blast_seg.c

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/* $Id: blast_seg.c 74060 2016-08-09 20:20:20Z rackerst $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author: Ilya Dondoshansky
 *
 */
 
/** @file blast_seg.c
 * A utility to find low complexity AA regions. This parallels functionality
 * of seg.c from the C toolkit, but without using the structures generated
 * from ASN.1 spec.
 * @todo FIXME needs comments
 */
 
#include <algo/blast/core/blast_seg.h>
#include <algo/blast/core/ncbi_math.h>
#include <algo/blast/core/blast_filter.h>
 
#include <algo/blast/core/blast_util.h>
 
 
/** Declared in blast_def.h. */
const int kSegWindow = 12;
const double kSegLocut = 2.2;
const double kSegHicut = 2.5;
 
/** Natural log of factorials: 0!, 1!, 2!, 3! */
double lnfact[] =
  {
   0.000000, 0.000000, 0.693147, 1.791759, 3.178054, 4.787492, 6.579251, 8.525161,
   10.604603, 12.801827, 15.104413, 17.502308, 19.987214, 22.552164, 25.191221, 27.899271,
   30.671860, 33.505073, 36.395445, 39.339884, 42.335616, 45.380139, 48.471181, 51.606676,
   54.784729, 58.003605, 61.261702, 64.557539, 67.889743, 71.257039, 74.658236, 78.092224,
   81.557959, 85.054467, 88.580828, 92.136176, 95.719695, 99.330612, 102.968199, 106.631760,
   110.320640, 114.034212, 117.771881, 121.533082, 125.317271, 129.123934, 132.952575, 136.802723,
   140.673924, 144.565744, 148.477767, 152.409593, 156.360836, 160.331128, 164.320112, 168.327445,
   172.352797, 176.395848, 180.456291, 184.533829, 188.628173, 192.739047, 196.866182, 201.009316,
   205.168199, 209.342587, 213.532241, 217.736934, 221.956442, 226.190548, 230.439044, 234.701723,
   238.978390, 243.268849, 247.572914, 251.890402, 256.221136, 260.564941, 264.921650, 269.291098,
   273.673124, 278.067573, 282.474293, 286.893133, 291.323950, 295.766601, 300.220949, 304.686857,
   309.164194, 313.652830, 318.152640, 322.663499, 327.185288, 331.717887, 336.261182, 340.815059,
   345.379407, 349.954118, 354.539086, 359.134205, 363.739376, 368.354496, 372.979469, 377.614198,
   382.258589, 386.912549, 391.575988, 396.248817, 400.930948, 405.622296, 410.322777, 415.032307,
   419.750806, 424.478193, 429.214392, 433.959324, 438.712914, 443.475088, 448.245773, 453.024896,
   457.812388, 462.608179, 467.412200, 472.224384, 477.044665, 481.872979, 486.709261, 491.553448,
   496.405478, 501.265291, 506.132825, 511.008023, 515.890825, 520.781174, 525.679014, 530.584288,
   535.496943, 540.416924, 545.344178, 550.278652, 555.220294, 560.169054, 565.124881, 570.087726,
   575.057539, 580.034273, 585.017879, 590.008312, 595.005524, 600.009471, 605.020106, 610.037386,
   615.061266, 620.091704, 625.128657, 630.172082, 635.221938, 640.278184, 645.340779, 650.409683,
   655.484857, 660.566261, 665.653857, 670.747608, 675.847474, 680.953420, 686.065407, 691.183401,
   696.307365, 701.437264, 706.573062, 711.714726, 716.862220, 722.015512, 727.174567, 732.339353,
   737.509837, 742.685987, 747.867770, 753.055156, 758.248113, 763.446610, 768.650617, 773.860103,
   779.075039, 784.295395, 789.521141, 794.752250, 799.988692, 805.230439, 810.477463, 815.729736,
   820.987232, 826.249922, 831.517780, 836.790780, 842.068894, 847.352098, 852.640365, 857.933670,
