# MafAlignments

Auto-generated from the config schema in the source — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Provided by the `maf` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/maf/src/LinearMafDisplay/mafAlignmentsConfigSchema.ts).

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

```js
{ 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](https://jbrowse.org/jb2/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface.

| Slot | Description |
| --- | --- |
| **show**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>DEFAULTS.showAlignments</code> | When off, only the bands above the rows render. |
| **rowProportion**<br>[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#number) = <code>DEFAULTS.rowProportion</code> | fraction of the row height each glyph fills |
| **showAllLetters**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>DEFAULTS.showAllLetters</code> | draw every base's letter, not only the mismatches' |
| **showAsUpperCase**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>DEFAULTS.showAsUpperCase</code> | uppercase all base letters |
| **showInversions**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>DEFAULTS.showInversions</code> | Inverted blocks get a diagonal hatch. |
| **showAnnotations**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>DEFAULTS.showAnnotations</code> | The per-species CDS reading frames from the MAF adapter's `annotationAdapter` (UCSC `mafFrames`). No effect without one. |