Merge pull request #794 from biocryst/stoichiometry

josemduarte · web-flow · commit 2bb08570f8a7 · 2018-08-24T11:15:23.000-07:00
Biological assembly builder, transformation ordering fix
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java
@@ -145,12 +145,11 @@ public void test4OPJ() throws IOException, StructureException {
 		assertEquals(3, multiModelBioAssemblies.get(0).getPolyChains(0).size() + multiModelBioAssemblies.get(0).getPolyChains(1).size());
 		// 3 chains in flattened structure in bioassembly 1
 		assertEquals(3, flattenedBioAssemblies.get(0).getPolyChains().size());
-		
+
 		// 3 chains divided into 2 models in bioassembly 2
-		assertEquals(3, multiModelBioAssemblies.get(1).getPolyChains(0).size() + multiModelBioAssemblies.get(0).getPolyChains(1).size());
+		assertEquals(3, multiModelBioAssemblies.get(1).getPolyChains(0).size() + multiModelBioAssemblies.get(1).getPolyChains(1).size());
 		// 3 chains in flattened structure in bioassembly 2
 		assertEquals(3, flattenedBioAssemblies.get(1).getPolyChains().size());
-		
 
 		// chain ids and names don't contain underscores in multimodel
 		for (int modelIdx = 0; modelIdx<multiModelBioAssemblies.get(0).nrModels(); modelIdx++) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -144,8 +144,9 @@ public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransf
 				// set sort order only if the two ids are identical
 				if (t1.getId().equals(t2.getId())) {
 					 return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());
+				} else {
+					return t1.getId().compareTo(t2.getId());
 				}
-			    return 0;
 		    }
 		});
 	}

Original file line number	Diff line number	Diff line change
`@@ -144,8 +144,9 @@ public int compare(BiologicalAssemblyTransformation t1, BiologicalAssemblyTransf`
`144`	`144`	`// set sort order only if the two ids are identical`
`145`	`145`	`if (t1.getId().equals(t2.getId())) {`
`146`	`146`	`return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());`
	`147`	`+ } else {`
	`148`	`+ return t1.getId().compareTo(t2.getId());`
`147`	`149`	`}`
`148`		`- return 0;`
`149`	`150`	`}`
`150`	`151`	`});`
`151`	`152`	`}`