+
+ /**
+ * Answers true if the character is one of aAcCgGtTuU
+ *
+ * @param c
+ * @return
+ */
+ public static boolean isNucleotide(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= TO_UPPER_CASE;
+ }
+
+ switch (c)
+ {
+ case 'A':
+ case 'C':
+ case 'G':
+ case 'T':
+ case 'U':
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Answers true if every character in the string is one of aAcCgGtTuU, or
+ * (optionally) a gap character (dot, dash, space), else false
+ *
+ * @param s
+ * @param allowGaps
+ * @return
+ */
+ public static boolean isNucleotideSequence(String s, boolean allowGaps)
+ {
+ if (s == null)
+ {
+ return false;
+ }
+ for (int i = 0; i < s.length(); i++)
+ {
+ char c = s.charAt(i);
+ if (!isNucleotide(c))
+ {
+ if (!allowGaps || !isGap(c))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * 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);
+ }
+ }