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ensembl-gh-mirror
zmap
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4746777c
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4746777c
authored
16 years ago
by
edgrif
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example keyword-value format file.
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src/zmapFeature/Style.keyword_value.txt
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4746777c
#
# A sample zmap style in the keyword/value format
#
[test_style]
# parent is the name of a parent style used for inheritance.
parent = some style
# description is plain text about what the style represents.
description = Base style for all wublast features.
# defines how features that use this style should be interpreted (e.g. as a transcript).
mode = [basic | alignment | transcript | raw_sequence | pep_sequence | text | graph | glyph | meta]
# All colours have two flavours: normal and selected, for each of those there are fill, draw and border.
#
colours = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
colours_frame0 = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
colours_frame1 = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
colours_frame2 = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
colours_strand_rev = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
# column display state controls how column is displayed:
col_display_state = [ hide | show_hide | show ]
# overlap modes: curr is what column will be displayed with, default is what column will displayed with
# if just bumped. bump_spacing sets distance between sub-columns of bumped features.
default_overlap_mode = [ Complete | Overlap | Item_overlap | Start | Name | Oscillate | Simple | Ends_range | Compact | Compact_no_interleave | Range | Range_colinear ]
overlap_mode = [ Complete | Overlap | Item_overlap | Start | Name | Oscillate | Simple | Ends_range | Compact | Compact_no_interleave | Range | Range_colinear ]
bump_spacing = 2
min_mag = 0.5
max_mag = 10
width = 16
score_mode = [ width | offset | histogram | percent ]
min_score = 10
max_score = 100
gff_source = arbitary name
gff_feature = rubbish feature
displayable = true
show_when_empty = false
show_text = false
strand_specific = true
show_reverse_strand = true
frame_mode = [ never | always | only_3 | only_1 ]
show_only_in_separator = false
directional_end = false
deferred = false
loaded = true
# mode specific fields will all have to be prefixed with the mode name....
# only one of these modes should be specified and it must match the mode set
# with the "mode" keyword above.
#
# graph mode
#
graph_mode = [ line | histogram ]
graph_baseline = 2
# glyph mode
#
glyph_mode = [ splice ]
# alignment mode
#
alignment_parse_gaps = true
alignment_align_gaps = true
alignment_pfetchable = false
alignment_within_error = 2
alignment_between_error = 3
alignment_perfect = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
alignment_colinear = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
alignment_noncolinear = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
# transcript mode
#
transcript_CDS_colours = normal fill #ffff00 ; normal draw #ff0000 ; normal border #000000 ; selected fill #ffff00 ; selected draw #ff0000 ; selected border #000000 ;
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