+
+ SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
+ AlignmentI al = new Alignment(newseqs);
+ ((Alignment) al).createDatasetAlignment();
+ return al;
+ }
+
+ /**
+ * Returns a reversed, and optionally complemented, sequence. The new
+ * sequence's name is the original name with "|rev" or "|revcomp" appended.
+ * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
+ * left unchanged.
+ *
+ * @param seq
+ * @param complement
+ * @return
+ */
+ public static SequenceI reverseSequence(String seqName, String sequence,
+ boolean complement)
+ {
+ String newName = seqName + "|rev" + (complement ? "comp" : "");
+ char[] originalSequence = sequence.toCharArray();
+ int length = originalSequence.length;
+ char[] reversedSequence = new char[length];
+ int bases = 0;
+ for (int i = 0; i < length; i++)
+ {
+ char c = complement ? getComplement(originalSequence[i])
+ : originalSequence[i];
+ reversedSequence[length - i - 1] = c;
+ if (!Comparison.isGap(c))
+ {
+ bases++;
+ }
+ }
+ SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
+ return reversed;
+ }
+
+ /**
+ * Answers the reverse complement of the input string
+ *
+ * @see #getComplement(char)
+ * @param s
+ * @return
+ */
+ public static String reverseComplement(String s)
+ {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i = s.length() - 1; i >= 0; i--)
+ {
+ sb.append(Dna.getComplement(s.charAt(i)));
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
+ * are treated as on http://reverse-complement.com/. Anything else is left
+ * unchanged.
+ *
+ * @param c
+ * @return
+ */
+ public static char getComplement(char c)
+ {
+ char result = c;
+ switch (c)
+ {
+ case '-':
+ case '.':
+ case ' ':
+ break;
+ case 'a':
+ result = 't';
+ break;
+ case 'A':
+ result = 'T';
+ break;
+ case 'c':
+ result = 'g';
+ break;
+ case 'C':
+ result = 'G';
+ break;
+ case 'g':
+ result = 'c';
+ break;
+ case 'G':
+ result = 'C';
+ break;
+ case 't':
+ result = 'a';
+ break;
+ case 'T':
+ result = 'A';
+ break;
+ case 'u':
+ result = 'a';
+ break;
+ case 'U':
+ result = 'A';
+ break;
+ case 'r':
+ result = 'y';
+ break;
+ case 'R':
+ result = 'Y';
+ break;
+ case 'y':
+ result = 'r';
+ break;
+ case 'Y':
+ result = 'R';
+ break;
+ case 'k':
+ result = 'm';
+ break;
+ case 'K':
+ result = 'M';
+ break;
+ case 'm':
+ result = 'k';
+ break;
+ case 'M':
+ result = 'K';
+ break;
+ case 'b':
+ result = 'v';
+ break;
+ case 'B':
+ result = 'V';
+ break;
+ case 'v':
+ result = 'b';
+ break;
+ case 'V':
+ result = 'B';
+ break;
+ case 'd':
+ result = 'h';
+ break;
+ case 'D':
+ result = 'H';
+ break;
+ case 'h':
+ result = 'd';
+ break;
+ case 'H':
+ result = 'D';
+ break;
+ }
+
+ return result;