+++ /dev/null
-package compbio.data.sequence;\r
-\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class FastaReaderTester {\r
-\r
- static FastaSequence s0 = new FastaSequence(\r
- "zedpshvyzg",\r
- "GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD");\r
-\r
- static FastaSequence s1 = new FastaSequence(\r
- "xovkactesa",\r
- "CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM"\r
- + "FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG"\r
- + "FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH"\r
- + "DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC");\r
- static FastaSequence s2 = new FastaSequence(\r
- "ntazzewyvv",\r
- "CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD"\r
- + "EASINM AQQWRSLPPSRIMKLNG HGCDCMHSHMEAD DTKQSGIKGTFWNG HDAQWLCRWG"\r
- + "EFITEA WWGRWGAITFFHAH ENKNEIQECSDQNLKE SRTTCEIID TCHLFTRHLDGW"\r
- + " RCEKCQANATHMTW ACTKSCAEQW FCAKELMMN "\r
- + "W KQMGWRCKIFRKLFRDNCWID FELPWWPICFCCKGLSTKSHSAHDGDQCRRW WPDCARDWLGPGIRGEF "\r
- + "FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI");\r
- static FastaSequence s3 = new FastaSequence(" 12 d t y wi k jbke ",\r
- " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"\r
- + " CCDQCQSWEAENWCASMRKAILF");\r
- static FastaSequence s4 = new FastaSequence(" 12 d t>y wi->foo k jbke ",\r
- " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"\r
- + " CCDQCQSWEAENWCASMRKAILF");\r
- @Test()\r
- public void test() {\r
-\r
- List<FastaSequence> old_seqs = null;\r
- final List<FastaSequence> list = new ArrayList<FastaSequence>();\r
- try {\r
- old_seqs = SequenceUtil.readFasta(new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "complicated.fasta"));\r
- final FastaReader fr = new FastaReader(AllTestSuit.TEST_DATA_PATH\r
- + "complicated.fasta");\r
-\r
- while (fr.hasNext()) {\r
- final FastaSequence fs = fr.next();\r
- list.add(fs);\r
- }\r
- } catch (final FileNotFoundException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- } catch (final IOException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- }\r
- System.out.println("OLD: " + old_seqs);\r
- System.out.println("NEW: " + list);\r
- Assert.assertEquals(old_seqs.size(), list.size());\r
- Assert.assertEquals(old_seqs.get(0), list.get(0));\r
- Assert.assertEquals(old_seqs.get(1), list.get(1));\r
- // Assert.assertEquals(old_seqs.get(2), list.get(2));\r
- // Assert.assertEquals(seqs.get(3), list.get(3));\r
-\r
- Assert.assertEquals(FastaReaderTester.s0, list.get(0));\r
- Assert.assertEquals(FastaReaderTester.s1, list.get(1));\r
- Assert.assertEquals(FastaReaderTester.s2, list.get(2));\r
- Assert.assertEquals(FastaReaderTester.s3, list.get(3));\r
- Assert.assertEquals(FastaReaderTester.s4, list.get(4));\r
-\r
- }\r
-}\r