#-------------------------------------------------------------------------------
# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
#
# This file is part of Jalview.
#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see .
#-------------------------------------------------------------------------------
Alignment Window Menus
Alignment Window Colour Menu
- Apply Colour To All Groups
If this is selected, any changes made to the background colour
will be applied to all currently defined groups.
- Colour
Text ...
Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
- Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage
Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
Turn Propensity, Buried Index, Nucleotide, User Defined
See colours for
a description of all colour schemes.
- By Conservation
See Colouring
by Conservation.
- Modify Conservation Threshold
Use this to display the conservation threshold slider window.
Useful if the window has been closed, or if the 'by conservation' option
appears to be doing nothing!
- Above Identity Threshold
See Above Percentage
Identity.
- Modify Identity Threshold
Use this to set the threshold value for colouring above Identity.
Useful if the window has been closed.
- By Annotation
Colours the alignment on a per-column value from a specified annotation.
See Annotation Colouring.