Added List<String> of comments with getter and setter into AbstractSequence.java;

jimty0511 · jimty0511 · commit 6fa0df9af72c · 2017-06-02T16:25:28.000-04:00
Added setComments into parseHeader() method in GenericGenbankHeaderParser.java;
Add new assert statement in GenbankReaderTest to check the comments
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -52,6 +52,7 @@ public void parseHeader(String header, S sequence) {
 		sequence.setOriginalHeader(header);
 		sequence.setAccession(new AccessionID(accession, DataSource.GENBANK, version, identifier));
 		sequence.setDescription(description);
+		sequence.setComments(comments);
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -73,6 +73,7 @@ public abstract class AbstractSequence<C extends Compound> implements Sequence<C
 			new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
 	private LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>> groupedFeatures =
 			new LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>>();
+	private List<String> comments = new ArrayList<>();
 
 	public AbstractSequence() {
 	}
@@ -427,6 +428,22 @@ public List<FeatureInterface<AbstractSequence<C>, C>> getFeaturesByType(String t
 		return features;
 	}
 
+	/**
+	 *
+	 * @return comments
+	 */
+	public List<String> getComments() {
+		return comments;
+	}
+
+	/**
+	 * Set comments.
+	 * @param comments
+	 */
+	public void setComments(List<String> comments) {
+		this.comments = comments;
+	}
+
 	/**
 	 * @return the featuresKeyWord
 	 */
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -46,6 +46,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.*;
 
 /**
@@ -96,6 +97,19 @@ public void testProcess() throws Exception {
 
 		LinkedHashMap<String, ProteinSequence> proteinSequences = genbankProtein.process();
 
+		assertThat(proteinSequences.get("NP_000257").getComments().get(0),is(
+				"VALIDATED REFSEQ: This record has undergone validation or\n" +
+				"preliminary review. The reference sequence was derived from\n" +
+				"AL034370.1, X65882.1 and BE139596.1.\n" +
+				"Summary: NDP is the genetic locus identified as harboring mutations\n" +
+				"that result in Norrie disease. Norrie disease is a rare genetic\n" +
+				"disorder characterized by bilateral congenital blindness that is\n" +
+				"caused by a vascularized mass behind each lens due to a\n" +
+				"maldeveloped retina (pseudoglioma).\n" +
+				"Publication Note:  This RefSeq record includes a subset of the\n" +
+				"publications that are available for this gene. Please see the\n" +
+				"Entrez Gene record to access additional publications."));
+
 		assertNotNull(proteinSequences);
 		assertEquals(1, proteinSequences.size());
 

Original file line number	Diff line number	Diff line change
`@@ -52,6 +52,7 @@ public void parseHeader(String header, S sequence) {`
`52`	`52`	`sequence.setOriginalHeader(header);`
`53`	`53`	`sequence.setAccession(new AccessionID(accession, DataSource.GENBANK, version, identifier));`
`54`	`54`	`sequence.setDescription(description);`
	`55`	`+ sequence.setComments(comments);`
`55`	`56`	`}`
`56`	`57`
`57`	`58`	`/**`