\r
public class SequenceUtilTester {\r
\r
- @Test()\r
- public void testisNonAmbNucleotideSequence() {\r
- String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
- assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
- String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
- assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
- String nonDna = "atgfctgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
- nonDna = "atgc1tgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
- nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
- // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
- }\r
-\r
- @Test()\r
- public void testCleanSequence() {\r
- String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
- SequenceUtil.cleanSequence(dirtySeq));\r
- }\r
-\r
- @Test()\r
- public void testDeepCleanSequence() {\r
- String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
- SequenceUtil.deepCleanSequence(dirtySeq));\r
+ @Test()\r
+ public void testisNonAmbNucleotideSequence() {\r
+ String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
+ assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
+ String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
+ assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
+ String nonDna = "atgfctgatgcatgcatgatgctga";\r
+ assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
+\r
+ nonDna = "atgc1tgatgcatgcatgatgctga";\r
+ assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
+\r
+ nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
+ assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
+ // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
+ assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
+\r
+ }\r
+\r
+ @Test()\r
+ public void testCleanSequence() {\r
+ String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
+ assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
+ SequenceUtil.cleanSequence(dirtySeq));\r
+ }\r
+\r
+ @Test()\r
+ public void testDeepCleanSequence() {\r
+ String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
+ assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
+ SequenceUtil.deepCleanSequence(dirtySeq));\r
+ }\r
+\r
+ @Test()\r
+ public void testisProteinSequence() {\r
+ String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
+ assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
+ String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
+ assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
+ String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
+ assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
+ AAseq += "XU";\r
+ assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
+\r
+ }\r
+\r
+ @Test()\r
+ public void testReadWriteFasta() {\r
+\r
+ try {\r
+ FileInputStream fio = new FileInputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
+ assertNotNull(fio);\r
+ List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
+ assertNotNull(fseqs);\r
+ assertEquals(3, fseqs.size());\r
+ assertEquals(3, fseqs.size());\r
+ fio.close();\r
+ FileOutputStream fou = new FileOutputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
+ SequenceUtil.writeFasta(fou, fseqs);\r
+ fou.close();\r
+ FileOutputStream fou20 = new FileOutputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
+ SequenceUtil.writeFasta(fou20, fseqs, 20);\r
+ fou20.close();\r
+\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
}\r
-\r
- @Test()\r
- public void testisProteinSequence() {\r
- String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
- String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
- String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
- assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
- AAseq += "XU";\r
- assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
-\r
+ }\r
+\r
+ /**\r
+ * This test tests the loading of horizontally formatted Jronn output file\r
+ */\r
+ @Test\r
+ public void loadJronnFile() {\r
+\r
+ FileInputStream fio;\r
+ try {\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
+ List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);\r
+ assertNotNull(aseqs);\r
+ assertEquals(aseqs.size(), 3);\r
+ AnnotatedSequence aseq = aseqs.get(0);\r
+ assertNotNull(aseq);\r
+ assertNotNull(aseq.getAnnotation());\r
+ //System.out.println(aseq);\r
+ assertEquals(aseq.getAnnotation().length, aseq.getSequence()\r
+ .length());\r
+ fio.close();\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (UnknownFileFormatException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
}\r
\r
- @Test()\r
- public void testReadWriteFasta() {\r
-\r
- try {\r
- FileInputStream fio = new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
- assertNotNull(fio);\r
- List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
- assertNotNull(fseqs);\r
- assertEquals(3, fseqs.size());\r
- assertEquals(3, fseqs.size());\r
- fio.close();\r
- FileOutputStream fou = new FileOutputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
- SequenceUtil.writeFasta(fou, fseqs);\r
- fou.close();\r
- FileOutputStream fou20 = new FileOutputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
- SequenceUtil.writeFasta(fou20, fseqs, 20);\r
- fou20.close();\r
-\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
+ }\r
\r
}\r