Add testing dirs

[proteocache.git] / testsrc / compbio / data / sequence / FastaReaderTester.java

diff --git a/testsrc/compbio/data/sequence/FastaReaderTester.java b/testsrc/compbio/data/sequence/FastaReaderTester.java
new file mode 100644 (file)
index 0000000..3a3b747
--- /dev/null
+++ b/testsrc/compbio/data/sequence/FastaReaderTester.java
@@ -0,0 +1,77 @@
+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