Embl Changes

NoorAldeenMB · NoorAldeenMB · commit d24230a23526 · 2017-12-03T17:05:37.000+02:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblReader.java
@@ -92,6 +92,7 @@ else if (lineIdentifier.equals("//")) {
                           emblRecord.setKeyword(keyword);
                           emblRecord.setEmblReference(emblReference);
                           emblRecord.setAccessionNumber(accessionNumber);
+                          emblRecord.setSequence(sequence.toString());
                     }
 
                 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/embl/EmblReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/embl/EmblReaderTest.java
@@ -1,5 +1,6 @@
 package org.biojava.nbio.core.sequence.io.embl;
 
+import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -13,24 +14,31 @@
  */
 public class EmblReaderTest {
 
-    private EmblReader emblReader;
-
-    @Before
-    public void setUp() {
-        emblReader = new EmblReader();
-    }
 
     @Test(expected = NullPointerException.class)
     public void givenNullFileParameterWhenProcessEmblFileThenThrowException() throws IOException {
         File file = null;
-        emblReader.process(file);
+        EmblReader.process(file);
 
     }
 
     @Test(expected = IllegalArgumentException.class)
     public void givenDirectoryWhenProcessEmblFileThenThrowException() throws IOException {
         File file = new File("./src/test/resources");
-        emblReader.process(file);
+        EmblReader.process(file);
+    }
+
+    @Test
+    public void givenAnEmilFileWhenProcessEmilFileThanTheSequenceShouldReturnAsExpected() throws IOException {
+        File file = new File("./src/test/resources/test.embl");
+        EmblRecord emblRecord = EmblReader.process(file);
+        Assert.assertEquals("acaagatgccattgtcccccggcctcctgctgctg" +
+                "ctgctctccggggccacggccaccgctgccctgcccctggagggtggccccaccggcc" +
+                "gagacagcgagcatatgcaggaagcggcaggaataaggaaaagcagcctcctgactttcc" +
+                "tcgcttggtggtttgagtggacctcccaggccagtgccgggcccctcataggagaggaagc" +
+                "tcgggaggtggccaggcggcaggaaggcgcacccccccagcaatccgcgcgccgggacagaa" +
+                "tgccctgcaggaacttcttctggaagaccttctcctcctgcaaataaaacctcacccatgaatgc" +
+                "tcacgcaagtttaattacagacctgaa",emblRecord.getSequence());
     }
 
 

Original file line number	Diff line number	Diff line change
`@@ -92,6 +92,7 @@ else if (lineIdentifier.equals("//")) {`
`92`	`92`	`emblRecord.setKeyword(keyword);`
`93`	`93`	`emblRecord.setEmblReference(emblReference);`
`94`	`94`	`emblRecord.setAccessionNumber(accessionNumber);`
	`95`	`+ emblRecord.setSequence(sequence.toString());`
`95`	`96`	`}`
`96`	`97`
`97`	`98`	`}`