From 4884e25f5b34c098cbfe5f207b2a3d938c9b82c4 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 23 Jan 2015 13:14:58 +0000 Subject: [PATCH] JAL-1628 tweak signature of core annotation printer for outputting hidden columns and view names via VIEW_HIDECOLS and VIEW_DEF --- help/html/features/annotationsFormat.html | 12 ++- src/jalview/io/AnnotationFile.java | 117 ++++++++++++++++++++++++++--- test/jalview/io/AnnotationFileIOTest.java | 5 +- 3 files changed, 117 insertions(+), 17 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 90dfd9b..72691ce 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -60,7 +60,7 @@ 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_SETREF and HIDE_INSERTIONS +
  • VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS for defining a reference sequence on the alignment and hiding regions based on gaps in a reference sequence
  • @@ -168,7 +168,7 @@ of sequence IDs.

    idColourColour for highlighting the Sequence ID labels for this group
    If idColour is given but colour is not, then idColor will also be used for the group background colour. showunconservedBoolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence hideBoolean (default false) indicating whether the rows in this group should be marked as hidden.
    Note: if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence. -hidecolsBoolean (default false) indicating whether columns in this groushould be marked as hidden +

    Specifying colours in PROPERTIES key-value pairs
    @@ -206,7 +206,7 @@ Group association is turned off for subsequent annotation rows by:

    GROUP_REF	ALIGNMENT


    -

    VIEW_SETREF, and HIDE_INSERTIONS
    +

    VIEW_SETREF, VIEW_HIDECOL 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.