From 666701168bbf6308964633ade95bfa3a84903ad7 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 18 Jul 2006 15:30:54 +0000 Subject: [PATCH] Takes strings, not seqs --- src/jalview/util/Comparison.java | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java index 9e0aef6..d35d84c 100755 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -116,21 +116,19 @@ public class Comparison * @param s2 SequenceI * @return float */ - public final static float PID(SequenceI seq1, SequenceI seq2) + public final static float PID(String seq1, String seq2) { - return PID(seq1, seq2, 0, seq1.getLength()); + return PID(seq1, seq2, 0, seq1.length()); } static final int caseShift = 'a' - 'A'; // Another pid with region specification - public final static float PID(SequenceI seq1, SequenceI seq2, int start, int end) + public final static float PID(String seq1, String seq2, int start, int end) { - String s1 = seq1.getSequence();//.toUpperCase(); - String s2 = seq2.getSequence();//.toUpperCase(); - int s1len = s1.length(); - int s2len = s2.length(); + int s1len = seq1.length(); + int s2len = seq2.length(); int len = Math.min(s1len, s2len); @@ -152,9 +150,9 @@ public class Comparison for (int i = start; i < len; i++) { - chr1 = s1.charAt(i) ; + chr1 = seq1.charAt(i) ; - chr2 = s2.charAt(i) ; + chr2 = seq2.charAt(i) ; if ('a' <= chr1 && chr1 <= 'z') { -- 1.7.10.2