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Rev: 639 - https://secure.bioinfweb.info/Code/svn/commons.java / trunk / test / src / info / bioinfweb / commons / bio / SequenceUtilsTest.java

Unified Diff View - SequenceUtilsTest.java

/trunk/test/src/info/bioinfweb/commons/bio/SequenceUtilsTest.java @ revision 638
/trunk/test/src/info/bioinfweb/commons/bio/SequenceUtilsTest.java @ revision 639
@@ -39,12 +39,13 @@ public class SequenceUtilsTest { @Test public void test_nucleotideConstituents() { - assertArrayEquals(new char[]{'A'}, SequenceUtils.nucleotideConstituents('A')); - assertArrayEquals(new char[]{'T'}, SequenceUtils.nucleotideConstituents('t')); - assertArrayEquals(new char[]{'-'}, SequenceUtils.nucleotideConstituents('-')); - assertArrayEquals(new char[]{'U'}, SequenceUtils.nucleotideConstituents('U')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('A')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('t')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('-')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('U')); assertArrayEquals(new char[]{'A', 'T', 'C', 'G'}, SequenceUtils.nucleotideConstituents('N')); assertArrayEquals(new char[]{'A', 'T', 'C', 'G'}, SequenceUtils.nucleotideConstituents('x')); + assertArrayEquals(new char[]{'A', 'T', 'C', 'G', '-'}, SequenceUtils.nucleotideConstituents('?')); } @@ -68,6 +69,7 @@ assertTrue(SequenceUtils.isNucleotideAmbuguityCode('B')); assertTrue(SequenceUtils.isNucleotideAmbuguityCode('H')); assertTrue(SequenceUtils.isNucleotideAmbuguityCode('D')); + assertTrue(SequenceUtils.isNucleotideAmbuguityCode('?')); } @@ -120,7 +122,7 @@ @Test public void test_oneLetterAminoAcidConstituents() { - assertArrayEquals(new char[]{'P'}, SequenceUtils.oneLetterAminoAcidConstituents("Pro")); + assertArrayEquals(new char[0], SequenceUtils.oneLetterAminoAcidConstituents("Pro")); assertArrayEquals(new char[]{'N', 'D'}, SequenceUtils.oneLetterAminoAcidConstituents("B")); assertArrayEquals(new char[]{'N', 'D'}, SequenceUtils.oneLetterAminoAcidConstituents("Asx")); assertArrayEquals(new char[]{'Q', 'E'}, SequenceUtils.oneLetterAminoAcidConstituents("Z")); @@ -132,7 +134,7 @@ @Test public void test_threeLetterAminoAcidConstituents() { - assertArrayEquals(new String[]{"Pro"}, SequenceUtils.threeLetterAminoAcidConstituents("Pro")); + assertArrayEquals(new String[0], SequenceUtils.threeLetterAminoAcidConstituents("Pro")); assertArrayEquals(new String[]{"Asn", "Asp"}, SequenceUtils.threeLetterAminoAcidConstituents("B")); assertArrayEquals(new String[]{"Asn", "Asp"}, SequenceUtils.threeLetterAminoAcidConstituents("Asx")); assertArrayEquals(new String[]{"Gln", "Glu"}, SequenceUtils.threeLetterAminoAcidConstituents("Z"));

/trunk/test/src/info/bioinfweb/commons/bio/SequenceUtilsTest.java @ revision 638

/trunk/test/src/info/bioinfweb/commons/bio/SequenceUtilsTest.java @ revision 639

@@ -39,12 +39,13 @@ public class SequenceUtilsTest { @Test public void test_nucleotideConstituents() { - assertArrayEquals(new char[]{'A'}, SequenceUtils.nucleotideConstituents('A')); - assertArrayEquals(new char[]{'T'}, SequenceUtils.nucleotideConstituents('t')); - assertArrayEquals(new char[]{'-'}, SequenceUtils.nucleotideConstituents('-')); - assertArrayEquals(new char[]{'U'}, SequenceUtils.nucleotideConstituents('U')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('A')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('t')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('-')); + assertArrayEquals(new char[0], SequenceUtils.nucleotideConstituents('U')); assertArrayEquals(new char[]{'A', 'T', 'C', 'G'}, SequenceUtils.nucleotideConstituents('N')); assertArrayEquals(new char[]{'A', 'T', 'C', 'G'}, SequenceUtils.nucleotideConstituents('x')); + assertArrayEquals(new char[]{'A', 'T', 'C', 'G', '-'}, SequenceUtils.nucleotideConstituents('?')); } @@ -68,6 +69,7 @@ assertTrue(SequenceUtils.isNucleotideAmbuguityCode('B')); assertTrue(SequenceUtils.isNucleotideAmbuguityCode('H')); assertTrue(SequenceUtils.isNucleotideAmbuguityCode('D')); + assertTrue(SequenceUtils.isNucleotideAmbuguityCode('?')); } @@ -120,7 +122,7 @@ @Test public void test_oneLetterAminoAcidConstituents() { - assertArrayEquals(new char[]{'P'}, SequenceUtils.oneLetterAminoAcidConstituents("Pro")); + assertArrayEquals(new char[0], SequenceUtils.oneLetterAminoAcidConstituents("Pro")); assertArrayEquals(new char[]{'N', 'D'}, SequenceUtils.oneLetterAminoAcidConstituents("B")); assertArrayEquals(new char[]{'N', 'D'}, SequenceUtils.oneLetterAminoAcidConstituents("Asx")); assertArrayEquals(new char[]{'Q', 'E'}, SequenceUtils.oneLetterAminoAcidConstituents("Z")); @@ -132,7 +134,7 @@ @Test public void test_threeLetterAminoAcidConstituents() { - assertArrayEquals(new String[]{"Pro"}, SequenceUtils.threeLetterAminoAcidConstituents("Pro")); + assertArrayEquals(new String[0], SequenceUtils.threeLetterAminoAcidConstituents("Pro")); assertArrayEquals(new String[]{"Asn", "Asp"}, SequenceUtils.threeLetterAminoAcidConstituents("B")); assertArrayEquals(new String[]{"Asn", "Asp"}, SequenceUtils.threeLetterAminoAcidConstituents("Asx")); assertArrayEquals(new String[]{"Gln", "Glu"}, SequenceUtils.threeLetterAminoAcidConstituents("Z"));

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