Fixed modfinder tests

josemduarte · josemduarte · commit 8459e6f5ff58 · 2016-05-10T21:51:33.000-07:00
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
@@ -272,7 +272,7 @@ public void identify(final List<Chain> chains,
 		Map<Component, Set<Group>> mapCompGroups = new HashMap<Component, Set<Group>>();
 
 		for (Chain chain : chains) {
-			mapChainIdChain.put(chain.getChainID(), chain);
+			mapChainIdChain.put(chain.getName(), chain);
 
 			List<Group> ress = StructureUtil.getAminoAcids(chain);
 
@@ -288,7 +288,7 @@ public void identify(final List<Chain> chains,
 		if (residues.isEmpty()) {
 			String pdbId = "?";
 			if ( chains.size() > 0) {
-				Structure struc = chains.get(0).getParent();
+				Structure struc = chains.get(0).getStructure();
 				if ( struc != null)
 					pdbId = struc.getPDBCode();
 			}
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -291,15 +291,11 @@ public void testParser() throws IOException, StructureException {
 		multiTest();
 	}
 
-	public void multiTest() {
+	public void multiTest() throws IOException, StructureException {
 		for ( String[] name : strucs){
-			try {
-//				parserTest(name[0], (String)null);
-				parserTest(name[0], name[1]);
-			} catch (Exception e){
-				logger.error("Exception: ", e);
-				fail(e.getMessage());
-			}
+			parserTest(name[0], (String)null);
+			parserTest(name[0], name[1]);
+
 		}
 	}
 

Original file line number	Diff line number	Diff line change
`@@ -291,15 +291,11 @@ public void testParser() throws IOException, StructureException {`
`291`	`291`	`multiTest();`
`292`	`292`	`}`
`293`	`293`
`294`		`- public void multiTest() {`
	`294`	`+ public void multiTest() throws IOException, StructureException {`
`295`	`295`	`for ( String[] name : strucs){`
`296`		`- try {`
`297`		`-// parserTest(name[0], (String)null);`
`298`		`- parserTest(name[0], name[1]);`
`299`		`- } catch (Exception e){`
`300`		`- logger.error("Exception: ", e);`
`301`		`- fail(e.getMessage());`
`302`		`- }`
	`296`	`+ parserTest(name[0], (String)null);`
	`297`	`+ parserTest(name[0], name[1]);`
	`298`	`+`
`303`	`299`	`}`
`304`	`300`	`}`
`305`	`301`