   863.231987, 868.535292, 873.843560, 879.156766, 884.474886, 889.797896, 895.125772, 900.458491,
   905.796029, 911.138363, 916.485471, 921.837329, 927.193915, 932.555207, 937.921183, 943.291821,
   948.667100, 954.046997, 959.431492, 964.820564, 970.214191, 975.612354, 981.015031, 986.422203,
   991.833849, 997.249950, 1002.670485, 1008.095435, 1013.524780, 1018.958502, 1024.396582, 1029.838999,
   1035.285737, 1040.736775, 1046.192096, 1051.651682, 1057.115514, 1062.583574, 1068.055844, 1073.532308,
   1079.012947, 1084.497744, 1089.986681, 1095.479743, 1100.976911, 1106.478169, 1111.983501, 1117.492889,
   1123.006318, 1128.523771, 1134.045232, 1139.570685, 1145.100114, 1150.633503, 1156.170838, 1161.712101,
   1167.257279, 1172.806355, 1178.359314, 1183.916142, 1189.476824, 1195.041344, 1200.609689, 1206.181843,
   1211.757792, 1217.337522, 1222.921018, 1228.508267, 1234.099254, 1239.693965, 1245.292387, 1250.894506,
   1256.500308, 1262.109780, 1267.722908, 1273.339679, 1278.960080, 1284.584097, 1290.211718, 1295.842930,
   1301.477720, 1307.116075, 1312.757982, 1318.403428, 1324.052403, 1329.704892, 1335.360884, 1341.020366,
   1346.683326, 1352.349753, 1358.019634, 1363.692957, 1369.369711, 1375.049884, 1380.733463, 1386.420439,
   1392.110798, 1397.804530, 1403.501624, 1409.202067, 1414.905850, 1420.612960, 1426.323387, 1432.037120,
   1437.754148, 1443.474460, 1449.198045, 1454.924892, 1460.654992, 1466.388333, 1472.124906, 1477.864699,
   1483.607702, 1489.353905, 1495.103298, 1500.855871, 1506.611613, 1512.370515, 1518.132566, 1523.897757,
   1529.666078, 1535.437519, 1541.212071, 1546.989723, 1552.770467, 1558.554292, 1564.341189, 1570.131149,
   1575.924163, 1581.720221, 1587.519313, 1593.321432, 1599.126567, 1604.934709, 1610.745850, 1616.559981,
   1622.377092, 1628.197175, 1634.020221, 1639.846221, 1645.675166, 1651.507049, 1657.341860, 1663.179590,
   1669.020232, 1674.863776, 1680.710215, 1686.559540, 1692.411742, 1698.266814, 1704.124747, 1709.985533,
   1715.849165, 1721.715633, 1727.584930, 1733.457047, 1739.331978, 1745.209714, 1751.090247, 1756.973569,
   1762.859673, 1768.748551, 1774.640196, 1780.534598, 1786.431752, 1792.331650, 1798.234283, 1804.139645,
   1810.047728, 1815.958524, 1821.872027, 1827.788229, 1833.707123, 1839.628702, 1845.552957, 1851.479884,
   1857.409473, 1863.341718, 1869.276612, 1875.214148, 1881.154319, 1887.097119, 1893.042539, 1898.990574,
   1904.941217, 1910.894460, 1916.850298, 1922.808722, 1928.769728, 1934.733307, 1940.699454, 1946.668161,
   1952.639423, 1958.613233, 1964.589584, 1970.568470, 1976.549884, 1982.533820, 1988.520272, 1994.509233,
   2000.500698, 2006.494659, 2012.491111, 2018.490048, 2024.491463, 2030.495350, 2036.501703, 2042.510516,
   2048.521784, 2054.535499, 2060.551656, 2066.570249, 2072.591272, 2078.614720, 2084.640586, 2090.668864,
   2096.699550, 2102.732636, 2108.768117, 2114.805988, 2120.846243, 2126.888876, 2132.933881, 2138.981253,
   2145.030987, 2151.083076, 2157.137515, 2163.194299, 2169.253423, 2175.314879, 2181.378665, 2187.444773,
   2193.513198, 2199.583936, 2205.656981, 2211.732327, 2217.809969, 2223.889902, 2229.972121, 2236.056620,
