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[jalview.git]
/
src
/
jalview
/
util
/
Comparison.java
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
d8e599b
..
3a831d0
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-13,27
+13,17
@@
public class Comparison {
String si = ii.getSequence();
\r
String sj = jj.getSequence();
\r
\r
String si = ii.getSequence();
\r
String sj = jj.getSequence();
\r
\r
- int ilen = end-start+1;
\r
- int jlen = end-start+1;
\r
+ int ilen = si.length()-1;
\r
+ int jlen = sj.length()-1;
\r
\r
\r
- if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
\r
- {
\r
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
\r
+ {
\r
ilen--;
\r
ilen--;
\r
-
\r
- while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
\r
- {
\r
- ilen--;
\r
- }
\r
}
\r
\r
}
\r
\r
- if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
\r
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
\r
{
\r
jlen--;
\r
{
\r
jlen--;
\r
-
\r
- while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
\r
- {
\r
- jlen--;
\r
- }
\r
}
\r
\r
int count = 0;
\r
}
\r
\r
int count = 0;
\r
@@
-63,7
+53,7
@@
public class Comparison {
}
\r
\r
/** */
\r
}
\r
\r
/** */
\r
- public static float PID(Sequence s1 , Sequence s2)
\r
+ public static float PID(SequenceI s1 , SequenceI s2)
\r
{
\r
int len;
\r
\r
{
\r
int len;
\r
\r