Step towards supporting MMCIF version 5

lafita · lafita · commit 28a8ff379782 · 2017-06-29T22:49:29.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -1371,15 +1371,16 @@ public void newDatabasePDBrevRecord(DatabasePdbrevRecord record) {
 
 	@Override
 	public void newDatabasePDBrev(DatabasePDBrev dbrev) {
-		//System.out.println("got a database revision:" + dbrev);
+		
+		logger.debug("got a database revision:" + dbrev);
+		
 		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
 		PDBHeader header = structure.getPDBHeader();
 
 		if ( header == null) {
 			header = new PDBHeader();
 		}
 
-
 		if (dbrev.getNum().equals("1")){
 
 			try {
@@ -1391,8 +1392,8 @@ public void newDatabasePDBrev(DatabasePDBrev dbrev) {
 			}
 
 			try {
-				Date mod = dateFormat.parse(dbrev.getDate());
-				header.setModDate(mod);
+				Date rel = dateFormat.parse(dbrev.getDate());
+				header.setRelDate(rel);
 
 			} catch (ParseException e){
 				logger.warn("Could not parse date string '{}', modification date will be unavailable", dbrev.getDate());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -647,7 +647,15 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 					loopFields, lineData, loopWarnings);
 
 			triggerNewDatabasePDBrevRecord(dbrev);
+			
+		// MMCIF version 5 dates
+		} else if ( category.equals("_pdbx_database_status")){
+			// TODO
 
+		// MMCIF version 5 dates
+		} else if ( category.equals("_pdbx_audit_revision_history")){
+			// TODO
+			
 		}else if (  category.equals("_database_PDB_remark")){
 			DatabasePDBremark remark = (DatabasePDBremark) buildObject(
 					DatabasePDBremark.class.getName(),
diff --git a/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmcif/1stp_v5.cif b/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmcif/1stp_v5.cif
