X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Fdata%2Fsequence%2FSequenceUtilTester.java;h=7db01eecf1c9528bada4c93abdf988b8c1c39d4a;hb=99ab39d360a99ec101152070146b63773a1d6453;hp=edb57a49b33254009ec6c7ee5ff070adbc25cfe8;hpb=4d6083e0cf39c4989e08bdaf9384e9d44c0da607;p=jabaws.git

diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index edb57a4..7db01ee 100644
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -24,6 +24,8 @@ import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.PrintWriter;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -82,6 +84,31 @@ public class SequenceUtilTester {
 	}
 
 	@Test()
+	public void testCleanProteinSequence() {
+		String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
+		assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
+		// This will still be NON protein sequence despite having only correct
+		// letters because the letters match perfectly the nucleotide sequence!
+		assertFalse(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(dirtySeq)));
+
+		String notaSeq = "atgc1tgatgcatgcatgatgmctga";
+		assertFalse(SequenceUtil.isProteinSequence(notaSeq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(notaSeq)));
+
+		String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
+		assertTrue(SequenceUtil.isProteinSequence(AAseq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(AAseq)));
+		AAseq += "XU";
+
+		assertFalse(SequenceUtil.isProteinSequence(AAseq));
+		assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
+				.cleanProteinSequence(AAseq)));
+	}
+
+	@Test()
 	public void testReadWriteFasta() {
 
 		try {
@@ -149,11 +176,11 @@ public class SequenceUtilTester {
 	/**
 	 * This test tests the loading of horizontally formatted Jronn output file
 	 * 
-	 * First seq 
+	 * First seq
 	 * 
-	 * M	0.86010	0.88512	0.37094
+	 * M 0.86010 0.88512 0.37094
 	 * 
-	 * T	0.79983	0.85864	0.44331
+	 * T 0.79983 0.85864 0.44331
 	 * 
 	 */
 	@SuppressWarnings("unchecked")
@@ -163,18 +190,90 @@ public class SequenceUtilTester {
 		FileInputStream fio;
 		try {
 			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
-					+ "scores.out");
-			Map<FastaSequence, Set<Score>> aseqs = SequenceUtil
-					.readDisembl(fio);
+					+ "disembl.out");
+			Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);
 			assertNotNull(aseqs);
-			assertEquals(aseqs.size(), 3); 
-			System.out.println(aseqs);
-			for(FastaSequence fs: aseqs.keySet()) {
-				assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));
-				Set<Score> scores = aseqs.get(fs); 
-				assertEquals(scores.size(),3);
+			assertEquals(aseqs.size(), 3);
+			ScoreManager sman = ScoreManager.newInstance(aseqs);
+
+			for (String fs : aseqs.keySet()) {
+				assertTrue(" Foobar_dundeefriends Foobar dundeefriends "
+						.contains(fs));
+				Set<Score> scores = aseqs.get(fs);
+				assertEquals(scores.size(), 3);
 			}
-			  fio.close();
+			fio.close();
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (UnknownFileFormatException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+
+	/**
+	 * This test tests the loading of horizontally formatted Jronn output file
+	 * 
+	 * First sequence:
+	 * 
+	 * >Foobar_dundeefriends
+	 * 
+	 * # GlobDoms 2-358, 373-568
+	 * 
+	 * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481
+	 * 
+	 * # RESIDUE DYDX RAW SMOOTHED
+	 * 
+	 * M 0.0044 -0.2259 -0.2259
+	 * 
+	 * T -0.1308 -0.2170 -0.2170
+	 * 
+	 * ............
+	 * 
+	 * > Second sequence
+	 */
+	@SuppressWarnings("unchecked")
+	@Test
+	public void testReadGlobPlotResults() {
+
+		FileInputStream fio;
+		try {
+			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
+					+ "globplot.out");
+			HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);
+			assertNotNull(aseqs);
+			assertEquals(aseqs.size(), 3);
+
+			String fsdf = null;
+			Set<Score> scores = null;
+			for (String fs : aseqs.keySet()) {
+				if ("Foobar_dundeefriends".contains(fs)) {
+					fsdf = fs;
+					scores = aseqs.get(fs);
+				}
+				assertEquals(scores.size(), 5);
+			}
+
+			ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);
+			sm.writeOut(new PrintWriter(System.out, true));
+
+			for (Score score : scores) {
+
+				if (score.getMethod()
+						.equals(GlobProtResult.Disorder.toString())) {
+					assertEquals(score.getRanges().size(), 7);
+					assertTrue(score.getScores().isEmpty());
+				}
+				if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {
+					assertFalse(score.getScores().isEmpty());
+					assertTrue(score.getRanges().isEmpty());
+				}
+			}
+			fio.close();
 		} catch (FileNotFoundException e) {
 			e.printStackTrace();
 			fail(e.getLocalizedMessage());