@@ -72,7 +72,7 @@ public class AlignmentTools {
7272 * Since algorithms which create non-sequential alignments split the
7373 * alignment into multiple blocks, some computational time can be saved
7474 * by only checking block boundaries for sequentiality. Setting
75- * <tt >checkWithinBlocks</tt > to <tt >true</tt > makes this function slower,
75+ * <code >checkWithinBlocks</code > to <code >true</code > makes this function slower,
7676 * but detects AFPChains with non-sequential blocks.
7777 *
7878 * Note that this method should give the same results as
@@ -209,7 +209,7 @@ public static <T> Map<T,T> applyAlignment(Map<T, T> alignmentMap, int k) {
209209 * @param <T>
210210 * @param alignmentMap The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
211211 * @param identity An identity-like function providing the isomorphism between
212- * the codomain of alignmentMap (of type <T> ) and the domain (type <S> ).
212+ * the codomain of alignmentMap (of type T ) and the domain (type S ).
213213 * @param k The number of times to apply the alignment
214214 * @return A new alignment. If the input function is not automorphic
215215 * (one-to-one), then some inputs may map to null, indicating that the
@@ -303,7 +303,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
303303 * identity. If <i>n</i> corresponds to the intrinsic order of the alignment,
304304 * this will be small. This algorithm tries increasing values of <i>n</i>
305305 * and looks for abrupt decreases in the root mean squared offset.
306- * If none are found at <i>n</i>< =maxSymmetry, the alignment is reported as
306+ * If none are found at <i>n</i>< =maxSymmetry, the alignment is reported as
307307 * non-symmetric.
308308 *
309309 * @param alignment The alignment to test for symmetry
@@ -314,7 +314,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
314314 * the calculation time and can lead to overfitting.
315315 * @param minimumMetricChange Percent decrease in root mean squared offsets
316316 * in order to declare symmetry. 0.4f seems to work well for CeSymm.
317- * @return The order of symmetry of alignment, or 1 if no order < =
317+ * @return The order of symmetry of alignment, or 1 if no order < =
318318 * maxSymmetry is found.
319319 *
320320 * @see IdentityMap For a simple identity function
@@ -472,7 +472,8 @@ public static Map<Integer, Integer> guessSequentialAlignment(
472472 * {@link AFPChain#getOptAln()}, but has the correct size().
473473 * <pre>
474474 * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
475- * aln.get(blockNum).get(structureNum={0,1}).get(pos)</pre>
475+ * aln.get(blockNum).get(structureNum={0,1}).get(pos)
476+ * </pre>
476477 *
477478 * @param afpChain
478479 * @return
@@ -850,7 +851,7 @@ public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
850851 * @param ca1
851852 * @param ca2 Second set of ca atoms. Will be modified based on the superposition
852853 * @throws StructureException
853- * @see {@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)}
854+ * @see CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)
854855 * contains much of the same code, but stores results in a CECalculator
855856 * instance rather than an AFPChain
856857 */
@@ -979,12 +980,13 @@ public static Object resizeArray (Object oldArray, int newSize) {
979980 * <p>Note that more concise representations may be possible.</p>
980981 *
981982 * Examples:
983+ * <ul>
982984 * <li>1>2>3>1</li>
983985 * <li>1>2>3>2 4>3</li>
984- *
986+ * </ul>
985987 * @param alignment The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
986988 * @param identity An identity-like function providing the isomorphism between
987- * the codomain of alignment (of type <T> ) and the domain (type <S> ).
989+ * the codomain of alignment (of type T ) and the domain (type S ).
988990 * @return
989991 */
990992 public static <S ,T > String toConciseAlignmentString (Map <S ,T > alignment , Map <T ,S > identity ) {
@@ -1197,7 +1199,6 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain,
11971199 * Does NOT rotate anything.
11981200 * @param ca
11991201 * @return a list of Chains that is built up from the Atoms in the ca array
1200- * @throws StructureException
12011202 */
12021203 public static final List <Chain > getAlignedModel (Atom [] ca ){
12031204
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