Remove Annotated and MuptiAnnotated Sequence use Score instead

[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 f526578..1460b52 100644 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -26,6 +26,8 @@ import java.io.IOException;
 import java.io.InputStream;\r
 import java.util.HashSet;\r
 import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
 \r
 import org.testng.annotations.Test;\r
 \r
@@ -118,15 +120,14 @@ public class SequenceUtilTester {
                FileInputStream fio;\r
                try {\r
                        fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
-                       List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);\r
+                       Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
                        assertNotNull(aseqs);\r
                        assertEquals(aseqs.size(), 3);\r
-                       AnnotatedSequence aseq = aseqs.get(0);\r
+                       Score aseq = aseqs.get(0);\r
                        assertNotNull(aseq);\r
-                       assertNotNull(aseq.getAnnotation());\r
+                       assertNotNull(aseq.getScores());\r
                        // System.out.println(aseq);\r
-                       assertEquals(aseq.getAnnotation().length, aseq.getSequence()\r
-                                       .length());\r
+                       assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
                        fio.close();\r
                } catch (FileNotFoundException e) {\r
                        e.printStackTrace();\r
@@ -156,7 +157,7 @@ public class SequenceUtilTester {
                try {\r
                        fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
                                        + "disembl.out");\r
-                       List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil\r
+                       Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
                                        .readDisembl(fio);\r
                        assertNotNull(aseqs);\r
 \r