More work to disorder prediction client & services.

[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 b6e74ae..7db01ee 100644 (file)
--- a/testsrc/compbio/data/sequence/SequenceUtilTester.java
+++ b/testsrc/compbio/data/sequence/SequenceUtilTester.java
@@ -24,6 +24,7 @@ import java.io.FileNotFoundException;
 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
@@ -83,6 +84,31 @@ public class SequenceUtilTester {
        }\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
@@ -168,7 +194,8 @@ public class SequenceUtilTester {
                        Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
                        assertNotNull(aseqs);\r
                        assertEquals(aseqs.size(), 3);\r
-                       // System.out.println(aseqs);\r
+                       ScoreManager sman = ScoreManager.newInstance(aseqs);\r
+\r
                        for (String fs : aseqs.keySet()) {\r
                                assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
                                                .contains(fs));\r
@@ -230,6 +257,10 @@ public class SequenceUtilTester {
                                }\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