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Add a util class for coloring features
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| define( [ | ||
| ], | ||
| function() { | ||
| var orientationTypes = { | ||
| "fr": { | ||
|
|
||
| "F1R2": "LR", | ||
| "F2R1": "LR", | ||
|
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| "F1F2": "LL", | ||
| "F2F1": "LL", | ||
|
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| "R1R2": "RR", | ||
| "R2R1": "RR", | ||
|
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| "R1F2": "RL", | ||
| "R2F1": "RL" | ||
| }, | ||
|
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| "rf": { | ||
|
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| "R1F2": "LR", | ||
| "R2F1": "LR", | ||
|
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| "R1R2": "LL", | ||
| "R2R1": "LL", | ||
|
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| "F1F2": "RR", | ||
| "F2F1": "RR", | ||
|
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| "F1R2": "RL", | ||
| "F2R1": "RL" | ||
| }, | ||
|
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| "ff": { | ||
|
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| "F2F1": "LR", | ||
| "R1R2": "LR", | ||
|
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| "F2R1": "LL", | ||
| "R1F2": "LL", | ||
|
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| "R2F1": "RR", | ||
| "F1R2": "RR", | ||
|
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| "R2R1": "RL", | ||
| "F1F2": "RL" | ||
| } | ||
| }; | ||
|
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| var PairUtils = { | ||
| colorAlignment( feature, path, glyph, track ) { | ||
| var strand = feature.get('strand'); | ||
| if (Math.abs(strand) != 1 && strand != '+' && strand != '-') { | ||
| return track.colorForBase('reference'); | ||
| } | ||
| else if (track.config.colorByOrientation) { | ||
| if (track.upperPercentile < Math.abs(feature.get('template_length'))) { | ||
| return 'red' | ||
| } else if (track.lowerPercentile > Math.abs(feature.get('template_length'))) { | ||
| return 'pink' | ||
| } | ||
| const type = orientationTypes[track.config.orientationType] | ||
| const orientation = type[feature.get('pair_orientation')] | ||
| const map = { | ||
| 'LR': 'color_pair_lr', | ||
| 'RR': 'color_pair_rr', | ||
| 'RL': 'color_pair_rl', | ||
| 'LL': 'color_pair_ll' | ||
| }; | ||
| return glyph.getStyle(feature, map[orientation] || 'color_nostrand'); | ||
| } | ||
| else if (track.config.useXS) { | ||
| var xs = feature.get('xs') | ||
| var strand = { | ||
| '-':'color_rev_strand', | ||
| '+':'color_fwd_strand' | ||
| }; | ||
| if (!strand[xs]) { | ||
| strand = 'color_nostrand'; | ||
| } | ||
| return glyph.getStyle(feature, strand[xs]); | ||
| } | ||
| else if (feature.get('multi_segment_template')) { | ||
| var revflag = feature.get('multi_segment_first'); | ||
| if (feature.get('multi_segment_all_correctly_aligned')) { | ||
| if (revflag || !track.config.useReverseTemplate) { | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_fwd_strand' ) | ||
| : glyph.getStyle( feature, 'color_rev_strand' ); | ||
| } else { | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_rev_strand' ) | ||
| : glyph.getStyle( feature, 'color_fwd_strand' ); | ||
| } | ||
| } | ||
| if (feature.get('multi_segment_next_segment_unmapped')) { | ||
| if (revflag || !track.config.useReverseTemplate) { | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_fwd_missing_mate' ) | ||
| : glyph.getStyle( feature, 'color_rev_missing_mate' ); | ||
| } else{ | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_rev_missing_mate' ) | ||
| : glyph.getStyle( feature, 'color_fwd_missing_mate' ); | ||
| } | ||
| } | ||
| if (feature.get('seq_id') == feature.get('next_seq_id')) { | ||
| if (revflag || !track.config.useReverseTemplate) { | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_fwd_strand_not_proper' ) | ||
| : glyph.getStyle( feature, 'color_rev_strand_not_proper' ); | ||
| } else { | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_rev_strand_not_proper' ) | ||
| : glyph.getStyle( feature, 'color_fwd_strand_not_proper' ); | ||
| } | ||
| } | ||
| // should only leave aberrant chr | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_fwd_diff_chr' ) | ||
| : glyph.getStyle( feature, 'color_rev_diff_chr' ); | ||
| } | ||
| return strand == 1 || strand == '+' | ||
| ? glyph.getStyle( feature, 'color_fwd_strand' ) | ||
| : glyph.getStyle( feature, 'color_rev_strand' ); | ||
| }, | ||
| colorAlignmentArc( feature, score, glyph, track ) { | ||
| if (track.config.colorByOrientation) { | ||
| if (track.upperPercentile < Math.abs(feature.get('template_length'))) { | ||
| return 'red' | ||
| } else if (track.lowerPercentile > Math.abs(feature.get('template_length'))) { | ||
| return 'pink' | ||
| } | ||
| const type = orientationTypes[track.config.orientationType] | ||
| const orientation = type[feature.get('pair_orientation')] | ||
| const map = { | ||
| 'LR': 'color_pair_lr', | ||
| 'RR': 'color_pair_rr', | ||
| 'RL': 'color_pair_rl', | ||
| 'LL': 'color_pair_ll' | ||
| }; | ||
| return glyph.getStyle(feature, map[orientation] || 'color_nostrand'); | ||
| } | ||
|
|
||
| return 'hsl(' + Math.abs(score / 10) + ',50%,50%)'; | ||
| } | ||
| }; | ||
|
|
||
| return PairUtils; | ||
|
|
||
| }); |
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