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igv

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Embeddable genomic visualization component based on the Integrative Genomics Viewer

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function createElementWithString(htmlString){ const tempDiv = document.createElement('div'); tempDiv.innerHTML = htmlString; return tempDiv.firstElementChild; } function div(options) { return create$1("div", options); } function create$1(tag, options) { const elem = document.createElement(tag); if (options) { if (options.class) { elem.classList.add(options.class); } if (options.id) { elem.id = options.id; } if(options.style) { applyStyle(elem, options.style); } } return elem; } function hide(elem) { const cssStyle = getComputedStyle(elem); if(cssStyle.display !== "none") { elem._initialDisplay = cssStyle.display; } elem.style.display = "none"; } function show(elem) { //const currentDisplay = getComputedStyle(elem).display; //if (currentDisplay === "none") { const d = elem._initialDisplay || "block"; elem.style.display = d; // } } function pageCoordinates(e) { if (e.type.startsWith("touch")) { const touch = e.touches[0]; return {x: touch.pageX, y: touch.pageY}; } else { return {x: e.pageX, y: e.pageY} } } function applyStyle(elem, style) { for (let key of Object.keys(style)) { elem.style[key] = style[key]; } } function guid$2 () { return ("0000" + (Math.random() * Math.pow(36, 4) << 0).toString(36)).slice(-4); } let getMouseXY = (domElement, { clientX, clientY }) => { // DOMRect object with eight properties: left, top, right, bottom, x, y, width, height const { left, top, width, height } = domElement.getBoundingClientRect(); const x = clientX - left; const y = clientY - top; return { x, y, xNormalized: x/width, yNormalized: y/height, width, height }; }; /** * Translate the mouse coordinates for the event to the coordinates for the given target element * @param event * @param domElement * @returns {{x: number, y: number}} */ function translateMouseCoordinates(event, domElement) { const { clientX, clientY } = event; return getMouseXY(domElement, { clientX, clientY }); } /** * Generic container for UI components */ class Panel { constructor() { this.elem = create$1('div', { class: 'igv-ui-panel-column' }); } add(component) { if(component instanceof Node) { this.elem.appendChild(component); } else if(typeof component === 'object') { this.elem.appendChild(component.elem); } else { // Assuming a string, possibly html const wrapper = div(); wrapper.innerHTML = component; this.elem.appendChild(wrapper); this.html = wrapper; } } } function createCheckbox$1(name, initialState) { const container = div({class: 'igv-ui-trackgear-popover-check-container'}); const svg = iconMarkup('check', (true === initialState ? 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This is not a general purprose function, * it makes several options specific to igv dialogs, the primary one being that the * target is absolutely positioned in pixel coordinates */ let dragData; // Its assumed we are only dragging one element at a time. function makeDraggable(target, handle, constraint) { handle.addEventListener('mousedown', dragStart.bind(target)); function dragStart(event) { event.stopPropagation(); event.preventDefault(); const dragFunction = drag.bind(this); const dragEndFunction = dragEnd.bind(this); const computedStyle = getComputedStyle(this); const boundingClientRect = this.getBoundingClientRect(); dragData = { constraint, dragFunction, dragEndFunction, screenX: event.screenX, screenY: event.screenY, minDy: -boundingClientRect.top, // Don't slide upwards more than this minDx: -boundingClientRect.left, top: parseInt(computedStyle.top.replace("px", "")), left: parseInt(computedStyle.left.replace("px", "")) }; document.addEventListener('mousemove', dragFunction); document.addEventListener('mouseup', dragEndFunction); document.addEventListener('mouseleave', dragEndFunction); document.addEventListener('mouseexit', dragEndFunction); } } function drag(event) { if (!dragData) { console.error("No drag data!"); return } event.stopPropagation(); event.preventDefault(); const dx = Math.max(dragData.minDx, event.screenX - dragData.screenX); const dy = Math.max(dragData.minDy, event.screenY - dragData.screenY); const left = dragData.left + dx; const top = dragData.top + dy; this.style.left = `${left}px`; this.style.top = `${top}px`; } function