   2242.143395, 2248.232440, 2254.323750, 2260.417320, 2266.513144, 2272.611219, 2278.711537, 2284.814096,
   2290.918889, 2297.025912, 2303.135160, 2309.246627, 2315.360309, 2321.476201, 2327.594299, 2333.714596,
   2339.837089, 2345.961772, 2352.088641, 2358.217692, 2364.348918, 2370.482316, 2376.617881, 2382.755608,
   2388.895493, 2395.037530, 2401.181716, 2407.328045, 2413.476513, 2419.627116, 2425.779849, 2431.934707,
   2438.091686, 2444.250781, 2450.411988, 2456.575303, 2462.740721, 2468.908238, 2475.077848, 2481.249549,
   2487.423335, 2493.599202, 2499.777146, 2505.957163, 2512.139248, 2518.323397, 2524.509606, 2530.697870,
   2536.888185, 2543.080548, 2549.274953, 2555.471397, 2561.669876, 2567.870385, 2574.072920, 2580.277478,
   2586.484054, 2592.692644, 2598.903244, 2605.115850, 2611.330458, 2617.547065, 2623.765665, 2629.986255,
   2636.208831, 2642.433390, 2648.659926, 2654.888437, 2661.118919, 2667.351367, 2673.585777, 2679.822147,
   2686.060472, 2692.300747, 2698.542971, 2704.787138, 2711.033244, 2717.281287, 2723.531263, 2729.783166,
   2736.036995, 2742.292745, 2748.550413, 2754.809994, 2761.071486, 2767.334884, 2773.600185, 2779.867386,
   2786.136482, 2792.407471, 2798.680348, 2804.955110, 2811.231753, 2817.510275, 2823.790671, 2830.072937,
   2836.357071, 2842.643070, 2848.930928, 2855.220644, 2861.512213, 2867.805632, 2874.100898, 2880.398007,
   2886.696957, 2892.997742, 2899.300361, 2905.604810, 2911.911085, 2918.219184, 2924.529102, 2930.840837,
   2937.154385, 2943.469743, 2949.786908, 2956.105876, 2962.426644, 2968.749209, 2975.073568, 2981.399718,
   2987.727655, 2994.057376, 3000.388877, 3006.722157, 3013.057211, 3019.394037, 3025.732631, 3032.072990,
   3038.415112, 3044.758992, 3051.104629, 3057.452018, 3063.801157, 3070.152043, 3076.504672, 3082.859042,
   3089.215150, 3095.572992, 3101.932566, 3108.293868, 3114.656896, 3121.021647, 3127.388118, 3133.756305,
   3140.126206, 3146.497818, 3152.871137, 3159.246162, 3165.622889, 3172.001315, 3178.381438, 3184.763254,
   3191.146760, 3197.531955, 3203.918834, 3210.307396, 3216.697636, 3223.089553, 3229.483144, 3235.878406,
   3242.275335, 3248.673930, 3255.074188, 3261.476105, 3267.879679, 3274.284908, 3280.691788, 3287.100316,
   3293.510491, 3299.922310, 3306.335768, 3312.750865, 3319.167598, 3325.585963, 3332.005958, 3338.427580,
   3344.850827, 3351.275696, 3357.702184, 3364.130290, 3370.560009, 3376.991340, 3383.424280, 3389.858827,
   3396.294977, 3402.732729, 3409.172079, 3415.613026, 3422.055566, 3428.499697, 3434.945417, 3441.392723,
   3447.841612, 3454.292083, 3460.744132, 3467.197757, 3473.652955, 3480.109725, 3486.568063, 3493.027968,
   3499.489436, 3505.952465, 3512.417053, 3518.883198, 3525.350897, 3531.820147, 3538.290947, 3544.763293,
   3551.237184, 3557.712616, 3564.189589, 3570.668098, 3577.148143, 3583.629720, 3590.112827, 3596.597463,
   3603.083624, 3609.571308, 3616.060512, 3622.551236, 3629.043476, 3635.537230, 3642.032495, 3648.529270,
   3655.027552, 3661.527339, 3668.028629, 3674.531419, 3681.035707, 3687.541491, 3694.048769, 3700.557538,
   3707.067797, 3713.579542, 3720.092772, 3726.607485, 3733.123678, 3739.641349, 3746.160496, 3752.681117,
