2 * PCA calculation treatment of gaps (and C->R score) changed in Jalview 2.10.2.
3 * To restore behaviour prior as at 2.10.1, run the script below
4 * NB this will change Tree calculations using similarity matrices
8 * START 2.10.1 mode script
10 import jalview.schemes.ResidueProperties
12 for (int row = 0 ; row <= ResidueProperties.maxProteinIndex; row++)
14 ResidueProperties.BLOSUM62[row][23] = ResidueProperties.BLOSUM62[row][22]
15 ResidueProperties.BLOSUM62[23][row] = ResidueProperties.BLOSUM62[row][22]
16 ResidueProperties.PAM250[row][23] = ResidueProperties.PAM250[row][22]
17 ResidueProperties.PAM250[23][row] = ResidueProperties.PAM250[row][22]
19 ResidueProperties.BLOSUM62[4][1]=3 // C-R score
20 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
22 ResidueProperties.DNA[row][10] = ResidueProperties.DNA[row][9]
23 ResidueProperties.DNA[10][row] = ResidueProperties.DNA[row][9]
26 * END 2.10.1 mode script
30 * To reinstate 2.10.2 calculation mode, including Tree calculations,
31 * run the script below
34 * START 2.10.2 mode script
36 import jalview.schemes.ResidueProperties
38 for (int row = 0 ; row < ResidueProperties.maxProteinIndex; row++)
40 ResidueProperties.BLOSUM62[row][23] = -4
41 ResidueProperties.BLOSUM62[23][row] = -4
42 ResidueProperties.PAM250[row][23] = -8
43 ResidueProperties.PAM250[23][row] = -8
45 ResidueProperties.BLOSUM62[23][23] = 1
46 ResidueProperties.PAM250[23][23] = 1
47 ResidueProperties.BLOSUM62[4][1]=-3 // C-R score
48 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
50 ResidueProperties.DNA[row][10] = 1
51 ResidueProperties.DNA[10][row] = 1
54 * END 2.10.2 mode script