dragEnd(event) { if (!dragData) { console.error("No drag data!"); return } event.stopPropagation(); event.preventDefault(); const dragFunction = dragData.dragFunction; const dragEndFunction = dragData.dragEndFunction; document.removeEventListener('mousemove', dragFunction); document.removeEventListener('mouseup', dragEndFunction); document.removeEventListener('mouseleave', dragEndFunction); document.removeEventListener('mouseexit', dragEndFunction); dragData = undefined; } class Dialog { constructor({parent, label, content, okHandler, cancelHandler}) { this.parent = parent; const cancel = () => { this.elem.style.display = 'none'; if (typeof cancelHandler === 'function') { cancelHandler(this); } }; // dialog container this.elem = div(); this.elem.classList.add('igv-ui-generic-dialog-container', 'igv-ui-center-fixed'); // dialog header const header = div({class: 'igv-ui-generic-dialog-header'}); this.elem.appendChild(header); attachDialogCloseHandlerWithParent(header, cancel); // dialog label if(label) { const labelDiv = div({class: 'igv-ui-dialog-one-liner'}); this.elem.appendChild(labelDiv); labelDiv.innerHTML = label; } // input container content.elem.style.margin = '16px'; this.elem.appendChild(content.elem); this.content = content; // ok | cancel const buttons = div({class: 'igv-ui-generic-dialog-ok-cancel'}); this.elem.appendChild(buttons); // ok this.ok = div(); buttons.appendChild(this.ok); this.ok.textContent = 'OK'; // cancel this.cancel = div(); buttons.appendChild(this.cancel); this.cancel.textContent = 'Cancel'; this.callback = undefined; this.ok.addEventListener('click', e => { this.elem.style.display = 'none'; if (typeof okHandler === 'function') { okHandler(this); } else if (this.callback && typeof this.callback === 'function') { this.callback(this); } }); this.cancel.addEventListener('click', cancel); makeDraggable(this.elem, header); // Consume all clicks in component this.elem.addEventListener('click', (e) => { e.preventDefault(); e.stopPropagation(); }); } present(options, e) { if (options.label && this.label) { this.label.textContent = options.label; } if (options.html) { const div = this.content.html; div.innerHTML = options.html; } if (options.text) { const div = this.content.html; div.innerText = options.text; } if (options.value && this.input) { this.input.value = options.value; } if (options.callback) { this.callback = options.callback; } const { top} = e.currentTarget.parentElement.getBoundingClientRect(); this.elem.style.top = `${ top }px`; this.elem.style.display = 'flex'; } } /** * Covers string literals and String objects * @param x * @returns {boolean} */ function isString$3(x) { return typeof x === "string" || x instanceof String } // StackOverflow: http://stackoverflow.com/a/10810674/116169 function numberFormatter$1(rawNumber) { var dec = String(rawNumber).split(/[.,]/), sep = ',', decsep = '.'; return dec[0].split('').reverse().reduce(function (prev, now, i) { return i % 3 === 0 ? prev + sep + now : prev + now; }).split('').reverse().join('') + (dec[1] ? decsep + dec[1] : ''); } const splitLines$3 = function (string) { return string.split(/\n|\r\n|\r/g); }; function splitStringRespectingQuotes(string, delim) { var tokens = [], len = string.length, i, n = 0, quote = false, c; if (len > 0) { tokens[n] = string.charAt(0); for (i = 1; i < len; i++) { c = string.charAt(i); if (c === '"') { quote = !quote; } else if (!quote && c === delim) { n++; tokens[n] = ""; } else { tokens[n] += c; } } } return tokens; } function stripQuotes$2(str) { if(str === undefined) { return str; } if(str.startsWith("'") || str.startsWith('"')) { str = str.substring(1); } if (str.endsWith("'") || str.endsWith('"')) { str = str.substring(0, str.length - 1); } return str; } function capitalize(str) { return str.length > 0 ? str.charAt(0).toUpperCase() + str.slice(1) : str; } /** * Parse a locus string and return a range object. Locus string is of the form chr:start-end. End is optional * */ function parseLocusString$1(string) { const t1 = string.split(":"); const t2 = t1[1].split("-"); const range = { chr: t1[0], start: Number.parseInt(t2[0].replace(/,/g, '')) - 1 }; if (t2.length > 1) { range.end = Number.parseInt(t2[1].replace(/,/g, '')); } else { range.end = range.start + 1; } return range; } /** * Return the filename from the path. Example * https://foo.com/bar.bed?param=2 => bar.bed * @param urlOrFile */ function getFilename$2(urlOrFile) { if (urlOrFile.name !