   3759.203210, 3765.726773, 3772.251802, 3778.778297, 3785.306255, 3791.835674, 3798.366551, 3804.898886,
   3811.432675, 3817.967916, 3824.504607, 3831.042747, 3837.582333, 3844.123363, 3850.665835, 3857.209747,
   3863.755097, 3870.301882, 3876.850101, 3883.399752, 3889.950832, 3896.503340, 3903.057274, 3909.612630,
   3916.169409, 3922.727607, 3929.287222, 3935.848253, 3942.410697, 3948.974552, 3955.539817, 3962.106490,
   3968.674567, 3975.244049, 3981.814932, 3988.387214, 3994.960895, 4001.535970, 4008.112440, 4014.690301,
   4021.269553, 4027.850192, 4034.432217, 4041.015626, 4047.600417, 4054.186589, 4060.774139, 4067.363066,
   4073.953367, 4080.545040, 4087.138085, 4093.732498, 4100.328279, 4106.925425, 4113.523934, 4120.123804,
   4126.725034, 4133.327622, 4139.931566, 4146.536864, 4153.143514, 4159.751515, 4166.360864, 4172.971560,
   4179.583601, 4186.196985, 4192.811711, 4199.427776, 4206.045179, 4212.663918, 4219.283991, 4225.905397,
   4232.528133, 4239.152198, 4245.777591, 4252.404308, 4259.032350, 4265.661713, 4272.292396, 4278.924398,
   4285.557717, 4292.192350, 4298.828297, 4305.465555, 4312.104122, 4318.743998, 4325.385180, 4332.027667,
   4338.671457, 4345.316548, 4351.962938, 4358.610627, 4365.259611, 4371.909890, 4378.561462, 4385.214325,
   4391.868478, 4398.523918, 4405.180645, 4411.838656, 4418.497950, 4425.158525, 4431.820380, 4438.483512,
   4445.147921, 4451.813605, 4458.480562, 4465.148790, 4471.818288, 4478.489054, 4485.161087, 4491.834385,
   4498.508947, 4505.184770, 4511.861853, 4518.540196, 4525.219795, 4531.900649, 4538.582758, 4545.266119,
   4551.950731, 4558.636592, 4565.323700, 4572.012055, 4578.701654, 4585.392497, 4592.084580, 4598.777904,
   4605.472466, 4612.168265, 4618.865299, 4625.563567, 4632.263068, 4638.963799, 4645.665759, 4652.368947,
   4659.073361, 4665.779001, 4672.485863, 4679.193947, 4685.903251, 4692.613774, 4699.325515, 4706.038471,
   4712.752642, 4719.468025, 4726.184620, 4732.902424, 4739.621438, 4746.341658, 4753.063083, 4759.785713,
   4766.509546, 4773.234579, 4779.960813, 4786.688244, 4793.416873, 4800.146697, 4806.877715, 4813.609926,
   4820.343328, 4827.077919, 4833.813700, 4840.550666, 4847.288819, 4854.028156, 4860.768675, 4867.510376,
   4874.253256, 4880.997315, 4887.742552, 4894.488964, 4901.236550, 4907.985310, 4914.735241, 4921.486343,
   4928.238613, 4934.992051, 4941.746655, 4948.502424, 4955.259356, 4962.017451, 4968.776706, 4975.537121,
   4982.298694, 4989.061423, 4995.825308, 5002.590347, 5009.356539, 5016.123882, 5022.892375, 5029.662017,
   5036.432806, 5043.204742, 5049.977822, 5056.752046, 5063.527412, 5070.303919, 5077.081566, 5083.860351,
   5090.640273, 5097.421330, 5104.203522, 5110.986848, 5117.771305, 5124.556892, 5131.343609, 5138.131454,
   5144.920426, 5151.710523, 5158.501745, 5165.294089, 5172.087555, 5178.882142, 5185.677848, 5192.474671,
   5199.272612, 5206.071668, 5212.871838, 5219.673121, 5226.475515, 5233.279021, 5240.083635, 5246.889358,
   5253.696187, 5260.504122, 5267.313161, 5274.123304, 5280.934548, 5287.746893, 5294.560338, 5301.374881,
   5308.190521, 5315.007257, 5321.825087, 5328.644011, 5335.464028, 5342.285135, 5349.107333, 5355.930619,
