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JAL-4235 JAL-3599 Try and report Eclipse Product Version for jalviewjsTranspile....
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
65fd110
..
02b3f41
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-890,7
+890,8
@@
public class AlignSeq
pdbpos++;
}
pdbpos++;
}
- if (allowmismatch || c1 == c2)
+ // ignore case differences
+ if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
{
// extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
{
// extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)