seqviz-plus/dist/elements.d.ts

An extension for Seqviz

/** Range is a single element with a range and direction in the viewer */
export interface Range {
    direction: -1 | 0 | 1;
    end: number;
    start: number;
}
/** NameRange elements have been parsed to include an id and name */
export interface NameRange extends Range {
    color?: string;
    id: string;
    name: string;
}
/** AnnotationProp is an annotation provided to SeqViz via the annotations prop. */
export interface AnnotationProp {
    color?: string;
    direction?: number | string;
    end: number;
    name: string;
    start: number;
}
/** Annotation is an annotation after parsing. */
export interface Annotation extends NameRange {
    color: string;
}
/** Translation is a single translated CDS. */
export interface Translation extends NameRange {
    AAseq: string;
    direction: -1 | 1;
}
/** Primer is a single primer for PCR. Not visualized right now. */
export interface Primer extends NameRange {
    color: string;
    direction: 1 | -1;
}
/** HighlightProp is a region of the plasmid and the desired highlight for that region. */
export interface HighlightProp {
    color?: string;
    end: number;
    start: number;
}
/** Highlight is the processed version of HighlightProp */
export interface Highlight extends HighlightProp {
    direction: 1 | -1;
    id: string;
    name: string;
}
export interface Part {
    annotations: Annotation[];
    compSeq: string;
    cutSites: CutSite[];
    name: string;
    primers: Primer[];
    seq: string;
}
export interface Size {
    height: number;
    width: number;
}
export interface Coor {
    x: number;
    y: number;
}
/** a single enzyme to use to digest the sequence with */
export interface Enzyme {
    /** an optional color to highlight the recognition site with */
    color?: string;
    /** the index of the cut-site on the forward strand relative to the start of the recognition site */
    fcut: number;
    /** name is the name of the enzyme. Used in the label above a cut-site */
    name: string;
    /** an optional range over which this enzyme's cut-sites should be limited */
    range?: {
        end: number;
        start: number;
    };
    /** the index of the cut-site on the reverse strand relative to the start of the recognition site */
    rcut: number;
    /** the recognition sequence */
    rseq: string;
}
/**
 * a single recognition site on the sequence
 *
 * TODO: it should be possible to remove name from below (it's on the enzyme)
 * and calc fcut/rcut from start/end + enzyme.fcut/rcut
 */
export interface CutSite extends NameRange {
    /** `1` if top strand (`seq`), `-1` if bottom strand (`compSeq`) */
    direction: 1 | -1;
    /** enzyme used to create this cut-site */
    enzyme: Enzyme;
    /** index relative to start index of the cut on the top strand */
    fcut: number;
    /** index relative to start index of the cut on the bottom strand */
    rcut: number;
}
/** supported input sequence types */
export declare type SeqType = "dna" | "rna" | "aa" | "unknown";