+ /**
+ * Convenience overload of isNucleotide
+ *
+ * @param seqs
+ * @return
+ */
+ public static boolean isNucleotide(SequenceI[][] seqs)
+ {
+ if (seqs == null)
+ {
+ return false;
+ }
+ List<SequenceI> flattened = new ArrayList<SequenceI>();
+ for (SequenceI[] ss : seqs)
+ {
+ for (SequenceI s : ss)
+ {
+ flattened.add(s);
+ }
+ }
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
+ return isNucleotide(oneDArray);
+ }
+
+ /**
+ * Compares two residues either case sensitively or case insensitively
+ * depending on the caseSensitive flag
+ *
+ * @param c1
+ * first char
+ * @param c2
+ * second char to compare with
+ * @param caseSensitive
+ * if true comparison will be case sensitive otherwise its not
+ * @return
+ */
+ public static boolean isSameResidue(char c1, char c2,
+ boolean caseSensitive)
+ {
+ if (caseSensitive)
+ {
+ return (c1 == c2);
+ }
+ else
+ {
+ return Character.toUpperCase(c1) == Character.toUpperCase(c2);
+ }