   5362.754992, 5369.580452, 5376.406998, 5383.234627, 5390.063339, 5396.893133, 5403.724007, 5410.555960,
   5417.388992, 5424.223101, 5431.058286, 5437.894545, 5444.731878, 5451.570283, 5458.409759, 5465.250306,
   5472.091921, 5478.934605, 5485.778355, 5492.623170, 5499.469050, 5506.315993, 5513.163998, 5520.013065,
   5526.863191, 5533.714376, 5540.566618, 5547.419917, 5554.274272, 5561.129681, 5567.986143, 5574.843657,
   5581.702222, 5588.561837, 5595.422500, 5602.284212, 5609.146970, 5616.010773, 5622.875621, 5629.741512,
   5636.608445, 5643.476419, 5650.345434, 5657.215487, 5664.086579, 5670.958707, 5677.831871, 5684.706069,
   5691.581301, 5698.457566, 5705.334862, 5712.213188, 5719.092544, 5725.972928, 5732.854339, 5739.736777,
   5746.620240, 5753.504726, 5760.390236, 5767.276768, 5774.164320, 5781.052893, 5787.942484, 5794.833093,
   5801.724719, 5808.617361, 5815.511017, 5822.405687, 5829.301370, 5836.198064, 5843.095769, 5849.994483,
   5856.894207, 5863.794937, 5870.696674, 5877.599417, 5884.503164, 5891.407915, 5898.313668, 5905.220423,
   5912.128178, 5919.036933, 5925.946687, 5932.857437, 5939.769185, 5946.681927, 5953.595665, 5960.510396,
   5967.426119, 5974.342834, 5981.260540, 5988.179235, 5995.098919, 6002.019590, 6008.941249, 6015.863892,
   6022.787521, 6029.712133, 6036.637729, 6043.564306, 6050.491864, 6057.420401, 6064.349918, 6071.280413,
   6078.211885, 6085.144333, 6092.077756, 6099.012153, 6105.947523, 6112.883866, 6119.821180, 6126.759465,
   6133.698719, 6140.638941, 6147.580131, 6154.522288, 6161.465410, 6168.409497, 6175.354548, 6182.300562,
   6189.247538, 6196.195476, 6203.144373, 6210.094229, 6217.045044, 6223.996816, 6230.949545, 6237.903229,
   6244.857868, 6251.813460, 6258.770006, 6265.727503, 6272.685952, 6279.645350, 6286.605698, 6293.566994,
   6300.529237, 6307.492427, 6314.456563, 6321.421643, 6328.387668, 6335.354635, 6342.322544, 6349.291394,
   6356.261185, 6363.231915, 6370.203584, 6377.176190, 6384.149733, 6391.124212, 6398.099626, 6405.075974,
   6412.053255, 6419.031469, 6426.010614, 6432.990690, 6439.971696, 6446.953631, 6453.936493, 6460.920283,
   6467.905000, 6474.890641, 6481.877208, 6488.864698, 6495.853111, 6502.842447, 6509.832703, 6516.823880,
   6523.815976, 6530.808991, 6537.802924, 6544.797774, 6551.793541, 6558.790222, 6565.787818, 6572.786328,
   6579.785750, 6586.786085, 6593.787330, 6600.789486, 6607.792552, 6614.796526, 6621.801408, 6628.807197,
   6635.813892, 6642.821493, 6649.829998, 6656.839407, 6663.849719, 6670.860933, 6677.873048, 6684.886064,
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   73533.239416, 73542.351592, 73551.463879, 73560.576276, 73569.688783, 73578.801400, 73587.914127, 73597.026965,
   73606.139913, 73615.252972, 73624.366140, 73633.479419, 73642.592808, 73651.706307, 73660.819916, 73669.933635,
   73679.047465, 73688.161404, 73697.275454, 73706.389614, 73715.503884, 73724.618264, 73733.732754, 73742.847354,
   73751.962064, 73761.076884, 73770.191814, 73779.306854, 73788.422005, 73797.537265, 73806.652635, 73815.768115,
   73824.883705, 73833.999405, 73843.115215, 73852.231135, 73861.347164, 73870.463304, 73879.579553, 73888.695913,
   73897.812382, 73906.928961, 73916.045650, 73925.162448, 73934.279357, 73943.396375, 73952.513503, 73961.630741,
