git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1479 improved Sifts PID calculation for determining an Entity to process
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
d4ae57d
..
7b3ce25
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-235,10
+235,7
@@
public class Conservation
c = '-';
}
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
}
values[c]++;
}
@@
-326,6
+323,7
@@
public class Conservation
}
else
{
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
nres++;
if (nres == 1)
@@
-347,6
+345,22
@@
public class Conservation
}
/**
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
* Calculates the conservation sequence
*
* @param consflag