Allow non-refined result, only self-alignment

lafita · lafita · commit 6beb84973b80 · 2015-08-04T10:17:50.000+02:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java b/biojava-structure-gui/src/main/java/demo/DemoCeSymm.java
@@ -73,7 +73,7 @@ public static void main(String[] args)
 		params.setMultipleAxes(true);
 
 		//Run the alignment
-		MultipleAlignment symmetry = ceSymm.align(atoms);
+		MultipleAlignment symmetry = ceSymm.align(atoms, params);
 
 		//Display the results in jmol
 		SymmetryDisplay.display(symmetry, ceSymm.getSymmetryAxes());
diff --git a/biojava-structure/src/main/java/demo/DemoCeSymm.java b/biojava-structure/src/main/java/demo/DemoCeSymm.java
@@ -73,7 +73,7 @@ public static void main(String[] args)
 		params.setMultipleAxes(true);
 
 		//Run the alignment
-		MultipleAlignment symmetry = ceSymm.align(atoms);
+		MultipleAlignment symmetry = ceSymm.align(atoms, params);
 
 		//Display the results in FatCat format
 		System.out.println(MultipleAlignmentWriter.toFatCat(symmetry));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -360,8 +360,11 @@ public AFPChain align(Atom[] ca10, Atom[] ca2O, Object param)
 		} catch (OrderDetectionFailedException e) {
 			e.printStackTrace();
 		}
-
-		//STEP 3: symmetry refinement, apply consistency in the subunit residues
+		
+		if (params.getRefineMethod() == RefineMethod.NOT_REFINED) 
+			return afpChain;
+		
+		//STEP 3: symmetry refinement, apply consistency in the subunit residues		
 		Refiner refiner = null;
 		try {
 			switch (type){
