/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.util;
* DOCUMENT ME!
*
* @param ii
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param jj
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* this was supposed to be an ungapped pid calculation
*
* @param ii
- * SequenceI
+ * SequenceI
* @param jj
- * SequenceI
+ * SequenceI
* @param start
- * int
+ * int
* @param end
- * int
+ * int
* @return float
*/
public static float compare(SequenceI ii, SequenceI jj, int start, int end)
* this is a gapped PID calculation
*
* @param s1
- * SequenceI
+ * SequenceI
* @param s2
- * SequenceI
+ * SequenceI
* @return float
*/
public final static float PID(String seq1, String seq2)
// Another pid with region specification
public final static float PID(String seq1, String seq2, int start, int end)
{
-
+ return PID(seq1, seq2, start, end, true,false);
+ }
+ /**
+ * Calculate percent identity for a pair of sequences over a particular range, with different options for ignoring gaps.
+ * @param seq1
+ * @param seq2
+ * @param start - position in seqs
+ * @param end - position in seqs
+ * @param wcGaps - if true - gaps match any character, if false, do not match anything
+ * @param ungappedOnly - if true - only count PID over ungapped columns
+ * @return
+ */
+ public final static float PID(String seq1, String seq2, int start, int end, boolean wcGaps, boolean ungappedOnly)
+ {
int s1len = seq1.length();
int s2len = seq2.length();
start = len - 1; // we just use a single residue for the difference
}
- int bad = 0;
+ int elen=len-start,bad = 0;
char chr1;
char chr2;
-
+ boolean agap;
for (int i = start; i < len; i++)
{
chr1 = seq1.charAt(i);
chr2 = seq2.charAt(i);
-
+ agap = isGap(chr1) || isGap(chr2);
if ('a' <= chr1 && chr1 <= 'z')
{
// TO UPPERCASE !!!
// Faster than toUpperCase
chr2 -= caseShift;
}
-
- if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
+
+ if (chr1 != chr2)
{
- bad++;
+ if (agap)
+ {
+ if (ungappedOnly)
+ {
+ elen--;
+ } else if (!wcGaps) {
+ bad++;
+ }
+ } else {
+ bad++;
+ }
}
+
}
-
- return ((float) 100 * (len - bad)) / len;
+ if (elen<1) { return 0f; }
+ return ((float) 100 * (elen - bad)) / elen;
}
/**
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/