From: jprocter Date: Mon, 30 May 2011 06:34:28 +0000 (+0100) Subject: first patch for JAL-838 - allow new typed of PID calcs X-Git-Tag: Release_2_7~178 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bd37829796d6d9f9b8340967eea49eb0d98f70a7;p=jalview.git first patch for JAL-838 - allow new typed of PID calcs --- diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java old mode 100755 new mode 100644 index 32e049d..60f21c8 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -133,7 +133,20 @@ public class Comparison // 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(); @@ -149,16 +162,16 @@ public class Comparison 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 !!! @@ -171,14 +184,25 @@ public class Comparison // 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; } /**