1 package compbio.data.sequence;
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3 import java.io.FileInputStream;
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4 import java.io.FileNotFoundException;
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5 import java.io.IOException;
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6 import java.util.ArrayList;
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7 import java.util.List;
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9 import org.testng.Assert;
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10 import org.testng.annotations.Test;
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12 import compbio.metadata.AllTestSuit;
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14 public class FastaReaderTester {
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16 static FastaSequence s0 = new FastaSequence(
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18 "GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD");
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20 static FastaSequence s1 = new FastaSequence(
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22 "CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM"
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23 + "FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG"
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24 + "FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH"
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25 + "DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC");
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26 static FastaSequence s2 = new FastaSequence(
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28 "CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD"
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29 + "EASINM AQQWRSLPPSRIMKLNG HGCDCMHSHMEAD DTKQSGIKGTFWNG HDAQWLCRWG"
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30 + "EFITEA WWGRWGAITFFHAH ENKNEIQECSDQNLKE SRTTCEIID TCHLFTRHLDGW"
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31 + " RCEKCQANATHMTW ACTKSCAEQW FCAKELMMN "
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32 + "W KQMGWRCKIFRKLFRDNCWID FELPWWPICFCCKGLSTKSHSAHDGDQCRRW WPDCARDWLGPGIRGEF "
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33 + "FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI");
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34 static FastaSequence s3 = new FastaSequence(" 12 d t y wi k jbke ",
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35 " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"
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36 + " CCDQCQSWEAENWCASMRKAILF");
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37 static FastaSequence s4 = new FastaSequence(" 12 d t>y wi->foo k jbke ",
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38 " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"
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39 + " CCDQCQSWEAENWCASMRKAILF");
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41 public void test() {
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43 List<FastaSequence> old_seqs = null;
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44 final List<FastaSequence> list = new ArrayList<FastaSequence>();
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46 old_seqs = SequenceUtil.readFasta(new FileInputStream(
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47 AllTestSuit.TEST_DATA_PATH + "complicated.fasta"));
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48 final FastaReader fr = new FastaReader(AllTestSuit.TEST_DATA_PATH
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49 + "complicated.fasta");
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51 while (fr.hasNext()) {
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52 final FastaSequence fs = fr.next();
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55 } catch (final FileNotFoundException e) {
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56 e.printStackTrace();
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57 Assert.fail(e.getLocalizedMessage());
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58 } catch (final IOException e) {
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59 e.printStackTrace();
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60 Assert.fail(e.getLocalizedMessage());
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62 System.out.println("OLD: " + old_seqs);
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63 System.out.println("NEW: " + list);
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64 Assert.assertEquals(old_seqs.size(), list.size());
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65 Assert.assertEquals(old_seqs.get(0), list.get(0));
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66 Assert.assertEquals(old_seqs.get(1), list.get(1));
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67 // Assert.assertEquals(old_seqs.get(2), list.get(2));
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68 // Assert.assertEquals(seqs.get(3), list.get(3));
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70 Assert.assertEquals(FastaReaderTester.s0, list.get(0));
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71 Assert.assertEquals(FastaReaderTester.s1, list.get(1));
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72 Assert.assertEquals(FastaReaderTester.s2, list.get(2));
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73 Assert.assertEquals(FastaReaderTester.s3, list.get(3));
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74 Assert.assertEquals(FastaReaderTester.s4, list.get(4));
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