Parser for DisEMBL results and finished runner, few test cases. DisemblTester has...

[jabaws.git] / testsrc / compbio / data / sequence / SequenceUtilTester.java

diff --git a/testsrc/compbio/data/sequence/SequenceUtilTester.java b/testsrc/compbio/data/sequence/SequenceUtilTester.java
index 82aa4a3..edb57a4 100644 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -148,27 +148,33 @@ public class SequenceUtilTester {
 \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
                FileInputStream fio;\r
                try {\r
                        fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
-                                       + "disembl.out");\r
+                                       + "scores.out");\r
                        Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
                                        .readDisembl(fio);\r
                        assertNotNull(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
-                       fio.close();\r
+                       assertEquals(aseqs.size(), 3); \r
+                       System.out.println(aseqs);\r
+                       for(FastaSequence fs: aseqs.keySet()) {\r
+                               assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));\r
+                               Set<Score> scores = aseqs.get(fs); \r
+                               assertEquals(scores.size(),3);\r
+                       }\r
+                         fio.close();\r
                } catch (FileNotFoundException e) {\r
                        e.printStackTrace();\r
                        fail(e.getLocalizedMessage());\r