"Fix" biojava#88. Improve documentation with a warning about getSymmetryOrder

sbliven · sbliven · commit 08340fbdbf61 · 2016-03-08T15:44:22.000+01:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -383,6 +383,12 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment, Map<Integer,
 	 * to determine the the symmetry order. For the identity alignment, sorts
 	 * the aligned residues of each protein sequentially, then defines the ith
 	 * residues of each protein to be equivalent.
+	 * 
+	 * <p>Note that the selection of the identity alignment here is <i>very</i>
+	 * naive, and only works for proteins with very good coverage. Wherever
+	 * possible, it is better to construct an identity function explicitly
+	 * from a sequence alignment (or use an {@link IdentityMap} for internally
+	 * symmetric proteins) and use {@link #getSymmetryOrder(Map, Map, int, float)}.
 	 */
 	public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange) throws StructureException {
 		// alignment comes from the afpChain alignment
