From 24c13cae7ab462fb159be2daa62ef7e7c812e0e9 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 22 Jan 2015 17:28:43 +0000 Subject: [PATCH] JAL-1372 JAL-1169 documentation for new commands HIDE_INSERTIONS AND VIEW_SETREF --- help/html/features/annotationsFormat.html | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 5012124..90dfd9b 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -60,8 +60,10 @@ ignored. The sections below describe the structure of an annotation file.
  • SEQUENCE_GROUP to define groups of sequences for further annotation
  • PROPERTIES to set visualisation properties for sequence groups
  • SEQUENCE_REF and GROUP_REF for attaching annotation to sequences and groups
    • -
  • VIEW_DEF and HIDE_INSERTIONS for creating new views and hiding regions based on gaps in a reference sequence
    • - +
  • VIEW_SETREF and HIDE_INSERTIONS + for defining a reference sequence on the alignment and hiding regions + based on gaps in a reference sequence
    • +

    At the end of this document, you can also find notes on compatibility of annotation files across @@ -204,10 +206,27 @@ Group association is turned off for subsequent annotation rows by: 

    GROUP_REF	ALIGNMENT

    -

    VIEW_DEF and HIDE_INSERTIONS
    +

    VIEW_SETREF, and HIDE_INSERTIONS
    Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.

    - -
    + +

    + VIEW_SETREF takes either a single sequence ID string, or a + numeric index (second argument), and attempts to assign a + corresponding sequence as the reference + sequence for the alignment. +

    +

    + HIDE_INSERTIONS takes a either a single sequence ID or a + numeric index, or no arguments. This command marks all gapped + positions in a specified sequence (either the one located by the + arguments, the current SEQUENCE_REF, or the reference sequence for the + view). +

    COMPATIBILITY NOTES
    The interpretation of the COMBINE statement in Version 2.8.1 was refined so that only annotation line graphs with the given names ands the same -- 1.7.10.2