sourmash
Version:
tools for comparing biological sequences with k-mer sketches
522 lines (459 loc) • 14.8 kB
JavaScript
let wasm;
export function __wbg_set_wasm(val) {
wasm = val;
}
function addToExternrefTable0(obj) {
const idx = wasm.__externref_table_alloc();
wasm.__wbindgen_export_2.set(idx, obj);
return idx;
}
function handleError(f, args) {
try {
return f.apply(this, args);
} catch (e) {
const idx = addToExternrefTable0(e);
wasm.__wbindgen_exn_store(idx);
}
}
const lTextDecoder = typeof TextDecoder === 'undefined' ? (0, module.require)('util').TextDecoder : TextDecoder;
let cachedTextDecoder = new lTextDecoder('utf-8', { ignoreBOM: true, fatal: true });
cachedTextDecoder.decode();
let cachedUint8ArrayMemory0 = null;
function getUint8ArrayMemory0() {
if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
}
return cachedUint8ArrayMemory0;
}
function getStringFromWasm0(ptr, len) {
ptr = ptr >>> 0;
return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
}
function debugString(val) {
// primitive types
const type = typeof val;
if (type == 'number' || type == 'boolean' || val == null) {
return `${val}`;
}
if (type == 'string') {
return `"${val}"`;
}
if (type == 'symbol') {
const description = val.description;
if (description == null) {
return 'Symbol';
} else {
return `Symbol(${description})`;
}
}
if (type == 'function') {
const name = val.name;
if (typeof name == 'string' && name.length > 0) {
return `Function(${name})`;
} else {
return 'Function';
}
}
// objects
if (Array.isArray(val)) {
const length = val.length;
let debug = '[';
if (length > 0) {
debug += debugString(val[0]);
}
for(let i = 1; i < length; i++) {
debug += ', ' + debugString(val[i]);
}
debug += ']';
return debug;
}
// Test for built-in
const builtInMatches = /\[object ([^\]]+)\]/.exec(toString.call(val));
let className;
if (builtInMatches && builtInMatches.length > 1) {
className = builtInMatches[1];
} else {
// Failed to match the standard '[object ClassName]'
return toString.call(val);
}
if (className == 'Object') {
// we're a user defined class or Object
// JSON.stringify avoids problems with cycles, and is generally much
// easier than looping through ownProperties of `val`.
try {
return 'Object(' + JSON.stringify(val) + ')';
} catch (_) {
return 'Object';
}
}
// errors
if (val instanceof Error) {
return `${val.name}: ${val.message}\n${val.stack}`;
}
// TODO we could test for more things here, like `Set`s and `Map`s.
return className;
}
let WASM_VECTOR_LEN = 0;
const lTextEncoder = typeof TextEncoder === 'undefined' ? (0, module.require)('util').TextEncoder : TextEncoder;
let cachedTextEncoder = new lTextEncoder('utf-8');
const encodeString = (typeof cachedTextEncoder.encodeInto === 'function'
? function (arg, view) {
return cachedTextEncoder.encodeInto(arg, view);
}
: function (arg, view) {
const buf = cachedTextEncoder.encode(arg);
view.set(buf);
return {
read: arg.length,
written: buf.length
};
});
function passStringToWasm0(arg, malloc, realloc) {
if (realloc === undefined) {
const buf = cachedTextEncoder.encode(arg);
const ptr = malloc(buf.length, 1) >>> 0;
getUint8ArrayMemory0().subarray(ptr, ptr + buf.length).set(buf);
WASM_VECTOR_LEN = buf.length;
return ptr;
}
let len = arg.length;
let ptr = malloc(len, 1) >>> 0;
const mem = getUint8ArrayMemory0();
let offset = 0;
for (; offset < len; offset++) {
const code = arg.charCodeAt(offset);
if (code > 0x7F) break;
mem[ptr + offset] = code;
}
if (offset !== len) {
if (offset !== 0) {
arg = arg.slice(offset);
}
ptr = realloc(ptr, len, len = offset + arg.length * 3, 1) >>> 0;
const view = getUint8ArrayMemory0().subarray(ptr + offset, ptr + len);
const ret = encodeString(arg, view);
offset += ret.written;
ptr = realloc(ptr, len, offset, 1) >>> 0;
}
WASM_VECTOR_LEN = offset;
return ptr;
}
let cachedDataViewMemory0 = null;
function getDataViewMemory0() {
if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
}
return cachedDataViewMemory0;
}
function _assertClass(instance, klass) {
if (!(instance instanceof klass)) {
