/**
* Genetic test result per Bennett standard
*/
export interface GeneTest {
type: '-' | 'S' | 'T'; // - = unknown, S = screening, T = tested
result: '-' | 'P' | 'N'; // - = unknown/VUS, P = positive, N = negative
}
/**
* Condition/disease affecting an individual
* Per Bennett standard: free text condition name with optional age at diagnosis
*/
export interface Condition {
name: string; // Free text: "Huntington's disease", "Breast cancer", "Type 2 diabetes"
age?: number; // Age at diagnosis/onset
}
/**
* Individual in the pedigree
*/
export interface Individual {
name: string;
sex: 'M' | 'F' | 'U'; // Sex assigned at birth (Bennett 2008)
gender?: 'M' | 'F' | 'NB' | 'GNC' | 'TM' | 'TF'; // Gender identity (Bennett 2022): NB=non-binary, GNC=gender non-conforming, TM=trans male, TF=trans female
sex_assigned_at_birth?: 'M' | 'F' | 'U'; // Explicit SAAB when gender differs (Bennett 2022)
display_name?: string;
top_level?: boolean;
proband?: boolean;
mother?: string;
father?: string;
age?: number;
yob?: number;
generation?: number; // Generation number (I, II, III, etc.) - Bennett numbering system
status?: number; // 0 = alive, 1 = deceased
mztwin?: string; // MZ twin group identifier
dztwin?: string; // DZ twin group identifier
ashkenazi?: number; // 0=no, 1=yes (Bennett: A marker)
noparents?: boolean;
adoption_type?: 'in' | 'out' | 'foster'; // Bennett: adoption direction (in=adopted into family, out=placed for adoption, foster=temporary)
birth_order?: number; // Bennett: birth order in sibling group (1, 2, 3, etc.) - displayed as Roman numerals
carrier?: boolean; // Carrier status (Bennett: dot in center)
gene_copy_number?: 'heterozygous' | 'homozygous' | 'compound_heterozygous'; // Bennett: gene copy number for carrier testing
pregnant?: boolean; // Pregnancy (Bennett: P inside symbol)
terminated?: boolean; // Stillbirth/SAB/termination (Bennett: small/large triangle)
terminated_age?: number; // Gestational age in weeks (affects triangle size)
pregnancy_outcome?:
| 'miscarriage'
| 'induced_termination'
| 'ectopic'
| 'stillbirth'
| 'unknown'; // Bennett: specific pregnancy outcome type
divorced?: boolean; // Divorced/separated from partner (Bennett: hash marks)
anticipation?: boolean; // Genetic anticipation (Bennett: special marker)
ectopic?: boolean; // Ectopic pregnancy (Bennett: distinct marker)
consultand?: boolean; // Consultand (vs proband - person seeking counseling)
infertility?: boolean; // Infertility (Bennett: crossed-out symbol or marker)
no_children_by_choice?: boolean; // No children by choice (Bennett: line through offspring line)
yod?: number; // Year of death (to calculate age at death)
obligate_carrier?: boolean; // Obligate carrier (inferred from pedigree)
art_type?: 'egg_donor' | 'sperm_donor' | 'embryo_donor' | 'surrogate'; // Bennett: Assisted Reproductive Technology conception type
relationship_type?: 'married' | 'unmarried' | 'common_law' | 'consensual'; // Bennett: partnership type (applied to one partner)
// Conditions/diseases - FREE TEXT per Bennett standard
// Examples:
// conditions: [{ name: "Huntington's disease", age: 45 }]
// conditions: [{ name: "Breast cancer", age: 42 }, { name: "Ovarian cancer", age: 55 }]
// conditions: [{ name: "Cystic fibrosis" }] // no age = affected status only
conditions?: Condition[];
// Genetic tests - use pattern: {gene}_gene_test
// Examples: brca1_gene_test, htt_gene_test, apoe_gene_test
[key: string]:
| string
| number
| boolean
| GeneTest
| Condition[]
| undefined;
}
/**
* Color palette for auto-assigning colors to conditions
*/
export const COLOR_PALETTE = [
'#F68F35', // Orange
'#4DAA4D', // Green
'#4289BA', // Blue
'#D5494A', // Red
'#9370DB', // Purple
'#20B2AA', // Teal
'#FF6347', // Tomato
'#6A5ACD', // Slate blue
'#CD853F', // Peru
'#708090', // Slate gray
];
export interface PedigreeOptions {
width?: number;
height?: number;
symbol_size?: number;
background?: string;
node_background?: string;
font_size?: string;
font_family?: string;
labels?: string[];
}
export const DEFAULT_OPTIONS: Required<PedigreeOptions> = {
width: 800,
height: 600,
symbol_size: 35,
background: '#ffffff',
node_background: '#ffffff',
font_size: '12px',
font_family: 'Arial, sans-serif',
labels: ['age'],
};
export interface RenderedNode {
individual: Individual;
x: number;
y: number;
generation: number;
}
export interface FamilyUnit {
father: Individual;
mother: Individual;
children: Individual[];
}
