-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
+/*\r
+ * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
+ * and/or modify it under the terms of the Apache License version 2 as published\r
+ * by the Apache Software Foundation This library is distributed in the hope\r
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * Apache License for more details. A copy of the license is in\r
+ * apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
+ * derived work distributed in source code form must include this copyright and\r
+ * license notice.\r
*/\r
-\r
package compbio.data.sequence;\r
\r
import static org.testng.AssertJUnit.assertEquals;\r
\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
- }\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
+ @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
-\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
+ @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, 21);\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
+ * 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
+ }\r
+\r
+ enum Trial {\r
+ one, two, three\r
+ };\r
+\r
+ /**\r
+ * This test tests the loading of horizontally formatted Jronn output file\r
+ */\r
+ @SuppressWarnings("unchecked")\r
+ @Test\r
+ public void testMultiAnnotatedSequence() {\r
+\r
+ FileInputStream fio;\r
+ try {\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ + "disembl.out");\r
+ List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil\r
+ .readDisembl(fio);\r
+ assertNotNull(aseqs);\r
+\r
+ /*\r
+ * MultiAnnotatedSequence ma = new MultiAnnotatedSequence();\r
+ * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);\r
+ * List<Number> list = new ArrayList<Number>(); list.add(new\r
+ * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,\r
+ * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));\r
+ * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);\r
+ */\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
+ }\r
}\r
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