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Add JRonn runner, tester, methods to parse jronn output files.
[jabaws.git] / testsrc / compbio / data / sequence / SequenceUtilTester.java
diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index 3dd09ef..f2af670 100644 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -36,80 +36,112 @@ import compbio.metadata.AllTestSuit;
 \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