== undefined) { return urlOrFile.name } else if (isString$3(urlOrFile)) { let index = urlOrFile.lastIndexOf("/"); let filename = index < 0 ? urlOrFile : urlOrFile.substr(index + 1); //Strip parameters -- handle local files later index = filename.indexOf("?"); if (index > 0) { filename = filename.substr(0, index); } return filename } else { throw Error(`Expected File or string, got ${typeof urlOrFile}`) } } /** * Test if object is a File or File-like object. * * @param object */ function isFile(object) { if(!object) { return false; } return typeof object !== 'function' && (object instanceof File || (object.hasOwnProperty("name") && typeof object.slice === 'function' && typeof object.arrayBuffer === 'function')) } function download(filename, data) { const element = document.createElement('a'); element.setAttribute('href', data); element.setAttribute('download', filename); element.style.display = 'none'; document.body.appendChild(element); element.click(); document.body.removeChild(element); } if (typeof process === 'object' && typeof window === 'undefined') { global.atob = function (str) { return Buffer.from(str, 'base64').toString('binary'); }; } function parseUri(str) { var o = options, m = o.parser["loose"].exec(str), uri = {}, i = 14; while (i--) uri[o.key[i]] = m[i] || ""; uri[o.q.name] = {}; uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) { if ($1) uri[o.q.name][$1] = $2; }); return uri; } const options = { strictMode: false, key: ["source", "protocol", "authority", "userInfo", "user", "password", "host", "port", "relative", "path", "directory", "file", "query", "anchor"], q: { name: "queryKey", parser: /(?:^|&)([^&=]*)=?([^&]*)/g }, parser: { strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/, loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/ } }; /** * Resolve a url, which might be a string, function (that returns a string or Promse), or Promise (that resolves to a string) * * @param url * @returns {Promise<*>} */ async function resolveURL(url) { return (typeof url === 'function') ? url() : url; } /*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */ // (C) 1995-2013 Jean-loup Gailly and Mark Adler // (C) 2014-2017 Vitaly Puzrin and Andrey Tupitsin // // This software is provided 'as-is', without any express or implied // warranty. In no event will the authors be held liable for any damages // arising from the use of this software. // // Permission is granted to anyone to use this software for any purpose, // including commercial applications, and to alter it and redistribute it // freely, subject to the following restrictions: // // 1. The origin of this software must not be misrepresented; you must not // claim that you wrote the original software. If you use this software // in a product, an acknowledgment in the product documentation would be // appreciated but is not required. // 2. Altered source versions must be plainly marked as such, and must not be // misrepresented as being the original software. // 3. This notice may not be removed or altered from any source distribution. /* eslint-disable space-unary-ops */ /* Public constants ==========================================================*/ /* ===========================================================================*/ //const Z_FILTERED = 1; //const Z_HUFFMAN_ONLY = 2; //const Z_RLE = 3; const Z_FIXED$1 = 4; //const Z_DEFAULT_STRATEGY = 0; /* Possible values of the data_type field (though see inflate()) */ const Z_BINARY = 0; const Z_TEXT = 1; //const Z_ASCII = 1; // = Z_TEXT const Z_UNKNOWN$1 = 2; /*============================================================================*/ function zero$1$1(buf) { let len = buf.length; while (--len >= 0) { buf[len] = 0; } } // From zutil.h const STORED_BLOCK = 0; const STATIC_TREES = 1; const DYN_TREES = 2; /* The three kinds of block type */ const MIN_MATCH$1$1 = 3; const MAX_MATCH$1$1 = 258; /* The minimum and maximum match lengths */ // From deflate.h /* =========================================================================== * Internal compression state. */ const LENGTH_CODES$1$1 = 29; /* number of length codes, not counting the special END_BLOCK code */ const LITERALS$1$1 = 256; /* number of literal bytes 0..255 */ const L_CODES$1$1 = LITERALS$1$1 + 1 + LENGTH_CODES$1$1; /* number of Literal or Length codes, including the END_BLOCK code */ const D_CODES$1$1 = 30; /* number of distance codes */ const