   73970.748088, 73979.865545, 73988.983112, 73998.100789, 74007.218575, 74016.336472, 74025.454477, 74034.572593,
   74043.690818, 74052.809153, 74061.927597, 74071.046151, 74080.164814, 74089.283588, 74098.402470, 74107.521463,
   74116.640565, 74125.759776, 74134.879097, 74143.998528, 74153.118068, 74162.237717, 74171.357476, 74180.477344,
   74189.597322, 74198.717410, 74207.837607, 74216.957913, 74226.078329, 74235.198854, 74244.319488, 74253.440232,
   74262.561085, 74271.682048, 74280.803120, 74289.924301, 74299.045591, 74308.166991, 74317.288500, 74326.410119,
   74335.531847, 74344.653684, 74353.775630, 74362.897685, 74372.019850, 74381.142124, 74390.264507, 74399.386999,
   74408.509601, 74417.632311, 74426.755131, 74435.878060, 74445.001098, 74454.124245, 74463.247501, 74472.370867,
   74481.494341, 74490.617925, 74499.741617, 74508.865419, 74517.989330, 74527.113349, 74536.237478, 74545.361716,
   74554.486062, 74563.610518, 74572.735082, 74581.859756, 74590.984538, 74600.109430, 74609.234430, 74618.359539,
   74627.484758, 74636.610085, 74645.735520, 74654.861065, 74663.986719, 74673.112481, 74682.238352, 74691.364332,
   74700.490421, 74709.616619, 74718.742925, 74727.869340, 74736.995864, 74746.122497, 74755.249238, 74764.376088,
   74773.503047, 74782.630114, 74791.757290, 74800.884575, 74810.011969, 74819.139471, 74828.267082, 74837.394801,
   74846.522629, 74855.650565, 74864.778611, 74873.906764, 74883.035026, 74892.163397, 74901.291877, 74910.420465,
   74919.549161, 74928.677966, 74937.806879, 74946.935901, 74956.065031, 74965.194270, 74974.323617, 74983.453073,
   74992.582637, 75001.712309, 75010.842090, 75019.971980, 75029.101977, 75038.232083, 75047.362298, 75056.492620,
   75065.623051, 75074.753590, 75083.884238, 75093.014994, 75102.145858, 75111.276831, 75120.407911, 75129.539100,
   75138.670397, 75147.801803, 75156.933316, 75166.064938, 75175.196668, 75184.328506, 75193.460453, 75202.592507,
   75211.724670, 75220.856940, 75229.989319, 75239.121806, 75248.254401, 75257.387104, 75266.519915, 75275.652835,
   75284.785862, 75293.918997, 75303.052240, 75312.185592, 75321.319051, 75330.452618, 75339.586294, 75348.720077,
   75357.853968, 75366.987967, 75376.122074, 75385.256289, 75394.390612, 75403.525043, 75412.659582, 75421.794228,
   75430.928983, 75440.063845, 75449.198815, 75458.333893, 75467.469078, 75476.604372, 75485.739773, 75494.875282,
   75504.010899, 75513.146624, 75522.282456, 75531.418396, 75540.554444, 75549.690599, 75558.826863, 75567.963233,
   75577.099712, 75586.236298, 75595.372992, 75604.509793, 75613.646702, 75622.783719, 75631.920843, 75641.058075,
   75650.195415, 75659.332862, 75668.470417, 75677.608079, 75686.745848, 75695.883726, 75705.021710, 75714.159802,
   75723.298002, 75732.436309, 75741.574724, 75750.713246, 75759.851876, 75768.990613, 75778.129457, 75787.268409,
   75796.407468, 75805.546634, 75814.685908, 75823.825290, 75832.964778, 75842.104374, 75851.244077, 75860.383888,
   75869.523806, 75878.663831, 75887.803964, 75896.944203, 75906.084550, 75915.225005, 75924.365566, 75933.506235,
   75942.647011, 75951.787894, 75960.928884, 75970.069982, 75979.211186, 75988.352498, 75997.493917, 76006.635443,
