Test parsing dates from PDB format

lafita · lafita · commit a145f9c62885 · 2017-06-29T22:06:46.000-07:00
biojava#677
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
@@ -32,6 +32,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
+import java.util.Calendar;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
@@ -50,6 +51,12 @@
 import org.junit.Before;
 import org.junit.Test;
 
+/**
+ * Test the {@link PDBFileParser}.
+ * 
+ * @author Aleix Lafita
+ *
+ */
 public class PDBFileParserTest {
 
 	private static PDBFileParser parser;
@@ -555,8 +562,6 @@ public void testCorrectAtomNamePadding() throws IOException {
 	
 	/**
 	 * Test handling of missing Element column. Issue 537 in github.
-	 * @author Aleix Lafita
-	 * @throws IOException 
 	 */
 	@Test
 	public void testMissingElements() throws IOException {
@@ -627,4 +632,28 @@ public void testMissingElements() throws IOException {
 		assertTrue("the Element column has not been filled correctly", pdb.equals(original));
 		
 	}
+	
+	/**
+	 * Test the parsing of release and last modified dates.
+	 */
+	@Test
+	public void testDates() throws IOException {
+		
+		String revisionDates = 
+		"REVDAT   5   13-JUL-11 1STP    1       VERSN                                    "+newline+
+		"REVDAT   4   24-FEB-09 1STP    1       VERSN                                    " + newline+
+		"REVDAT   3   01-APR-03 1STP    1       JRNL                                     " + newline+
+		"REVDAT   2   15-OCT-94 1STP    1       AUTHOR                                   " + newline+
+		"REVDAT   1   15-OCT-92 1STP    0                                                " + newline;
+	
+		BufferedReader br = new BufferedReader(new StringReader(revisionDates));
+		Structure s = parser.parsePDBFile(br);
+		
+		// The latest modified date should be 2011
+		assertEquals(s.getPDBHeader().getModDate().getYear() + 1900, 2011);
+		
+		// The release date should be 1992
+		assertEquals(s.getPDBHeader().getRelDate().getYear() + 1900, 1992);
+	
+	}
 }
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/StructureIOTest.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure.test.io;
 
-
 import static org.junit.Assert.*;
 
 import java.io.IOException;
@@ -29,15 +28,16 @@
 import org.biojava.nbio.structure.StructureIO;
 import org.junit.Test;
 
-
-
+/**
+ * Test StructureIO methods.
+ * 
+ */
 public class StructureIOTest {
 	
 	@Test
 	public void testStructureIO() throws IOException, StructureException {
 
 		String pdbId = "1gav";
-
 		int nrAssembls = StructureIO.getBiologicalAssemblies(pdbId).size();
 		assertEquals(1,nrAssembls);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -672,31 +672,32 @@ private void pdb_TURN_Handler( String line){
 	 */
 	private void pdb_REVDAT_Handler(String line) {
 
-		// keep the first as release date and the last as modification date
-		Date relDate = pdbHeader.getRelDate();
+		// keep the first as latest modified date and the last as release date
+		Date modDate = pdbHeader.getModDate();
 
-		if ( relDate == null || relDate.equals(new Date(0)) ) {
+		if ( modDate == null || modDate.equals(new Date(0)) ) {
 			
-			// release date is still uninitialized
-			String releaseDate = line.substring (13, 22).trim() ;
+			// modified date is still uninitialized
+			String modificationDate = line.substring (13, 22).trim() ;
 
 			try {
-				Date dep = dateFormat.parse(releaseDate);
+				Date dep = dateFormat.parse(modificationDate);
 				pdbHeader.setModDate(dep);
+				pdbHeader.setRelDate(dep);
 			} catch (ParseException e){
-				logger.info("Could not parse modification date string '"+releaseDate+"'. Will continue without modification date");
+				logger.info("Could not parse revision date string '"+modificationDate+"'. ");
 			}
 
 		} else {
 			
-			// set as the latest modification date
-			String modificationDate = line.substring (13, 22).trim() ;
+			// set as the release date
+			String releaseDate = line.substring (13, 22).trim() ;
 
 			try {
-				Date dep = dateFormat.parse(modificationDate);
-				pdbHeader.setModDate(dep);
+				Date dep = dateFormat.parse(releaseDate);
+				pdbHeader.setRelDate(dep);
 			} catch (ParseException e){
-				logger.info("Could not parse modification date string '"+modificationDate+"'. Will continue without modification date");
+				logger.info("Could not parse revision date string '"+releaseDate+"'. ");
 			}
 		}
 	}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseHeader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseHeader.java
@@ -12,7 +12,7 @@
 import org.junit.Test;
 
 /**
- * A class to test the parsing of R-work from files
+ * Test the parsing header informationof R-work from files
  * @author Anthony Bradley
  *
  */

Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,7 @@`
`12`	`12`	`import org.junit.Test;`
`13`	`13`
`14`	`14`	`/**`
`15`		`- * A class to test the parsing of R-work from files`
	`15`	`+ * Test the parsing header informationof R-work from files`
`16`	`16`	`* @author Anthony Bradley`
`17`	`17`	`*`
`18`	`18`	`*/`