWagctuagcua");
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
+    seq = new Sequence("nineyfivepercent+tenpercent",
+            "agctuagcgEWWctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence("eightyfivepercent+fifteenpercent",
+            "agctuagcgWWWctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
     seq = new Sequence("eightyfivepercentgapped",
             "--agc--tuA--GCPV-a---gct-uA-GC---UV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
-    seq = new Sequence("nineypercentgapped",
-            "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
+    seq = new Sequence("ninetyfivepercentgapped",
+            "ag--ct-u-a---gc---g----aag--c---tuagcuV");
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("allgap", "---------");
@@ -108,8 +133,10 @@ public class ComparisonTest
                 new SequenceI[]
                 { seq, seq, seq, seq, seq2, seq2, null } }));
 
-    seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
-    // 12/14 = 85.7%
+    String seqString = "aaatatatatgEcctgagtcgt";
+    seq = new Sequence("ShortProteinThatLooksLikeDNA", seqString);
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+    seq = new Sequence("LongProteinThatLooksLikeDNA", seqString.repeat(10));
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     assertFalse(Comparison.isNucleotide((SequenceI[]) null));
@@ -165,6 +192,25 @@ public class ComparisonTest
     assertFalse(Comparison.isNucleotide('P'));
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsNucleotideAmbiguity()
+  {
+    assertTrue(Comparison.isNucleotide('b', true));
+    assertTrue(Comparison.isNucleotide('B', true));
+    assertTrue(Comparison.isNucleotide('d', true));
+    assertTrue(Comparison.isNucleotide('V', true));
+    assertTrue(Comparison.isNucleotide('M', true));
+    assertTrue(Comparison.isNucleotide('s', true));
+    assertTrue(Comparison.isNucleotide('W', true));
+    assertTrue(Comparison.isNucleotide('x', true));
+    assertTrue(Comparison.isNucleotide('Y', true));
+    assertTrue(Comparison.isNucleotide('r', true));
+    assertTrue(Comparison.isNucleotide('i', true));
+    assertFalse(Comparison.isNucleotide('-', true));
+    assertFalse(Comparison.isNucleotide('n', true));
+    assertFalse(Comparison.isNucleotide('P', true));
+  }
+
   /**
    * Test the percentage identity calculation for two sequences
    */
@@ -206,6 +252,30 @@ public class ComparisonTest
     assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
     assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
     assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("gatactawgataca", false));
+    // including nucleotide ambiguity
+    assertTrue(
+            Comparison.isNucleotideSequence("gatacaWgataca", true, true));
+    assertFalse(
+            Comparison.isNucleotideSequence("gatacaEgataca", true, true));
+
+    // not quite all nucleotides and ambiguity codes
+    Sequence seq = new Sequence("Ambiguity DNA codes", "gatacagatacabve");
+    assertFalse(Comparison.isNucleotide(seq));
+    // all nucleotide and nucleotide ambiguity codes
+    seq = new Sequence("Ambiguity DNA codes", "gatacagatacabvt");
+    assertFalse(Comparison.isNucleotide(seq));
+    seq = new Sequence("Ambiguity DNA codes", "agatacabb");
+    assertFalse(Comparison.isNucleotide(seq));
+    // 55% nucleotide with only Xs or Ns
+    assertTrue(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacaXXXX")));
+    assertTrue(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacaNNNN")));
+    assertFalse(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacXXXXX")));
+    assertFalse(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacNNNNN")));
   }
 
   @Test(groups = { "Functional" })
@@ -219,4 +289,23 @@ public class ComparisonTest
     assertFalse(Comparison.isSameResidue('a', 'A', true));
     assertFalse(Comparison.isSameResidue('A', 'a', true));
   }
+
+  @Test(groups = { "Functional" })
+  public void testNucleotideProportion()
+  {
+    assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 3));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 3));
+    assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 4));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 4));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(17, 20));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(18, 20));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(38, 50));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(39, 50));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(54, 100));
+    assertTrue(
+            Comparison.myShortSequenceNucleotideProportionCount(55, 100));
+  }
 }