import static org.testng.AssertJUnit.assertTrue;\r
import static org.testng.AssertJUnit.fail;\r
\r
+import java.io.File;\r
import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.InputStream;\r
+import java.io.PrintWriter;\r
+import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
import java.util.Map;\r
import org.testng.annotations.Test;\r
\r
import compbio.metadata.AllTestSuit;\r
+import compbio.runner.disorder.Disembl;\r
\r
public class SequenceUtilTester {\r
\r
}\r
\r
@Test()\r
+ public void testCleanProteinSequence() {\r
+ String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
+ assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
+ // This will still be NON protein sequence despite having only correct\r
+ // letters because the letters match perfectly the nucleotide sequence!\r
+ assertFalse(SequenceUtil.isProteinSequence(SequenceUtil\r
+ .cleanProteinSequence(dirtySeq)));\r
+\r
+ String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
+ assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
+ .cleanProteinSequence(notaSeq)));\r
+\r
+ String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
+ assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
+ .cleanProteinSequence(AAseq)));\r
+ AAseq += "XU";\r
+\r
+ assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
+ .cleanProteinSequence(AAseq)));\r
+ }\r
+\r
+ @Test()\r
public void testReadWriteFasta() {\r
\r
try {\r
Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
assertNotNull(aseqs);\r
assertEquals(aseqs.size(), 3);\r
- Score aseq = aseqs.get(0);\r
+ Score aseq = aseqs.get("Foobar");\r
assertNotNull(aseq);\r
assertNotNull(aseq.getScores());\r
// System.out.println(aseq);\r
\r
/**\r
* This test tests the loading of horizontally formatted Jronn output file\r
+ * \r
+ * First seq\r
+ * \r
+ * M 0.86010 0.88512 0.37094\r
+ * \r
+ * T 0.79983 0.85864 0.44331\r
+ * \r
*/\r
@SuppressWarnings("unchecked")\r
@Test\r
- public void testMultiAnnotatedSequence() {\r
+ public void testReadDisemblResults() {\r
+\r
\r
+ Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
+ Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
+ Map<String,Map<String, Float>> _values=new HashMap<String, Map<String,Float>>();\r
+ Map<String, Float> values = new HashMap<String, Float>();\r
+ Set<Range> rset;\r
+ rset = new HashSet<Range>();\r
+ for (String[] se:new String[][] { { "34","41"},{"50","58"},{"83","91"},{"118","127"},{" 160","169"},{" 191","220"},{" 243","252"},{" 287","343"},{" 350","391"},{" 429","485"},{" 497","506"},{"539","547"}})\r
+ {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.COILS.toString(), rset);\r
+ values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
+ rset = new HashSet<Range>();\r
+ for (String[] se:new String[][] { { "355","368"}})\r
+ {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.REM465.toString(), rset);\r
+ values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
+ rset = new HashSet<Range>();\r
+ for (String[] se:new String[][] { { "190","204"}})\r
+ {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
+ values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
+ _ranges.put("Foobar_dundeefriends", ranges);\r
+ _values.put("Foobar_dundeefriends", values);\r
FileInputStream fio;\r
try {\r
fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ "disembl.out");\r
- Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
- .readDisembl(fio);\r
+ Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
assertNotNull(aseqs);\r
+ assertEquals(aseqs.size(), 3);\r
+ ScoreManager sman = ScoreManager.newInstance(aseqs);\r
\r
- /*\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
+ for (String fs : aseqs.keySet()) {\r
+ assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
+ .contains(fs));\r
+ Set<Score> scores = aseqs.get(fs);\r
+ assertEquals(scores.size(), 3);\r
+ for (Score sc:scores) {\r
+ if (_ranges.containsKey(fs))\r
+ {\r
+ assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
+ assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
+ }\r
+ }\r
+ }\r
fio.close();\r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
}\r
+ /**\r
+ * This test tests the loading of horizontally formatted Jronn output file\r
+ * \r
+ * First sequence:\r
+ * \r
+ * >Foobar_dundeefriends\r
+ * \r
+ * # GlobDoms 2-358, 373-568\r
+ * \r
+ * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
+ * \r
+ * # RESIDUE DYDX RAW SMOOTHED\r
+ * \r
+ * M 0.0044 -0.2259 -0.2259\r
+ * \r
+ * T -0.1308 -0.2170 -0.2170\r
+ * \r
+ * ............\r
+ * \r
+ * > Second sequence\r
+ */\r
+ @SuppressWarnings("unchecked")\r
+ @Test\r
+ public void testReadGlobPlotResults() {\r
+\r
+ FileInputStream fio;\r
+ try {\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ + "globplot.out");\r
+ HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
+ assertNotNull(aseqs);\r
+ assertEquals(aseqs.size(), 3);\r
+\r
+ String fsdf = null;\r
+ Set<Score> scores = null;\r
+ for (String fs : aseqs.keySet()) {\r
+ if ("Foobar_dundeefriends".contains(fs)) {\r
+ fsdf = fs;\r
+ scores = aseqs.get(fs);\r
+ }\r
+ assertEquals(scores.size(), 5);\r
+ }\r
+\r
+ ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
+ sm.writeOut(new PrintWriter(System.out, true));\r
+\r
+ for (Score score : scores) {\r
\r
+ if (score.getMethod()\r
+ .equals(GlobProtResult.Disorder.toString())) {\r
+ assertEquals(score.getRanges().size(), 7);\r
+ assertTrue(score.getScores().isEmpty());\r
+ }\r
+ if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
+ assertFalse(score.getScores().isEmpty());\r
+ assertTrue(score.getRanges().isEmpty());\r
+ }\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
+ @Test\r
+ public void testReadIUPredForShortAndLongDisorder() {\r
+ try {\r
+ Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
+ AllTestSuit.TEST_DATA_PATH, "out.long"));\r
+ ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
+ // man.writeOut(new PrintWriter(System.out, true));\r
+ assertNotNull(scores);\r
+ assertEquals(3, scores.size());\r
+\r
+ Score score = scores.get("Foobar_dundeefriends");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(568, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+\r
+ score = scores.get("Foobar");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(481, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+\r
+ score = scores.get("dundeefriends");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(513, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+\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
+ @Test\r
+ public void testReadIUPredForGlobDomain() {\r
+ try {\r
+ Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
+ AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
+ assertNotNull(scores);\r
+ assertEquals(2, scores.size());\r
+ ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
+ // man.writeOut(new PrintWriter(System.out, true));\r
+ assertEquals(2, man.getNumberOfSeq());\r
+ Score score = scores.get("P53_HUMA");\r
+ assertNotNull(score);\r
+ assertEquals(2, score.getRanges().size());\r
+ assertEquals(0, score.getScores().size());\r
+ assertEquals("Glob", score.getMethod());\r
+\r
+ score = scores.get("Foobar_dundeefriends");\r
+ assertEquals(0, score.getRanges().size());\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 testReadAAConResults() {\r
try {\r
git://source.jalview.org / jabaws.git / blobdiff