   76015.777076, 76024.918816, 76034.060664, 76043.202618, 76052.344680, 76061.486848, 76070.629124, 76079.771507,
   76088.913996, 76098.056593, 76107.199297, 76116.342108, 76125.485025, 76134.628050, 76143.771182, 76152.914420,
   76162.057766, 76171.201218, 76180.344777, 76189.488444, 76198.632217, 76207.776097, 76216.920084, 76226.064177,
   76235.208378, 76244.352685, 76253.497100, 76262.641621, 76271.786248, 76280.930983, 76290.075824, 76299.220773,
   76308.365828, 76317.510989, 76326.656258, 76335.801633, 76344.947114, 76354.092703, 76363.238398, 76372.384200,
   76381.530108, 76390.676124, 76399.822245, 76408.968474, 76418.114809, 76427.261251, 76436.407799, 76445.554454,
   76454.701215, 76463.848083, 76472.995057, 76482.142138, 76491.289326, 76500.436620, 76509.584021, 76518.731528,
   76527.879141, 76537.026861, 76546.174688, 76555.322621, 76564.470660, 76573.618806, 76582.767058, 76591.915417,
   76601.063882, 76610.212453, 76619.361131, 76628.509915, 76637.658805, 76646.807802, 76655.956905, 76665.106114,
   76674.255430, 76683.404852, 76692.554380, 76701.704015, 76710.853755, 76720.003602, 76729.153556, 76738.303615,
   76747.453781, 76756.604052, 76765.754431, 76774.904915, 76784.055505, 76793.206202, 76802.357004, 76811.507913,
   76820.658928, 76829.810049, 76838.961276, 76848.112609, 76857.264049, 76866.415594, 76875.567245, 76884.719003,
   76893.870866, 76903.022836, 76912.174911, 76921.327092, 76930.479380, 76939.631773, 76948.784273, 76957.936878,
   76967.089589, 76976.242406, 76985.395330, 76994.548359, 77003.701493, 77012.854734, 77022.008081, 77031.161533,
   77040.315092, 77049.468756, 77058.622526, 77067.776402, 77076.930383, 77086.084471, 77095.238664, 77104.392963,
   77113.547368, 77122.701878, 77131.856495, 77141.011216, 77150.166044, 77159.320977, 77168.476017, 77177.631161,
   77186.786412, 77195.941768, 77205.097229, 77214.252797, 77223.408470, 77232.564248, 77241.720133, 77250.876122,
   77260.032218, 77269.188419, 77278.344725, 77287.501137, 77296.657655, 77305.814278, 77314.971006, 77324.127840,
   77333.284780, 77342.441825, 77351.598976, 77360.756232, 77369.913593, 77379.071060, 77388.228632, 77397.386310,
   77406.544093, 77415.701982, 77424.859976, 77434.018075, 77443.176279, 77452.334589, 77461.493005, 77470.651525,
   77479.810151, 77488.968883, 77498.127719, 77507.286661, 77516.445708, 77525.604860, 77534.764118, 77543.923481,
   77553.082949, 77562.242522, 77571.402200, 77580.561984, 77589.721873, 77598.881867, 77608.041966, 77617.202170,
   77626.362480, 77635.522894, 77644.683414, 77653.844039, 77663.004769, 77672.165604, 77681.326544, 77690.487589,
   77699.648739, 77708.809994, 77717.971354, 77727.132819, 77736.294390, 77745.456065, 77754.617845, 77763.779730,
   77772.941720, 77782.103815, 77791.266015, 77800.428320, 77809.590730, 77818.753245, 77827.915864, 77837.078589,
   77846.241418, 77855.404353, 77864.567392, 77873.730536, 77882.893784, 77892.057138, 77901.220596, 77910.384160,
   77919.547828, 77928.711600, 77937.875478, 77947.039460, 77956.203547, 77965.367739, 77974.532035, 77983.696436,
   77992.860942, 78002.025553, 78011.190268, 78020.355088, 78029.520012, 78038.685041, 78047.850175, 78057.015414,
