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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

github.com/sillitoe/biojs-vis-pdbviewer

sillitoe/biojs-vis-pdbviewer

159 lines (155 loc) • 7.59 kB
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Clazz.declarePackage ("JU"); c$ = Clazz.decorateAsClass (function () { this.dyn_tree = null; this.max_code = 0; this.stat_desc = null; Clazz.instantialize (this, arguments); }, JU, "Tree"); c$.d_code = Clazz.defineMethod (c$, "d_code", function (dist) { return ((dist) < 256 ? JU.Tree._dist_code[dist] : JU.Tree._dist_code[256 + ((dist) >>> 7)]); }, "~N"); Clazz.defineMethod (c$, "gen_bitlen", function (s) { var tree = this.dyn_tree; var stree = this.stat_desc.static_tree; var extra = this.stat_desc.extra_bits; var base = this.stat_desc.extra_base; var max_length = this.stat_desc.max_length; var h; var n; var m; var bits; var xbits; var f; var overflow = 0; for (bits = 0; bits <= 15; bits++) s.bl_count[bits] = 0; tree[s.heap[s.heap_max] * 2 + 1] = 0; for (h = s.heap_max + 1; h < 573; h++) { n = s.heap[h]; bits = tree[tree[n * 2 + 1] * 2 + 1] + 1; if (bits > max_length) { bits = max_length; overflow++; }tree[n * 2 + 1] = bits; if (n > this.max_code) continue; s.bl_count[bits]++; xbits = 0; if (n >= base) xbits = extra[n - base]; f = tree[n * 2]; s.opt_len += f * (bits + xbits); if (stree != null) s.static_len += f * (stree[n * 2 + 1] + xbits); } if (overflow == 0) return; do { bits = max_length - 1; while (s.bl_count[bits] == 0) bits--; s.bl_count[bits]--; s.bl_count[bits + 1] += 2; s.bl_count[max_length]--; overflow -= 2; } while (overflow > 0); for (bits = max_length; bits != 0; bits--) { n = s.bl_count[bits]; while (n != 0) { m = s.heap[--h]; if (m > this.max_code) continue; if (tree[m * 2 + 1] != bits) { s.opt_len += (bits - tree[m * 2 + 1]) * tree[m * 2]; tree[m * 2 + 1] = bits; }n--; } } }, "JU.Deflate"); Clazz.defineMethod (c$, "build_tree", function (s) { var tree = this.dyn_tree; var stree = this.stat_desc.static_tree; var elems = this.stat_desc.elems; var n; var m; var max_code = -1; var node; s.heap_len = 0; s.heap_max = 573; for (n = 0; n < elems; n++) { if (tree[n * 2] != 0) { s.heap[++s.heap_len] = max_code = n; s.depth[n] = 0; } else { tree[n * 2 + 1] = 0; }} while (s.heap_len < 2) { node = s.heap[++s.heap_len] = (max_code < 2 ? ++max_code : 0); tree[node * 2] = 1; s.depth[node] = 0; s.opt_len--; if (stree != null) s.static_len -= stree[node * 2 + 1]; } this.max_code = max_code; for (n = Clazz.doubleToInt (s.heap_len / 2); n >= 1; n--) s.pqdownheap (tree, n); node = elems; do { n = s.heap[1]; s.heap[1] = s.heap[s.heap_len--]; s.pqdownheap (tree, 1); m = s.heap[1]; s.heap[--s.heap_max] = n; s.heap[--s.heap_max] = m; tree[node * 2] = (tree[n * 2] + tree[m * 2]); s.depth[node] = (Math.max (s.depth[n], s.depth[m]) + 1); tree[n * 2 + 1] = tree[m * 2 + 1] = node; s.heap[1] = node++; s.pqdownheap (tree, 1); } while (s.heap_len >= 2); s.heap[--s.heap_max] = s.heap[1]; this.gen_bitlen (s); JU.Tree.gen_codes (tree, max_code, s.bl_count); }, "JU.Deflate"); c$.gen_codes = Clazz.defineMethod (c$, "gen_codes", function (tree, max_code, bl_count) { var code = 0; var bits; var n; JU.Tree.next_code[0] = 0; for (bits = 1; bits <= 15; bits++) { JU.Tree.next_code[bits] = code = ((code + bl_count[bits - 1]) << 1); } for (n = 0; n <= max_code; n++) { var len = tree[n * 2 + 1]; if (len == 0) continue; tree[n * 2] = (JU.Tree.bi_reverse (JU.Tree.next_code[len]++, len)); } }, "~A,~N,~A"); c$.bi_reverse = Clazz.defineMethod (c$, "bi_reverse", function (code, len) { var res = 0; do { res |= code & 1; code >>>= 1; res <<= 1; } while (--len > 0); return res >>> 1; }, "~N,~N"); Clazz.defineStatics (c$, "MAX_BITS", 15, "LITERALS", 256, "LENGTH_CODES", 29, "L_CODES", (286), "HEAP_SIZE", (573), "MAX_BL_BITS", 7, "END_BLOCK", 256, "REP_3_6", 16, "REPZ_3_10", 17, "REPZ_11_138", 18, "extra_lbits", [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], "extra_dbits", [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], "extra_blbits", [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 3, 7], "bl_order", [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15], "Buf_size", 16, "DIST_CODE_LEN", 512, "_dist_code", [0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17, 18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29], "_length_code", [0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28], "base_length", [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56, 64, 80, 96, 112, 128, 160, 192, 224, 0], "base_dist", [0, 1, 2, 3, 4, 6, 8, 12, 16, 24, 32, 48, 64, 96, 128, 192, 256, 384, 512, 768, 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576], "next_code", Clazz.newShortArray (16, 0));