fixing biojava#280 parser now can dealing with multiple "residueDetail" values.

andreasprlic · andreasprlic · commit b6bb812d783f · 2015-06-15T20:47:19.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java
@@ -26,6 +26,7 @@
 
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
+import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
@@ -199,9 +200,9 @@ private SiftsResidue getResidue(Element residue) {
 			
 			boolean observed = true;
 			
-			String detail = getTextValue(residue, "residueDetail");
-			//System.out.println(">"+detail+"<");
-			if ( detail != null && detail.trim().equalsIgnoreCase("Not_Observed")){
+			List<String> details = getTextValues(residue, "residueDetail");
+
+			if ( details != null && details.contains("Not_Observed")){
 				observed = false;
 			}
 			res.setNotObserved(! observed);
@@ -258,6 +259,25 @@ private String getTextValue(Element ele, String tagName) {
 			return textVal;
 		}
 
+	private List<String> getTextValues(Element ele, String tagName) {
+		List<String>values = new ArrayList<String>();
+		NodeList nl = ele.getElementsByTagName(tagName);
+		if(nl != null && nl.getLength() > 0) {
+			for ( int i = 0 ;i < nl.getLength() ; i ++) {
+
+				Element n = (Element) nl.item(i);
+
+				String k = n.getNodeName();
+
+				String val = n.getFirstChild().getNodeValue();
+				if ( val != null)
+					values.add(val);
+			}
+		}
+
+		return values;
+	}
+
 
 		
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
@@ -34,6 +34,49 @@
 
 public class TestSiftsParsing extends TestCase {
 
+
+	public void test4DIA(){
+		try {
+			List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("4DIA");
+
+			assertNotNull(entities);
+
+			assertTrue(entities.size() == 1);
+
+			for (SiftsEntity e : entities){
+				//System.out.println(e.getEntityId() + " " +e.getType());
+
+
+				assertTrue(e.getSegments().size() > 0 );
+				for ( SiftsSegment seg: e.getSegments()) {
+					assertTrue(seg.getResidues().size() > 0);
+					
+					for ( SiftsResidue res: seg.getResidues() ) {
+
+						if ( res.getUniProtResName() != null ) {
+							assertNotNull(res.getUniProtAccessionId() );
+							assertNotNull(res.getUniProtResName());
+
+							// test for github ticket #280
+							if ( res.getUniProtPos() == 129) {
+
+								assertTrue(res.getNotObserved());
+							}
+
+						}
+					}
+				}
+
+			}
+
+		} catch (Exception e){
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
+
+
+	}
+
 	public void test4jn3(){
 		try {
 			List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("4jn3");
