examples/groovy/pcaMode.groovy

   1 /*
   2  * PCA calculation treatment of gaps 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 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
  20 {
  21   ResidueProperties.DNA[row][10] = ResidueProperties.DNA[row][9]
  22   ResidueProperties.DNA[10][row] = ResidueProperties.DNA[row][9]
  23 }
  24 /*
  25  * END 2.10.1 mode script
  26  */
  27
  28 /*
  29  * To reinstate 2.10.2 calculation mode, including Tree calculations,
  30  * run the script below
  31  */
  32 /*
  33  * START 2.10.2 mode script
  34  */
  35  import jalview.schemes.ResidueProperties
  36
  37 for (int row = 0 ; row < ResidueProperties.maxProteinIndex; row++)
  38 {
  39   ResidueProperties.BLOSUM62[row][23] = -4
  40   ResidueProperties.BLOSUM62[23][row] = -4
  41   ResidueProperties.PAM250[row][23] = -8
  42   ResidueProperties.PAM250[23][row] = -8
  43 }
  44 ResidueProperties.BLOSUM62[23][23] = 1
  45 ResidueProperties.PAM250[23][23] = 1
  46 for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
  47 {
  48   ResidueProperties.DNA[row][10] = 1
  49   ResidueProperties.DNA[10][row] = 1
  50 }
  51 /*
  52  * END 2.10.2 mode script
  53  */