Fix integration tests (biojava#128), which I broke in 3c7315e

sbliven · sbliven · commit 21ac29ae7583 · 2014-05-13T19:22:43.000+02:00
- We now allow '_' as a synonym for chain 'A' (needed in old files), so
  the test specifically disallowing this was failing.
- I changed it to check for an actual missing chain
- BerkeleyScop has slightly different comments than MRC scop, and the
  test cases are inflexible.
diff --git a/integrationtest/src/test/java/org/biojava/structure/test/StructureToolsTest.java b/integrationtest/src/test/java/org/biojava/structure/test/StructureToolsTest.java
@@ -172,17 +172,27 @@ public void testGetSubRanges() throws StructureException {
 		range = "-";
 		substr = StructureTools.getSubRanges(structure2, range);
 		assertEquals("Should have gotten whole structure",structure2, substr);
-		
+
 		// Test single-chain syntax
 		range = "_:";
 		substr = StructureTools.getSubRanges(structure, range);
 		assertEquals("Wrong number of chains in "+range, 1, substr.size());
-		
+
 		chain = substr.getChain(0);
 		assertEquals("Did not find the expected number of residues in first chain of "+range, 123, chain.getAtomLength() );
+
+		// Test single-chain syntax in a multi-chain structure. Should give chain A.
+		range = "_:";
+		substr = StructureTools.getSubRanges(structure2, range);
+		assertEquals("Wrong number of chains in "+range, 1, substr.size());
+		
+		chain = substr.getChain(0);
+		assertEquals("Chain _ not converted to chain A.","A",chain.getChainID());
+		assertEquals("Did not find the expected number of residues in first chain of "+range, 411, chain.getAtomLength() );
 		
 		try {
-			range = "_:";
+			// Illegal chain name
+			range = "X:";
 			substr = StructureTools.getSubRanges(structure2, range);
 			fail("Illegal chain name in '"+range+"'. Should throw StructureException");
 		} catch(StructureException ex) {} //expected 
diff --git a/integrationtest/src/test/java/org/biojava/structure/test/scop/ScopDatabaseTest.java b/integrationtest/src/test/java/org/biojava/structure/test/scop/ScopDatabaseTest.java
@@ -208,7 +208,8 @@ public void testComments() {
             assertEquals(tag+"Wrong number of comments", 1, comments.size());
             assertEquals(tag+"Wrong comment", "complexed with cmo, hem", comments.get(0).trim());
         }
-        if(scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_75) >= 0 ) {
+        if(scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_73) >= 0 &&
+        		scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_75) <= 0) {
             // Note: only tested so far with 1.75, so may need some modification for earlier versions
 
             comments = scop.getComments(127355);

Original file line number	Diff line number	Diff line change
`@@ -208,7 +208,8 @@ public void testComments() {`
`208`	`208`	`assertEquals(tag+"Wrong number of comments", 1, comments.size());`
`209`	`209`	`assertEquals(tag+"Wrong comment", "complexed with cmo, hem", comments.get(0).trim());`
`210`	`210`	`}`
`211`		`- if(scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_75) >= 0 ) {`
	`211`	`+ if(scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_73) >= 0 &&`
	`212`	`+ scop.getScopVersion().compareToIgnoreCase( ScopFactory.VERSION_1_75) <= 0) {`
`212`	`213`	`// Note: only tested so far with 1.75, so may need some modification for earlier versions`
`213`	`214`
`214`	`215`	`comments = scop.getComments(127355);`