MafAlignments
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the maf plugin. View source.
The MAF display's alignments setting: the per-species rows, the band
that takes the height the bands above it leave, and what each row draws.
Example usage
{ type: 'LinearMafDisplay', alignments: { showAllLetters: true } }Config slots
A setting written to it names members one by one: a member left out stays as it is, and null resets one. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.
| Slot | Description |
|---|---|
showboolean = DEFAULTS.showAlignments | When off, only the bands above the rows render. |
rowProportionnumber = DEFAULTS.rowProportion | fraction of the row height each glyph fills |
showAllLettersboolean = DEFAULTS.showAllLetters | draw every base's letter, not only the mismatches' |
showAsUpperCaseboolean = DEFAULTS.showAsUpperCase | uppercase all base letters |
showInversionsboolean = DEFAULTS.showInversions | Inverted blocks get a diagonal hatch. |
showAnnotationsboolean = DEFAULTS.showAnnotations | The per-species CDS reading frames from the MAF adapter's annotationAdapter (UCSC mafFrames). No effect without one. |