throw new Error(`expected instance of ${klass.name}`);
}
}
function takeFromExternrefTable0(idx) {
const value = wasm.__wbindgen_export_2.get(idx);
wasm.__externref_table_dealloc(idx);
return value;
}
function isLikeNone(x) {
return x === undefined || x === null;
}
let cachedUint32ArrayMemory0 = null;
function getUint32ArrayMemory0() {
if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
}
return cachedUint32ArrayMemory0;
}
function passArray32ToWasm0(arg, malloc) {
const ptr = malloc(arg.length * 4, 4) >>> 0;
getUint32ArrayMemory0().set(arg, ptr / 4);
WASM_VECTOR_LEN = arg.length;
return ptr;
}
const ComputeParametersFinalization = (typeof FinalizationRegistry === 'undefined')
? { register: () => {}, unregister: () => {} }
: new FinalizationRegistry(ptr => wasm.__wbg_computeparameters_free(ptr >>> 0, 1));
export class ComputeParameters {
__destroy_into_raw() {
const ptr = this.__wbg_ptr;
this.__wbg_ptr = 0;
ComputeParametersFinalization.unregister(this);
return ptr;
}
free() {
const ptr = this.__destroy_into_raw();
wasm.__wbg_computeparameters_free(ptr, 0);
}
constructor() {
const ret = wasm.computeparameters_new_with_params();
this.__wbg_ptr = ret >>> 0;
ComputeParametersFinalization.register(this, this.__wbg_ptr, this);
return this;
}
/**
* @param {Uint32Array} ksizes
*/
set_ksizes(ksizes) {
const ptr0 = passArray32ToWasm0(ksizes, wasm.__wbindgen_malloc);
const len0 = WASM_VECTOR_LEN;
wasm.computeparameters_set_ksizes(this.__wbg_ptr, ptr0, len0);
}
/**
* @param {number} scaled
*/
set_scaled(scaled) {
wasm.computeparameters_set_scaled(this.__wbg_ptr, scaled);
}
/**
* @param {number} num
*/
set_num(num) {
wasm.computeparameters_set_num(this.__wbg_ptr, num);
}
/**
* @param {boolean} is_protein
*/
set_protein(is_protein) {
wasm.computeparameters_set_protein(this.__wbg_ptr, is_protein);
}
/**
* @param {boolean} dayhoff
*/
set_dayhoff(dayhoff) {
wasm.computeparameters_set_dayhoff(this.__wbg_ptr, dayhoff);
}
/**
* @param {boolean} hp
*/
set_hp(hp) {
wasm.computeparameters_set_hp(this.__wbg_ptr, hp);
}
/**
* @param {boolean} track
*/
set_track_abundance(track) {
wasm.computeparameters_set_track_abundance(this.__wbg_ptr, track);
}
/**
* @param {number} seed
*/
set_seed(seed) {
wasm.computeparameters_set_seed(this.__wbg_ptr, seed);
}
}
const KmerMinHashFinalization = (typeof FinalizationRegistry === 'undefined')
? { register: () => {}, unregister: () => {} }
: new FinalizationRegistry(ptr => wasm.__wbg_kmerminhash_free(ptr >>> 0, 1));
export class KmerMinHash {
__destroy_into_raw() {
const ptr = this.__wbg_ptr;
this.__wbg_ptr = 0;
KmerMinHashFinalization.unregister(this);
return ptr;
}
free() {
const ptr = this.__destroy_into_raw();
wasm.__wbg_kmerminhash_free(ptr, 0);
}
/**
* @param {number} num
* @param {number} ksize
* @param {boolean} is_protein
* @param {boolean} dayhoff
* @param {boolean} hp
* @param {number} seed
* @param {number} scaled
* @param {boolean} track_abundance
*/
constructor(num, ksize, is_protein, dayhoff, hp, seed, scaled, track_abundance) {
const ret = wasm.kmerminhash_new_with_scaled(num, ksize, is_protein, dayhoff, hp, seed, scaled, track_abundance);
this.__wbg_ptr = ret >>> 0;
KmerMinHashFinalization.register(this, this.__wbg_ptr, this);
return this;
}
/**
* @param {string} buf
*/
add_sequence_js(buf) {
const ptr0 = passStringToWasm0(buf, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
const len0 = WASM_VECTOR_LEN;
const ret = wasm.kmerminhash_add_sequence_js(this.__wbg_ptr, ptr0, len0);
if (ret[1]) {
throw takeFromExternrefTable0(ret[0]);
}
}
/**
* @returns {string}
*/
to_json() {
let deferred2_0;
let deferred2_1;
try {
const ret = wasm.kmerminhash_to_json(this.__wbg_ptr);
var ptr1 = ret[0];
var len1 = ret[1];
if (ret[3]) {
ptr1 = 0; len1 = 0;
throw takeFromExternrefTable0(ret[2]);
}
deferred2_0 = ptr1;
deferred2_1 = len1;
return getStringFromWasm0(ptr1, len1);
} finally {
wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
}
}
}
const SignatureFinalization = (typeof FinalizationRegistry === 'undefined')
