From f777eebb4b991645bffdfe87b8702db943e94584 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 18 Aug 2017 14:13:28 +0100 Subject: [PATCH] JAL-1551 formatting --- help/html/releases.html | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index 485cf73..c331ae1 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -228,7 +228,9 @@ li:before { Updated JABAWS client to v2.2
  • - Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services + Filter non-standard amino acids and + nucleotides when submitting to AACon and other MSA + Analysis services
  • URLs for viewing database @@ -290,25 +292,23 @@ li:before { matrix - C->R should be '-3'
    Old matrix restored with this one-line groovy script:
    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
    • -
  • - Fixed Jalview's treatment of gaps in PCA - 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).

    Enter - the following in the Groovy console to restore pre-2.10.2 - behaviour:
    +
  • Fixed + Jalview's treatment of gaps in PCA 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).

    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) -
    • + calculations (not recommended)
  • Fixed off-by-one bug that affected scaling of branch lengths for trees computed using @@ -661,7 +661,8 @@ li:before { doesn't always add secondary structure annotation.
    • - + +
    2.10.1
    29/11/2016     -- 1.7.10.2