BL_CODES$1 = 19; /* number of codes used to transfer the bit lengths */ const HEAP_SIZE$1 = 2 * L_CODES$1$1 + 1; /* maximum heap size */ const MAX_BITS$1 = 15; /* All codes must not exceed MAX_BITS bits */ const Buf_size = 16; /* size of bit buffer in bi_buf */ /* =========================================================================== * Constants */ const MAX_BL_BITS = 7; /* Bit length codes must not exceed MAX_BL_BITS bits */ const END_BLOCK = 256; /* end of block literal code */ const REP_3_6 = 16; /* repeat previous bit length 3-6 times (2 bits of repeat count) */ const REPZ_3_10 = 17; /* repeat a zero length 3-10 times (3 bits of repeat count) */ const REPZ_11_138 = 18; /* repeat a zero length 11-138 times (7 bits of repeat count) */ /* eslint-disable comma-spacing,array-bracket-spacing */ const extra_lbits = /* extra bits for each length code */ new Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]); const extra_dbits = /* extra bits for each distance code */ new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]); const extra_blbits = /* extra bits for each bit length code */ new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]); const bl_order = new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]); /* eslint-enable comma-spacing,array-bracket-spacing */ /* The lengths of the bit length codes are sent in order of decreasing * probability, to avoid transmitting the lengths for unused bit length codes. */ /* =========================================================================== * Local data. These are initialized only once. */ // We pre-fill arrays with 0 to avoid uninitialized gaps const DIST_CODE_LEN$1 = 512; /* see definition of array dist_code below */ // !!!! Use flat array instead of structure, Freq = i*2, Len = i*2+1 const static_ltree$1 = new Array((L_CODES$1$1 + 2) * 2); zero$1$1(static_ltree$1); /* The static literal tree. Since the bit lengths are imposed, there is no * need for the L_CODES extra codes used during heap construction. However * The codes 286 and 287 are needed to build a canonical tree (see _tr_init * below). */ const static_dtree$1 = new Array(D_CODES$1$1 * 2); zero$1$1(static_dtree$1); /* The static distance tree. (Actually a trivial tree since all codes use * 5 bits.) */ const _dist_code$1 = new Array(DIST_CODE_LEN$1); zero$1$1(_dist_code$1); /* Distance codes. The first 256 values correspond to the distances * 3 .. 258, the last 256 values correspond to the top 8 bits of * the 15 bit distances. */ const _length_code$1 = new Array(MAX_MATCH$1$1 - MIN_MATCH$1$1 + 1); zero$1$1(_length_code$1); /* length code for each normalized match length (0 == MIN_MATCH) */ const base_length$1 = new Array(LENGTH_CODES$1$1); zero$1$1(base_length$1); /* First normalized length for each code (0 = MIN_MATCH) */ const base_dist$1 = new Array(D_CODES$1$1); zero$1$1(base_dist$1); /* First normalized distance for each code (0 = distance of 1) */ function StaticTreeDesc(static_tree, extra_bits, extra_base, elems, max_length) { this.static_tree = static_tree; /* static tree or NULL */ this.extra_bits = extra_bits; /* extra bits for each code or NULL */ this.extra_base = extra_base; /* base index for extra_bits */ this.elems = elems; /* max number of elements in the tree */ this.max_length = max_length; /* max bit length for the codes */ // show if `static_tree` has data or dummy - needed for monomorphic objects this.has_stree = static_tree && static_tree.length; } let static_l_desc; let static_d_desc; let static_bl_desc; function TreeDesc(dyn_tree, stat_desc) { this.dyn_tree = dyn_tree; /* the dynamic tree */ this.max_code = 0; /* largest code with non zero frequency */ this.stat_desc = stat_desc; /* the corresponding static tree */ } const d_code = (dist) => { return dist < 256 ? _dist_code$1[dist] : _dist_code$1[256 + (dist >>> 7)]; }; /* =========================================================================== * Output a short LSB first on the stream. * IN assertion: there is enough room in pendingBuf. */ const put_short = (s, w) => { // put_byte(s, (uch)((w) & 0xff)); // put_byte(s, (uch)((ush)(w) >> 8)); s.pending_buf[s.pending++] = (w) & 0xff; s.pending_buf[s.pending++] = (w >>> 8) & 0xff; }; /* =========================================================================== * Send a value on a given number of bits. * IN assertion: length <= 16 and value fits in length bits. */ const send_bits = (s, value, length) => { if (s.bi_valid > (Buf_size - length)) { s.bi_buf |= (value << s.bi_valid) & 0xffff; put_short(s, s.bi_buf); s.bi_buf = value >> (Buf_size - s.bi_valid); s.bi_valid += length - Buf_size; } else { s.bi_buf |= (value << s.bi_valid) & 0xffff; s.bi_valid += length; } }; const send_code = (s, c, tree) => { send_bits(s, tree[c * 2]/*.Code*/, tree[c * 2 + 1]/*.Len*/); }; /* =========================================================================== * Reverse the first len bits of a code, using straightforward code (a faster * method would use a table) * IN assertion: 1 <= len <= 15 */ const bi_reverse = (code, len) => { let res = 0; do { res |= code & 1; code >>>= 1; res <<= 1; } while (--len > 0); return res >>> 1; }; /* =========================================================================== * Flush the bit buffer, keeping at most 7 bits in it. */ const bi_flush = (s) => { if (s.bi_valid === 16) { put_short(s, s.bi_buf); s.bi_buf = 0; s.bi_valid = 0; } else if (s.bi_valid >= 8) { s.pending_buf[s.pending++] = s.bi_buf & 0xff; s.bi_buf >>= 8; s.bi_valid -= 8; } }; /* =========================================================================== * Compute the optimal bit lengths for a tree and update the total bit length * for the current block. * IN assertion: the fields freq and dad are set, heap[heap_max] and * above are the tree nodes sorted by increasing frequency. * OUT assertions: the field len is set to the optimal bit length, the * array bl_count contains the frequencies for each bit length. * The length opt_len is updated; static_len is also updated if stree is * not null. */ const gen_bitlen = (s, desc) => { // deflate_state *s; // tree_desc *desc; /* the tree descriptor */ const tree = desc.dyn_tree; const max_code = desc.max_code; const stree = desc.stat_desc.static_tree; const has_stree = desc.stat_desc.has_stree; const extra = desc.stat_desc.extra_bits; const base = desc.stat_desc.extra_base; const max_length = desc.stat_desc.max_length; let h; /* heap index */ let n, m; /* iterate over the tree elements */ let bits; /* bit length */ let xbits; /* extra bits */ let f; /* frequency */ let overflow = 0; /* number of elements with bit length too large */ for (bits = 0; bits <= MAX_BITS$1; bits++) { s.bl_count[bits] = 0; } /* In a first pass, compute the optimal bit lengths (which may * overflow in the case of the bit length tree). */ tree[s.heap[s.heap_max] * 2 + 1]/*.Len*/ = 0; /* root of the heap */ for (h = s.heap_max + 1; h < HEAP_SIZE$1; h++) { n = s.heap[h]; bits = tree[tree[n * 2 + 1]/*.Dad*/ * 2 + 1]/*.Len*/ + 1; if (bits > max_length) { bits = max_length; overflow++; } tree[n * 2 + 1]/*.Len*/ = bits; /* We overwrite tree[n].Dad which is no longer needed */ if (n > max_code) { continue; } /* not a leaf node */ s.bl_count[bits]++; xbits = 0; if (n >= base) { xbits = extra[n - base]; } f = tree[n * 2]/*.Freq*/; s.opt_len += f * (bits + xbits); if (has_stree) { s.static_len += f * (stree[n * 2 + 1]/*.Len*/ + xbits); } } if (overflow === 0) { return; } // Tracev((stderr,"\nbit length overflow\n")); /* This happens for example on obj2 and pic of the Calgary corpus */ /* Find the first bit length which could increase: */ do { bits = max_length - 1; while (s.bl_count[bits] === 0) { bits--; } s.bl_count[bits]--; /* move one leaf down the tree */ s.bl_count[bits + 1] += 2; /* move one overflow item as its brother */ s.bl_count[max_length]--; /* The brother of the overflow item also moves one step up, * but this does not affect bl_count[max_length] */ overflow -= 2; } while (overflow > 0); /* Now recompute all bit lengths, scanning in increasing frequency. * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all * lengths instead of fixing only the wrong ones. This idea is taken * from 'ar' written by Haruhiko Okumura.) */ for (bits = max_length; bits !== 0; bits--) { n = s.bl_count[bits]; while (n !== 0) { m = s.heap[--h]; if (m > max_code) { continue; } if (tree[m * 2 + 1]/*.Len*/ !