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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

# 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

# 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

# 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: 10
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

On This Page
featureConfigurableProperties featureCoordinateHeight featureCoordinateShow featureDirColor featureFillColor featureHeightDefault featureNameAlign featureNameColor featureNameFontSize featureNameFontStyle featureNameMargin featureNameRotate featureNameScaleFontFactor featureQualityHeight featureQualityShow featureQualityValues featureSignalToNoiseHeight featureSignalToNoiseShow featureSignalToNoiseValues featureSpliceStyle featureStaggered featureTraceHeight featureTraceTrim featureTracesShow featureTranslateHeight featureTranslateShow featureTypeDefault featureWidthDefault genomeResolution genomeTicks maxFeatureStringLen periodTicksLabels sequenceAColor sequenceAlign sequenceBColor sequenceCColor sequenceColor sequenceDColor sequenceEColor sequenceEndColor sequenceFColor sequenceFillColor sequenceFontSize sequenceFontStyle sequenceGAPColor sequenceGColor sequenceHColor sequenceIColor sequenceKColor sequenceLColor sequenceMColor sequenceMargin sequenceNColor sequencePColor sequenceQColor sequenceRColor sequenceRotate sequenceSColor sequenceScaleFontFactor sequenceStartColor sequenceTColor sequenceUColor sequenceVColor sequenceWColor sequenceXColor sequenceYColor sequenceZColor showFeatureNameThereshold subtracksMaxDefault trackConfigurableProperties trackDirColor trackFillColor trackNameAlign trackNameColor trackNameFontSize trackNameFontStyle trackNameMargin trackNameRotate trackNameScaleFontFactor wireColor
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