examples/groovy/pcaMode.groovy

   1 /*
   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
   5  */
   6
   7 /*
   8  * START 2.10.1 mode script
   9  */
  10 import jalview.schemes.ResidueProperties
  11
  12 for (int row = 0 ; row <= ResidueProperties.maxProteinIndex; row++)
  13 {
  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]
  18 }
  19 ResidueProperties.BLOSUM62[4][1]=3 // C-R score
  20 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
  21 {
  22   ResidueProperties.DNA[row][10] = ResidueProperties.DNA[row][9]
  23   ResidueProperties.DNA[10][row] = ResidueProperties.DNA[row][9]
  24 }
  25 /*
  26  * END 2.10.1 mode script
  27  */
  28
  29 /*
  30  * To reinstate 2.10.2 calculation mode, including Tree calculations,
  31  * run the script below
  32  */
  33 /*
  34  * START 2.10.2 mode script
  35  */
  36  import jalview.schemes.ResidueProperties
  37
  38 for (int row = 0 ; row < ResidueProperties.maxProteinIndex; row++)
  39 {
  40   ResidueProperties.BLOSUM62[row][23] = -4
  41   ResidueProperties.BLOSUM62[23][row] = -4
  42   ResidueProperties.PAM250[row][23] = -8
  43   ResidueProperties.PAM250[23][row] = -8
  44 }
  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++)
  49 {
  50   ResidueProperties.DNA[row][10] = 1
  51   ResidueProperties.DNA[10][row] = 1
  52 }
  53 /*
  54  * END 2.10.2 mode script
  55  */