X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Fdata%2Fsequence%2FSequenceUtilTester.java;h=720037baa52a734b5baf94ec4654267d14394c8e;hb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;hp=3dd09efcde52c8ed7d276644682e82df6fba803d;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index 3dd09ef..720037b 100644
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -1,21 +1,16 @@
-/* Copyright (c) 2009 Peter Troshin
- *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
- * 
- *  This library is free software; you can redistribute it and/or modify it under the terms of the
- *  Apache License version 2 as published by the Apache Software Foundation
- * 
- *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
- *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
- *  License for more details.
- * 
- *  A copy of the license is in apache_license.txt. It is also available here:
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
- * 
- * Any republication or derived work distributed in source code form
- * must include this copyright and license notice.
+/*
+ * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
+ * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
+ * and/or modify it under the terms of the Apache License version 2 as published
+ * by the Apache Software Foundation This library is distributed in the hope
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * Apache License for more details. A copy of the license is in
+ * apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
+ * derived work distributed in source code form must include this copyright and
+ * license notice.
  */
-
 package compbio.data.sequence;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -100,7 +95,7 @@ public class SequenceUtilTester {
 			fou.close();
 			FileOutputStream fou20 = new FileOutputStream(
 					AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
-			SequenceUtil.writeFasta(fou20, fseqs, 20);
+			SequenceUtil.writeFasta(fou20, fseqs, 21);
 			fou20.close();
 
 		} catch (FileNotFoundException e) {
@@ -112,4 +107,76 @@ public class SequenceUtilTester {
 		}
 	}
 
+	/**
+	 * This test tests the loading of horizontally formatted Jronn output file
+	 */
+	@Test
+	public void loadJronnFile() {
+
+		FileInputStream fio;
+		try {
+			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
+			List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);
+			assertNotNull(aseqs);
+			assertEquals(aseqs.size(), 3);
+			AnnotatedSequence aseq = aseqs.get(0);
+			assertNotNull(aseq);
+			assertNotNull(aseq.getAnnotation());
+			// System.out.println(aseq);
+			assertEquals(aseq.getAnnotation().length, aseq.getSequence()
+					.length());
+			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());
+		}
+
+	}
+
+	enum Trial {
+		one, two, three
+	};
+
+	/**
+	 * This test tests the loading of horizontally formatted Jronn output file
+	 */
+	@SuppressWarnings("unchecked")
+	@Test
+	public void testMultiAnnotatedSequence() {
+
+		FileInputStream fio;
+		try {
+			fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
+					+ "disembl.out");
+			List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil
+					.readDisembl(fio);
+			assertNotNull(aseqs);
+
+			/*
+			 * MultiAnnotatedSequence ma = new MultiAnnotatedSequence();
+			 * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);
+			 * List<Number> list = new ArrayList<Number>(); list.add(new
+			 * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,
+			 * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));
+			 * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);
+			 */
+			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());
+		}
+
+	}
 }