diff --git a/src/zmapFeature/Style.keyword_value.txt b/src/zmapFeature/Style.keyword_value.txt new file mode 100755 index 0000000000000000000000000000000000000000..e7a9776321c3946149f6d47b7ba9390be9e90e2c --- /dev/null +++ b/src/zmapFeature/Style.keyword_value.txt @@ -0,0 +1,98 @@ +# +# 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 ;