From 38628e1c57ebc7dd900f0a9b6f807396873a7d67 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 16 Aug 2017 19:16:08 +0100 Subject: [PATCH] JAL-2418 check groovy script one-liners for restoring legacy score model behaviour --- help/html/releases.html | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index 89a39a3..23cfb84 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -270,19 +270,22 @@ li:before {
  • Fixed Jalview's treatment of gaps in PCA - and substitution matrix based Tree calculations.
    In + and substitution matrix based Tree calculations.

    In earlier versions of Jalview, gaps matching gaps were penalised, and gaps matching non-gaps penalised even more. In the PCA calculation, gaps were actually treated as non-gaps - so different costs were applied, which meant Jalview's PCAs were different to those produced by SeqSpace.
    Jalview now treats gaps in the same way as - SeqSpace (ie it scores them as 0). To restore pre-2.10.2 - behaviour
    - jalview.viewmodel.PCAModel.scoreGapAsAny=true // for - 2.10.1 mode
    - jalview.viewmodel.PCAModel.scoreGapAsAny=false // to - restore 2.10.2 mode + SeqSpace (ie it scores them as 0).

    Enter + the following in the Groovy console to restore pre-2.10.2 + behaviour:
    + jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true + // for 2.10.1 mode
    + jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false + // to restore 2.10.2 mode

    Note: + these settings will affect all subsequent tree and PCA + calculations (not recommended)
  • Fixed off-by-one bug that affected -- 1.7.10.2