JAL-2398 include 'compatibility mode' for C->R score correction

diff --git a/examples/groovy/pcaMode.groovy b/examples/groovy/pcaMode.groovy
index c106704..817e6e1 100644 (file)
--- a/examples/groovy/pcaMode.groovy
+++ b/examples/groovy/pcaMode.groovy
@@ -1,5 +1,5 @@
 /*
- * PCA calculation treatment of gaps changed in Jalview 2.10.2.
+ * PCA calculation treatment of gaps (and C->R score) changed in Jalview 2.10.2.
  * To restore behaviour prior as at 2.10.1, run the script below
  * NB this will change Tree calculations using similarity matrices
  */
@@ -16,6 +16,7 @@ for (int row = 0 ; row <= ResidueProperties.maxProteinIndex; row++)
   ResidueProperties.PAM250[row][23] = ResidueProperties.PAM250[row][22] 
   ResidueProperties.PAM250[23][row] = ResidueProperties.PAM250[row][22] 
 } 
+ResidueProperties.BLOSUM62[4][1]=3 // C-R score
 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++) 
 { 
   ResidueProperties.DNA[row][10] = ResidueProperties.DNA[row][9] 
@@ -43,6 +44,7 @@ for (int row = 0 ; row < ResidueProperties.maxProteinIndex; row++)
 } 
 ResidueProperties.BLOSUM62[23][23] = 1 
 ResidueProperties.PAM250[23][23] = 1 
+ResidueProperties.BLOSUM62[4][1]=-3 // C-R score
 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++) 
 { 
   ResidueProperties.DNA[row][10] = 1