git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
79cc408
)
Takes strings, not seqs
author
amwaterhouse
<Andrew Waterhouse>
Tue, 18 Jul 2006 15:30:54 +0000
(15:30 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 18 Jul 2006 15:30:54 +0000
(15:30 +0000)
src/jalview/util/Comparison.java
patch
|
blob
|
history
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
9e0aef6
..
d35d84c
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-116,21
+116,19
@@
public class Comparison
* @param s2 SequenceI
\r
* @return float
\r
*/
\r
* @param s2 SequenceI
\r
* @return float
\r
*/
\r
- public final static float PID(SequenceI seq1, SequenceI seq2)
\r
+ public final static float PID(String seq1, String seq2)
\r
{
\r
{
\r
- return PID(seq1, seq2, 0, seq1.getLength());
\r
+ return PID(seq1, seq2, 0, seq1.length());
\r
}
\r
\r
static final int caseShift = 'a' - 'A';
\r
\r
// Another pid with region specification
\r
}
\r
\r
static final int caseShift = 'a' - 'A';
\r
\r
// Another pid with region specification
\r
- public final static float PID(SequenceI seq1, SequenceI seq2, int start, int end)
\r
+ public final static float PID(String seq1, String seq2, int start, int end)
\r
{
\r
{
\r
- String s1 = seq1.getSequence();//.toUpperCase();
\r
- String s2 = seq2.getSequence();//.toUpperCase();
\r
- int s1len = s1.length();
\r
- int s2len = s2.length();
\r
\r
\r
+ int s1len = seq1.length();
\r
+ int s2len = seq2.length();
\r
\r
int len = Math.min(s1len, s2len);
\r
\r
\r
int len = Math.min(s1len, s2len);
\r
\r
@@
-152,9
+150,9
@@
public class Comparison
\r
for (int i = start; i < len; i++)
\r
{
\r
\r
for (int i = start; i < len; i++)
\r
{
\r
- chr1 = s1.charAt(i) ;
\r
+ chr1 = seq1.charAt(i) ;
\r
\r
\r
- chr2 = s2.charAt(i) ;
\r
+ chr2 = seq2.charAt(i) ;
\r
\r
if ('a' <= chr1 && chr1 <= 'z')
\r
{
\r
\r
if ('a' <= chr1 && chr1 <= 'z')
\r
{
\r