From 452985f004452b57379d566c7ec342162538ac22 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 7 Feb 2017 12:50:49 +0000 Subject: [PATCH] JAL-2398 include 'compatibility mode' for C->R score correction --- examples/groovy/pcaMode.groovy | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/examples/groovy/pcaMode.groovy b/examples/groovy/pcaMode.groovy index c106704..817e6e1 100644 --- 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 -- 1.7.10.2