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
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+ }
+
@Test(groups = { "Functional" })
public void testIsGap()
{
@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+tenpercent",
+ "agctuagcgVagctuagcuVE");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq } }));
- seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
+ seq = new Sequence(">nineyfivepercent+0percent",
+ "aagctuagcgEagctuagcua");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
+ seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ 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", "---------");
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
/*
- * 90% DNA:
+ * 90% DNA but one protein sequence - expect false
*/
- assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq, seq2 }));
- assertTrue(Comparison.isNucleotide(new SequenceI[][] {
- new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq, seq2 } }));
/*
- * 80% DNA:
+ * 80% DNA but one protein sequence - Expect false
*/
- assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq2, seq2 }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
-
- seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
- // 12/14 = 85.7%
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq2, seq2, null } }));
+
+ 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));
@Test(groups = { "Functional" })
public void testPID_includingGaps()
{
- String seq1 = "ABCDEF";
+ String seq1 = "ABCDEFG"; // extra length here is ignored
String seq2 = "abcdef";
assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
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
*/
public void testPID_ungappedOnly()
{
// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
- String seq1 = "a--b-cdefh";
+ // the extra length of seq1 is ignored
+ String seq1 = "a--b-cdefhr";
String seq2 = "a---bcdefg";
int length = seq1.length();
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" })
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff