Genome Browser : General parameters used in genome browser

# featureConfigurableProperties

Feature configurable properties
@features {id:[string];Feature id;[],fill:[color];Color for the feature;[]}
Type: array
Default: [id, name, label, hideName, fill, outline, dir, showDir, connect, offset, data, subtype, quality, signalToNoise, coordinate, sequence, trace, gaps, translate, hide, counter]
Used in: Genome

# featureCoordinateHeight

Default size in pixels of the coordinates height
Type: integer
Default: 14
Used in: Genome

# featureCoordinateShow

Flag use to show coordinates
Type: boolean
Default: true
Used in: Genome

# featureDirColor

Color for the strand direction of the feature in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# featureFillColor

Color for the fill of the feature in the genome browser
Type: color
Default: rgb(255,255,255)
Used in: Genome

# featureHeightDefault

Default size in pixels of the feature height
Type: integer
Default: 14
Used in: Genome

# featureNameAlign

Align for the feature name
Type: string
Default: center
Options: left, center, right
Used in: Genome

# featureNameBaseline

Baseline for the feature name
Type: string
Default: middle
Options: top, middle, bottom
Used in: Genome

# featureNameColor

Color for the text in feature name
Type: color
Default: rgb(0,0,0)
Used in: Genome

# featureNameFontSize

Font size for the text in feature name. Be aware that auto scaling font must be turned off for this property to take effect. A more convenient way to modify the size is to use the featureNameScaleFontFactor
Type: integer
Default: 12
Used in: Genome

# featureNameFontStyle

Font style for the feature name
Type: string
Default:
Options: , bold, italic, bold italic
Used in: Genome

# featureNameMargin

Margin used in feature name
Type: float
Default: 8
Used in: Genome

# featureNameRotate

Rotation in degrees for the feature name
Type: integer
Default:
Used in: Genome

# featureNameScaleFontFactor

Scaling factor used to increase or decrease the feature name font size in the canvas
Type: float
Default: 1
Used in: Genome

# featureQualityHeight

Default size in pixels of the quality height
Type: integer
Default: 14
Used in: Genome

# featureQualityShow

Flag use to show quality
Type: boolean
Default: true
Used in: Genome

# featureQualityValues

Flag use to show values for the quality
Type: boolean
Default: false
Used in: Genome

# featureSignalToNoiseHeight

Default size in pixels of the quality height
Type: integer
Default: 14
Used in: Genome

# featureSignalToNoiseShow

Flag use to show quality
Type: boolean
Default: true
Used in: Genome

# featureSignalToNoiseValues

Flag use to show values for the quality
Type: boolean
Default: false
Used in: Genome

# featureSpliceStyle

Default style for splicing in boxes
Type: string
Default: rect
Options: rect, broken
Used in: Genome

# featureStaggered

Flag use to stagger the features in the genome panel
Type: boolean
Default: false
Used in: Genome

# featureTraceHeight

Default size in pixels of the trace height
Type: integer
Default: 40
Used in: Genome

# featureTraceTrim

Default triming for nucleotide values in the traces (expressed in percent)
Type: integer
Default: 1
Used in: Genome

# featureTracesShow

Flag use to show traces
Type: boolean
Default: true
Used in: Genome

# featureTranslateHeight

Default size in pixels of the translation height
Type: integer
Default: 14
Used in: Genome

# featureTranslateShow

Flag use to show tranlation
Type: boolean
Default: true
Used in: Genome

# featureTypeDefault

Default type for the feature in the genome browser
Type: string
Default: line
Options: box, bar, heatmap, sequence, triangle, line
Used in: Genome

# featureWidthDefault

Default size in pixels of the feature width
Type: integer
Default: 3
Used in: Genome

# genomeResolution

Number to adjust the splines curvature
Type: string
Default: low
Options: low, medium, high
Used in: Genome

# genomeTicks

Number of ticks in the genome browser
Type: integer
Default: 50
Used in: Genome

# maxFeatureStringLen

Maximum length in characters a feature label can have so anything above is truncated
Type: integer
Default: 30
Used in: Genome

# periodTicksLabels

Number of ticks to skip between values in the genome browser
Type: integer
Default: 5
Used in: Genome

# sequenceAColor

Color for the adenines and alanines in the genome browser
Type: color
Default: rgb(0,103,0)
Used in: Genome

# sequenceAlign

Align for the sequence
Type: string
Default: center
Options: left, center, right
Used in: Genome

# sequenceBColor

Color for the degenerate C/G/T and asparagines in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceBaseline

Baseline for the sequence
Type: string
Default: middle
Options: top, middle, bottom
Used in: Genome

# sequenceCColor

Color for the cytosines and cysteins in the genome browser
Type: color
Default: rgb(0,0,255)
Used in: Genome

# sequenceColor

Color for the text in sequence
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceDColor

Color for the degenerate A/G/T and aspartic acids in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceEColor

Color for the glutamic acids in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceEndColor

Color for the end codon in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceFColor

Color for the phenylalanines in the genome browser
Type: color
Default: rgb(0,0,255)
Used in: Genome

# sequenceFillColor

Color for the background when showing sequnces in the box or sequence object in the Genome. The default is to use the background of the object. If specied a valid color then all the background of sequences will be uniform
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceFontSize

Font size for the text in sequence. Be aware that auto scaling font must be turned off for this property to take effect. A more convenient way to modify the size is to use the sequenceScaleFontFactor
Type: integer
Default: 12
Used in: Genome

# sequenceFontStyle

Font style for the sequence
Type: string
Default:
Options: , bold, italic, bold italic
Used in: Genome

# sequenceGAPColor

Color for the deletions, insertions and gaps in the genome browser
Type: color
Default: rgb(255,0,255)
Used in: Genome

# sequenceGColor

Color for the guanines and glycines in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceHColor

Color for the degenerate A/C/T and histidines in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceIColor

Color for the isoleucines in the genome browser
Type: color
Default: rgb(0,103,0)
Used in: Genome

# sequenceKColor

Color for the degenerate G/T and lysines in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceLColor

Color for the leucines in the genome browser
Type: color
Default: rgb(0,103,0)
Used in: Genome

# sequenceMColor

Color for the degenerate A/G and methionines in the genome browser
Type: color
Default: rgb(0,103,0)
Used in: Genome

# sequenceMargin

Margin used in sequence
Type: float
Default: 8
Used in: Genome

# sequenceNColor

Color for the degenerate A/C/G/T and asparagines in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequencePColor

Color for the prolines in the genome browser
Type: color
Default: rgb(255,165,0)
Used in: Genome

# sequenceQColor

Color for the glutamines in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceRColor

Color for the degenerate A/G and arginines in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceRotate

Rotation in degrees for the sequence
Type: integer
Default:
Used in: Genome

# sequenceSColor

Color for the degenerate G/C and serines in the genome browser
Type: color
Default: rgb(255,165,0)
Used in: Genome

# sequenceScaleFontFactor

Scaling factor used to increase or decrease the sequence font size in the canvas
Type: float
Default: 1
Used in: Genome

# sequenceStartColor

Color for the start codon in the genome browser
Type: color
Default: rgb(0,204,0)
Used in: Genome

# sequenceTColor

Color for the thymidines and threonines in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceUColor

Color for the uracils in the genome browser
Type: color
Default: rgb(255,0,0)
Used in: Genome

# sequenceVColor

Color for the degenerate A/C/G and valines in the genome browser
Type: color
Default: rgb(0,103,0)
Used in: Genome

# sequenceWColor

Color for the degenerate A/T and tryptophans in the genome browser
Type: color
Default: rgb(0,0,255)
Used in: Genome

# sequenceXColor

Color for the any aminoacid code in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# sequenceYColor

Color for the degenerate C/T and tyrosines in the genome browser
Type: color
Default: rgb(0,0,255)
Used in: Genome

# sequenceZColor

Color for the glutamines in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# showFeatureNameThereshold

Threshehold used to set te limit when there are too many features in the genome browser
Type: integer
Default: 20
Used in: Genome

# subtracksMaxDefault

Maximum number of subtracks to show in a track
Type: integer
Default: 8
Used in: Genome

# trackConfigurableProperties

Track configurable properties
@tracks {name:[string];Track name;[]}
Type: array
Default: [name, hideName, hideFeatureNames, type, height, fill, outline, data, hide, connect, subtracksMax, highlight]
Used in: Genome

# trackDirColor

Color for the strand direction of the tracks in the genome browser
Type: color
Default: rgb(0,0,0)
Used in: Genome

# trackFillColor

Color for the fill of the tracks in the genome browser
Type: color
Default: rgb(255,255,255)
Used in: Genome

# trackNameAlign

Align for the track name
Type: string
Default: center
Options: left, center, right
Used in: Genome

# trackNameBaseline

Baseline for the track name
Type: string
Default: middle
Options: top, middle, bottom
Used in: Genome

# trackNameColor

Color for the text in track name
Type: color
Default: rgb(0,0,0)
Used in: Genome

# trackNameFontSize

Font size for the text in track name. Be aware that auto scaling font must be turned off for this property to take effect. A more convenient way to modify the size is to use the trackNameScaleFontFactor
Type: integer
Default: 12
Used in: Genome

# trackNameFontStyle

Font style for the track name
Type: string
Default:
Options: , bold, italic, bold italic
Used in: Genome

# trackNameMargin

Margin used in track name
Type: float
Default: 8
Used in: Genome

# trackNameRotate

Rotation in degrees for the track name
Type: integer
Default:
Used in: Genome

# trackNameScaleFontFactor

Scaling factor used to increase or decrease the track name font size in the canvas
Type: float
Default: 1
Used in: Genome

# wireColor

Color for the ticks in the genome browser
Type: color
Default: rgba(204,204,204,0.1)
Used in: Genome