== bits) { // Tracev((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits)); s.opt_len += (bits - tree[m * 2 + 1]/*.Len*/) * tree[m * 2]/*.Freq*/; tree[m * 2 + 1]/*.Len*/ = bits; } n--; } } }; /* =========================================================================== * Generate the codes for a given tree and bit counts (which need not be * optimal). * IN assertion: the array bl_count contains the bit length statistics for * the given tree and the field len is set for all tree elements. * OUT assertion: the field code is set for all tree elements of non * zero code length. */ const gen_codes = (tree, max_code, bl_count) => { // ct_data *tree; /* the tree to decorate */ // int max_code; /* largest code with non zero frequency */ // ushf *bl_count; /* number of codes at each bit length */ const next_code = new Array(MAX_BITS$1 + 1); /* next code value for each bit length */ let code = 0; /* running code value */ let bits; /* bit index */ let n; /* code index */ /* The distribution counts are first used to generate the code values * without bit reversal. */ for (bits = 1; bits <= MAX_BITS$1; bits++) { code = (code + bl_count[bits - 1]) << 1; next_code[bits] = code; } /* Check that the bit counts in bl_count are consistent. The last code * must be all ones. */ //Assert (code + bl_count[MAX_BITS]-1 == (1<<MAX_BITS)-1, // "inconsistent bit counts"); //Tracev((stderr,"\ngen_codes: max_code %d ", max_code)); for (n = 0; n <= max_code; n++) { let len = tree[n * 2 + 1]/*.Len*/; if (len === 0) { continue; } /* Now reverse the bits */ tree[n * 2]/*.Code*/ = bi_reverse(next_code[len]++, len); //Tracecv(tree != static_ltree, (stderr,"\nn %3d %c l %2d c %4x (%x) ", // n, (isgraph(n) ? n : ' '), len, tree[n].Code, next_code[len]-1)); } }; /* =========================================================================== * Initialize the various 'constant' tables. */ const tr_static_init = () => { let n; /* iterates over tree elements */ let bits; /* bit counter */ let length; /* length value */ let code; /* code value */ let dist; /* distance index */ const bl_count = new Array(MAX_BITS$1 + 1); /* number of codes at each bit length for an optimal tree */ // do check in _tr_init() //if (static_init_done) return; /* For some embedded targets, global variables are not initialized: */ /*#ifdef NO_INIT_GLOBAL_POINTERS static_l_desc.static_tree = static_ltree; static_l_desc.extra_bits = extra_lbits; static_d_desc.static_tree = static_dtree; static_d_desc.extra_bits = extra_dbits; static_bl_desc.extra_bits = extra_blbits; #endif*/ /* Initialize the mapping length (0..255) -> length code (0..28) */ length = 0; for (code = 0; code < LENGTH_CODES$1$1 - 1; code++) { base_length$1[code] = length; for (n = 0; n < (1 << extra_lbits[code]); n++) { _length_code$1[length++] = code; } } //Assert (length == 256, "tr_static_init: length != 256"); /* Note that the length 255 (match length 258) can be represented * in two different ways: code 284 + 5 bits or code 285, so we * overwrite length_code[255] to use the best encoding: */ _length_code$1[length - 1] = code; /* Initialize the mapping dist (0..32K) -> dist code (0..29) */ dist = 0; for (code = 0; code < 16; code++) { base_dist$1[code] = dist; for (n = 0; n < (1 << extra_dbits[code]); n++) { _dist_code$1[dist++] = code; } } //Assert (dist == 256, "tr_static_init: dist != 256"); dist >>= 7; /* from now on, all distances are divided by 128 */ for (; code < D_CODES$1$1; code++) { base_dist$1[code] = dist << 7; for (n = 0; n < (1 << (extra_dbits[code] - 7)); n++) { _dist_code$1[256 + dist++] = code; } } //Assert (dist == 256, "tr_static_init: 256+dist != 512"); /* Construct the codes of the static literal tree */ for (bits = 0; bits <= MAX_BITS$1; bits++) { bl_count[bits] = 0; } n = 0; while (n <= 143) { static_ltree$1[n * 2 + 1]/*.Len*/ = 8; n++; bl_count[8]++; } while (n <= 255) { static_ltree$1[n * 2 + 1]/*.Len*/ = 9; n++; bl_count[9]++; } while (n <= 279) { static_ltree$1[n * 2 + 1]/*.Len*/ = 7; n++; bl_count[7]++; } while (n <= 287) { static_ltree$1[n * 2 + 1]/*.Len*/ = 8; n++; bl_count[8]++; } /* Codes 286 and 287 do not exist, but we must include them in the * tree construction to get a canonical Huffman tree (longest code * all ones) */ gen_codes(static_ltree$1, L_CODES$1$1 + 1, bl_count); /* The static distance tree is trivial: */ for (n = 0; n < D_CODES$1$1; n++) { static_dtree$1[n * 2 + 1]/*.Len*/ = 5; static_dtree$1[n * 2]/*.Code*/ = bi_reverse(n, 5); } // Now data ready and we can init static trees static_l_desc = new StaticTreeDesc(static_ltree$1, extra_lbits, LITERALS$1$1 + 1, L_CODES$1$1, MAX_BITS$1); static_d_desc = new StaticTreeDesc(static_dtree$1, extra_dbits, 0, D_CODES$1$1, MAX_BITS$1); static_bl_desc = new StaticTreeDesc(new Array(0), extra_blbits, 0, BL_CODES$1, MAX_BL_BITS); //static_init_done = true; }; /* =========================================================================== * Initialize