? { register: () => {}, unregister: () => {} }
: new FinalizationRegistry(ptr => wasm.__wbg_signature_free(ptr >>> 0, 1));
export class Signature {
__destroy_into_raw() {
const ptr = this.__wbg_ptr;
this.__wbg_ptr = 0;
SignatureFinalization.unregister(this);
return ptr;
}
free() {
const ptr = this.__destroy_into_raw();
wasm.__wbg_signature_free(ptr, 0);
}
/**
* @param {ComputeParameters} params
*/
constructor(params) {
_assertClass(params, ComputeParameters);
const ret = wasm.signature_new_from_params(params.__wbg_ptr);
this.__wbg_ptr = ret >>> 0;
SignatureFinalization.register(this, this.__wbg_ptr, this);
return this;
}
/**
* @param {string} buf
*/
add_sequence_js(buf) {
const ptr0 = passStringToWasm0(buf, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
const len0 = WASM_VECTOR_LEN;
const ret = wasm.signature_add_sequence_js(this.__wbg_ptr, ptr0, len0);
if (ret[1]) {
throw takeFromExternrefTable0(ret[0]);
}
}
/**
* @param {File} fp
* @param {Function | undefined} [callback]
*/
add_from_file(fp, callback) {
const ret = wasm.signature_add_from_file(this.__wbg_ptr, fp, isLikeNone(callback) ? 0 : addToExternrefTable0(callback));
if (ret[1]) {
throw takeFromExternrefTable0(ret[0]);
}
}
/**
* @returns {string}
*/
to_json() {
let deferred2_0;
let deferred2_1;
try {
const ret = wasm.signature_to_json(this.__wbg_ptr);
var ptr1 = ret[0];
var len1 = ret[1];
if (ret[3]) {
ptr1 = 0; len1 = 0;
throw takeFromExternrefTable0(ret[2]);
}
deferred2_0 = ptr1;
deferred2_1 = len1;
return getStringFromWasm0(ptr1, len1);
} finally {
wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
}
}
/**
* @returns {number}
*/
size() {
const ret = wasm.signature_size(this.__wbg_ptr);
return ret >>> 0;
}
}
export function __wbg_apply_e561e3b9b5a01b05() { return handleError(function (arg0, arg1, arg2) {
const ret = arg0.apply(arg1, arg2);
return ret;
}, arguments) };
export function __wbg_buffer_6e1d53ff183194fc(arg0) {
const ret = arg0.buffer;
return ret;
};
export function __wbg_byteLength_3c7a1d3824c799bc(arg0) {
const ret = arg0.byteLength;
return ret;
};
export function __wbg_length_2e63ba34c4121df5(arg0) {
const ret = arg0.length;
return ret;
};
export function __wbg_new_23362fa370a0a372(arg0) {
const ret = new Uint8Array(arg0);
return ret;
};
export function __wbg_new_4d81617a04bc1b5b(arg0, arg1) {
const ret = new Error(getStringFromWasm0(arg0, arg1));
return ret;
};
export function __wbg_new_57f8e10a89ba544b() { return handleError(function () {
const ret = new FileReaderSync();
return ret;
}, arguments) };
export function __wbg_newwithlength_7718eaa2b2cf3d39(arg0) {
const ret = new Array(arg0 >>> 0);
return ret;
};
export function __wbg_readAsArrayBuffer_4553a457b952e5f4() { return handleError(function (arg0, arg1) {
const ret = arg0.readAsArrayBuffer(arg1);
return ret;
}, arguments) };
export function __wbg_set_7b70226104a82921(arg0, arg1, arg2) {
arg0.set(arg1, arg2 >>> 0);
};
export function __wbg_set_a1fb6291729caffb(arg0, arg1, arg2) {
arg0[arg1 >>> 0] = arg2;
};
export function __wbg_size_965da315036ee58c(arg0) {
const ret = arg0.size;
return ret;
};
export function __wbg_slice_2f49f67ad5c9299a() { return handleError(function (arg0, arg1, arg2) {
const ret = arg0.slice(arg1, arg2);
return ret;
}, arguments) };
export function __wbindgen_debug_string(arg0, arg1) {
const ret = debugString(arg1);
const ptr1 = passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
const len1 = WASM_VECTOR_LEN;
getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
};
export function __wbindgen_init_externref_table() {
const table = wasm.__wbindgen_export_2;
const offset = table.grow(4);
table.set(0, undefined);
table.set(offset + 0, undefined);
table.set(offset + 1, null);
table.set(offset + 2, true);
table.set(offset + 3, false);
;
};
export function __wbindgen_memory() {
const ret = wasm.memory;
return ret;
};
export function __wbindgen_number_new(arg0) {
const ret = arg0;
return ret;
};
export function __wbindgen_throw(arg0, arg1) {
throw new Error(getStringFromWasm0(arg0, arg1));
};