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JAL-2398 include 'compatibility mode' for C->R score correction
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 7 Feb 2017 12:50:49 +0000
(12:50 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 7 Feb 2017 12:50:49 +0000
(12:50 +0000)
examples/groovy/pcaMode.groovy
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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
*/
* 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.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]
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[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
for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++)
{
ResidueProperties.DNA[row][10] = 1