a new block. */ const init_block = (s) => { let n; /* iterates over tree elements */ /* Initialize the trees. */ for (n = 0; n < L_CODES$1$1; n++) { s.dyn_ltree[n * 2]/*.Freq*/ = 0; } for (n = 0; n < D_CODES$1$1; n++) { s.dyn_dtree[n * 2]/*.Freq*/ = 0; } for (n = 0; n < BL_CODES$1; n++) { s.bl_tree[n * 2]/*.Freq*/ = 0; } s.dyn_ltree[END_BLOCK * 2]/*.Freq*/ = 1; s.opt_len = s.static_len = 0; s.sym_next = s.matches = 0; }; /* =========================================================================== * Flush the bit buffer and align the output on a byte boundary */ const bi_windup = (s) => { if (s.bi_valid > 8) { put_short(s, s.bi_buf); } else if (s.bi_valid > 0) { //put_byte(s, (Byte)s->bi_buf); s.pending_buf[s.pending++] = s.bi_buf; } s.bi_buf = 0; s.bi_valid = 0; }; /* =========================================================================== * Compares to subtrees, using the tree depth as tie breaker when * the subtrees have equal frequency. This minimizes the worst case length. */ const smaller = (tree, n, m, depth) => { const _n2 = n * 2; const _m2 = m * 2; return (tree[_n2]/*.Freq*/ < tree[_m2]/*.Freq*/ || (tree[_n2]/*.Freq*/ === tree[_m2]/*.Freq*/ && depth[n] <= depth[m])); }; /* =========================================================================== * Restore the heap property by moving down the tree starting at node k, * exchanging a node with the smallest of its two sons if necessary, stopping * when the heap property is re-established (each father smaller than its * two sons). */ const pqdownheap = (s, tree, k) => { // deflate_state *s; // ct_data *tree; /* the tree to restore */ // int k; /* node to move down */ const v = s.heap[k]; let j = k << 1; /* left son of k */ while (j <= s.heap_len) { /* Set j to the smallest of the two sons: */ if (j < s.heap_len && smaller(tree, s.heap[j + 1], s.heap[j], s.depth)) { j++; } /* Exit if v is smaller than both sons */ if (smaller(tree, v, s.heap[j], s.depth)) { break; } /* Exchange v with the smallest son */ s.heap[k] = s.heap[j]; k = j; /* And continue down the tree, setting j to the left son of k */ j <<= 1; } s.heap[k] = v; }; // inlined manually // const SMALLEST = 1; /* =========================================================================== * Send the block data compressed using the given Huffman trees */ const compress_block = (s, ltree, dtree) => { // deflate_state *s; // const ct_data *ltree; /* literal tree */ // const ct_data *dtree; /* distance tree */ let dist; /* distance of matched string */ let lc; /* match length or unmatched char (if dist == 0) */ let sx = 0; /* running index in sym_buf */ let code; /* the code to send */ let extra; /* number of extra bits to send */ if (s.sym_next !== 0) { do { dist = s.pending_buf[s.sym_buf + sx++] & 0xff; dist += (s.pending_buf[s.sym_buf + sx++] & 0xff) << 8; lc = s.pending_buf[s.sym_buf + sx++]; if (dist === 0) { send_code(s, lc, ltree); /* send a literal byte */ //Tracecv(isgraph(lc), (stderr," '%c' ", lc)); } else { /* Here, lc is the match length - MIN_MATCH */ code = _length_code$1[lc]; send_code(s, code + LITERALS$1$1 + 1, ltree); /* send the length code */ extra = extra_lbits[code]; if (extra !== 0) { lc -= base_length$1[code]; send_bits(s, lc, extra); /* send the extra length bits */ } dist--; /* dist is now the match distance - 1 */ code = d_code(dist); //Assert (code < D_CODES, "bad d_code"); send_code(s, code, dtree); /* send the distance code */ extra = extra_dbits[code]; if (extra !== 0) { dist -= base_dist$1[code]; send_bits(s, dist, extra); /* send the extra distance bits */ } } /* literal or match pair ? */ /* Check that the overlay between pending_buf and sym_buf is ok: */ //Assert(s->pending < s->lit_bufsize + sx, "pendingBuf overflow"); } while (sx < s.sym_next); } send_code(s, END_BLOCK, ltree); }; /* =========================================================================== * Construct one Huffman tree and assigns the code bit strings and lengths. * Update the total bit length for the current block. * IN assertion: the field freq is set for all tree elements. * OUT assertions: the fields len and code are set to the optimal bit length * and corresponding code. The length opt_len is updated; static_len is * also updated if stree is not null. The field max_code is set. */ const build_tree = (s, desc) => { // deflate_state *s; // tree_desc *desc; /* the tree descriptor */ const tree = desc.dyn_tree; const stree = desc.stat_desc.static_tree; const has_stree = desc.stat_desc.has_stree; const elems = desc.stat_desc.elems; let n, m; /* iterate over heap elements */ let max_code = -1; /* largest code with non zero frequency */ let node; /* new node being created */ /* Construct the initial heap, with least frequent element in * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1]. * heap[0] is not used. */ s.heap_len = 0; s.heap_max = HEAP_SIZE$1; for (n = 0; n < elems; n++) { if (tree[n * 2]/*.Freq*/ !