private static final int TO_UPPER_CASE = 'a' - 'A';
- private static final char GAP_SPACE = ' ';
+ public static final char GAP_SPACE = ' ';
- private static final char GAP_DOT = '.';
+ public static final char GAP_DOT = '.';
- private static final char GAP_DASH = '-';
+ public static final char GAP_DASH = '-';
public static final String GapChars = new String(new char[] { GAP_SPACE,
GAP_DOT, GAP_DASH });
* @param s2
* SequenceI
* @return float
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2)
{
return PID(seq1, seq2, 0, seq1.length());
static final int caseShift = 'a' - 'A';
// Another pid with region specification
+ /**
+ * @deprecated use PIDModel.computePID()
+ */
+ @Deprecated
public final static float PID(String seq1, String seq2, int start, int end)
{
return PID(seq1, seq2, start, end, true, false);
* @param ungappedOnly
* - if true - only count PID over ungapped columns
* @return
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2, int start,
int end, boolean wcGaps, boolean ungappedOnly)
{
}
/**
- * Compares two chars either case sensitively or case insensitively depending
- * on the caseSensitive flag
+ * Compares two residues either case sensitively or case insensitively
+ * depending on the caseSensitive flag
*
* @param c1
* first char
* if true comparison will be case sensitive otherwise its not
* @return
*/
- public static boolean compareChars(char c1, char c2, boolean caseSensitive)
+ public static boolean isSameResidue(char c1, char c2,
+ boolean caseSensitive)
{
- boolean sameCase = (Character.isUpperCase(c1) && Character
- .isUpperCase(c2))
- || (Character.isLowerCase(c1) && Character.isLowerCase(c2));
- if (sameCase)
+ if (caseSensitive)
{
- return c1 == c2;
- }
- else if (caseSensitive)
- {
- return false;
+ return (c1 == c2);
}
else
{