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fixed base lookup bug in dna pairwise alignment and ensured abiguous and non-standard...
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
62d8d92
..
b14d9c6
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-87,7
+87,7
@@
public class ResidueProperties
aaIndex['b'] = 20;
aaIndex['z'] = 21;
aaIndex['x'] = 22;
aaIndex['b'] = 20;
aaIndex['z'] = 21;
aaIndex['x'] = 22;
- aaIndex['u'] = 22;
+ aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also extend subt. matrices
}
static
}
static
@@
-1167,12
+1167,7
@@
public class ResidueProperties
public static int getPAM250(String A1, String A2)
{
public static int getPAM250(String A1, String A2)
{
- int a = aaIndex[A1.charAt(0)];
- int b = aaIndex[A2.charAt(0)];
-
- int pog = ResidueProperties.PAM250[a][b];
-
- return pog;
+ return getPAM250(A1.charAt(0), A2.charAt(0));
}
public static int getBLOSUM62(char c1, char c2)
}
public static int getBLOSUM62(char c1, char c2)
@@
-1246,4
+1241,14
@@
public class ResidueProperties
}
return null;
}
}
return null;
}
+
+ public static int getPAM250(char c, char d)
+ {
+ int a = aaIndex[c];
+ int b = aaIndex[d];
+
+ int pog = ResidueProperties.PAM250[a][b];
+
+ return pog;
+ }
}
}