== 0) { s.heap[++s.heap_len] = max_code = n; s.depth[n] = 0; } else { tree[n * 2 + 1]/*.Len*/ = 0; } } /* The pkzip format requires that at least one distance code exists, * and that at least one bit should be sent even if there is only one * possible code. So to avoid special checks later on we force at least * two codes of non zero frequency. */ while (s.heap_len < 2) { node = s.heap[++s.heap_len] = (max_code < 2 ? ++max_code : 0); tree[node * 2]/*.Freq*/ = 1; s.depth[node] = 0; s.opt_len--; if (has_stree) { s.static_len -= stree[node * 2 + 1]/*.Len*/; } /* node is 0 or 1 so it does not have extra bits */ } desc.max_code = max_code; /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree, * establish sub-heaps of increasing lengths: */ for (n = (s.heap_len >> 1/*int /2*/); n >= 1; n--) { pqdownheap(s, tree, n); } /* Construct the Huffman tree by repeatedly combining the least two * frequent nodes. */ node = elems; /* next internal node of the tree */ do { //pqremove(s, tree, n); /* n = node of least frequency */ /*** pqremove ***/ n = s.heap[1/*SMALLEST*/]; s.heap[1/*SMALLEST*/] = s.heap[s.heap_len--]; pqdownheap(s, tree, 1/*SMALLEST*/); /***/ m = s.heap[1/*SMALLEST*/]; /* m = node of next least frequency */ s.heap[--s.heap_max] = n; /* keep the nodes sorted by frequency */ s.heap[--s.heap_max] = m; /* Create a new node father of n and m */ tree[node * 2]/*.Freq*/ = tree[n * 2]/*.Freq*/ + tree[m * 2]/*.Freq*/; s.depth[node] = (s.depth[n] >= s.depth[m] ? s.depth[n] : s.depth[m]) + 1; tree[n * 2 + 1]/*.Dad*/ = tree[m * 2 + 1]/*.Dad*/ = node; /* and insert the new node in the heap */ s.heap[1/*SMALLEST*/] = node++; pqdownheap(s, tree, 1/*SMALLEST*/); } while (s.heap_len >= 2); s.heap[--s.heap_max] = s.heap[1/*SMALLEST*/]; /* At this point, the fields freq and dad are set. We can now * generate the bit lengths. */ gen_bitlen(s, desc); /* The field len is now set, we can generate the bit codes */ gen_codes(tree, max_code, s.bl_count); }; /* =========================================================================== * Scan a literal or distance tree to determine the frequencies of the codes * in the bit length tree. */ const scan_tree = (s, tree, max_code) => { // deflate_state *s; // ct_data *tree; /* the tree to be scanned */ // int max_code; /* and its largest code of non zero frequency */ let n; /* iterates over all tree elements */ let prevlen = -1; /* last emitted length */ let curlen; /* length of current code */ let nextlen = tree[0 * 2 + 1]/*.Len*/; /* length of next code */ let count = 0; /* repeat count of the current code */ let max_count = 7; /* max repeat count */ let min_count = 4; /* min repeat count */ if (nextlen === 0) { max_count = 138; min_count = 3; } tree[(max_code + 1) * 2 + 1]/*.Len*/ = 0xffff; /* guard */ for (n = 0; n <= max_code; n++) { curlen = nextlen; nextlen = tree[(n + 1) * 2 + 1]/*.Len*/; if (++count < max_count && curlen === nextlen) { continue; } else if (count < min_count) { s.bl_tree[curlen * 2]/*.Freq*/ += count; } else if (curlen !== 0) { if (curlen !== prevlen) { s.bl_tree[curlen * 2]/*.Freq*/++; } s.bl_tree[REP_3_6 * 2]/*.Freq*/++; } else if (count <= 10) { s.bl_tree[REPZ_3_10 * 2]/*.Freq*/++; } else { s.bl_tree[REPZ_11_138 * 2]/*.Freq*/++; } count = 0; prevlen = curlen; if (nextlen === 0) { max_count = 138; min_count = 3; } else if (curlen === nextlen) { max_count = 6; min_count = 3; } else { max_count = 7; min_count = 4; } } }; /* =========================================================================== * Send a literal or distance tree in compressed form, using the codes in * bl_tree. */ const send_tree = (s, tree, max_code) => { // deflate_state *s; // ct_data *tree; /* the tree to be scanned */ // int max_code; /* and its largest code of non zero frequency */ let n; /* iterates over all tree elements */ let prevlen = -1; /* last emitted length */ let curlen; /* length of current code */ let nextlen = tree[0 * 2