From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 7 Feb 2017 12:44:01 +0000 (+0000)
Subject: JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode
X-Git-Tag: Release_2_10_3b1~343^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=09b0818c06ad80b1ea684b1140975625afffdf25;p=jalview.git

JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode
---

diff --git a/examples/groovy/pcaMode.groovy b/examples/groovy/pcaMode.groovy
new file mode 100644
index 0000000..c106704
--- /dev/null
+++ b/examples/groovy/pcaMode.groovy
@@ -0,0 +1,53 @@
+/*
+ * PCA calculation treatment of gaps 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
+ */
+
+/*
+ * START 2.10.1 mode script
+ */
+import jalview.schemes.ResidueProperties 
+
+for (int row = 0 ; row <= ResidueProperties.maxProteinIndex; row++) 
+{ 
+  ResidueProperties.BLOSUM62[row][23] = ResidueProperties.BLOSUM62[row][22] 
+  ResidueProperties.BLOSUM62[23][row] = ResidueProperties.BLOSUM62[row][22] 
+  ResidueProperties.PAM250[row][23] = ResidueProperties.PAM250[row][22] 
+  ResidueProperties.PAM250[23][row] = ResidueProperties.PAM250[row][22] 
+} 
+for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++) 
+{ 
+  ResidueProperties.DNA[row][10] = ResidueProperties.DNA[row][9] 
+  ResidueProperties.DNA[10][row] = ResidueProperties.DNA[row][9] 
+}
+/*
+ * END 2.10.1 mode script
+ */
+
+/*
+ * To reinstate 2.10.2 calculation mode, including Tree calculations,
+ * run the script below
+ */
+/*
+ * START 2.10.2 mode script
+ */
+ import jalview.schemes.ResidueProperties 
+
+for (int row = 0 ; row < ResidueProperties.maxProteinIndex; row++) 
+{ 
+  ResidueProperties.BLOSUM62[row][23] = -4 
+  ResidueProperties.BLOSUM62[23][row] = -4 
+  ResidueProperties.PAM250[row][23] = -8 
+  ResidueProperties.PAM250[23][row] = -8 
+} 
+ResidueProperties.BLOSUM62[23][23] = 1 
+ResidueProperties.PAM250[23][23] = 1 
+for (int row = 0 ; row <= ResidueProperties.maxNucleotideIndex; row++) 
+{ 
+  ResidueProperties.DNA[row][10] = 1 
+  ResidueProperties.DNA[10][row] = 1 
+}
+/*
+ * END 2.10.2 mode script
+ */