   78066.180757, 78075.346204, 78084.511756, 78093.677413, 78102.843174, 78112.009040, 78121.175011, 78130.341086,
   78139.507265, 78148.673549, 78157.839938, 78167.006431, 78176.173028, 78185.339730, 78194.506536, 78203.673447,
   78212.840462, 78222.007582, 78231.174806, 78240.342135, 78249.509568, 78258.677105, 78267.844746, 78277.012492,
   78286.180343, 78295.348297, 78304.516356, 78313.684520, 78322.852787, 78332.021159, 78341.189635, 78350.358216,
   78359.526900, 78368.695689, 78377.864583, 78387.033580, 78396.202682, 78405.371887, 78414.541197, 78423.710612,
   78432.880130, 78442.049753, 78451.219479, 78460.389310, 78469.559245, 78478.729284, 78487.899427, 78497.069675,
   78506.240026, 78515.410481, 78524.581041, 78533.751704, 78542.922472, 78552.093344, 78561.264319, 78570.435399,
   78579.606583, 78588.777870, 78597.949262, 78607.120757, 78616.292357, 78625.464060, 78634.635868, 78643.807779,
   78652.979794, 78662.151914, 78671.324137, 78680.496464, 78689.668894, 78698.841429, 78708.014068, 78717.186810,
   78726.359656, 78735.532606, 78744.705660, 78753.878817, 78763.052079, 78772.225444, 78781.398913, 78790.572485,
   78799.746162, 78808.919942, 78818.093826, 78827.267813, 78836.441905, 78845.616100, 78854.790398, 78863.964800,
   78873.139306, 78882.313916, 78891.488629, 78900.663446, 78909.838366, 78919.013390, 78928.188518, 78937.363749,
   78946.539084, 78955.714522, 78964.890064, 78974.065710, 78983.241458, 78992.417311, 79001.593267, 79010.769326,
   79019.945489, 79029.121756, 79038.298125, 79047.474599, 79056.651175, 79065.827856, 79075.004639, 79084.181526,
   79093.358517, 79102.535610, 79111.712808, 79120.890108, 79130.067512, 79139.245019, 79148.422630, 79157.600344,
   79166.778161, 79175.956081, 79185.134105, 79194.312232, 79203.490462, 79212.668796, 79221.847233, 79231.025773,
   79240.204416, 79249.383163, 79258.562012, 79267.740965, 79276.920021, 79286.099181, 79295.278443, 79304.457809,
   79313.637277, 79322.816849, 79331.996524, 79341.176302, 79350.356183, 79359.536168, 79368.716255, 79377.896445,
   79387.076739, 79396.257135, 79405.437635, 79414.618237, 79423.798943, 79432.979751, 79442.160663, 79451.341678,
   79460.522795, 79469.704016, 79478.885339, 79488.066765, 79497.248295, 79506.429927, 79515.611662, 79524.793500,
   79533.975441, 79543.157485, 79552.339631, 79561.521881, 79570.704233, 79579.886688, 79589.069246, 79598.251907,
   79607.434671, 79616.617537, 79625.800506, 79634.983578, 79644.166753, 79653.350030, 79662.533410, 79671.716893,
   79680.900479, 79690.084167, 79699.267958, 79708.451852, 79717.635849, 79726.819948, 79736.004149, 79745.188454,
   79754.372861, 79763.557370, 79772.741982, 79781.926697, 79791.111515, 79800.296435, 79809.481457, 79818.666582,
   79827.851810, 79837.037140, 79846.222573, 79855.408108, 79864.593746, 79873.779486, 79882.965329, 79892.151274,
   79901.337322, 79910.523472, 79919.709725, 79928.896080, 79938.082537, 79947.269097, 79956.455759, 79965.642524,
   79974.829391, 79984.016360, 79993.203432, 80002.390606, 80011.577882, 80020.765261, 80029.952742, 80039.140326,
   80048.328011, 80057.515799, 80066.703690, 80075.891682, 80085.079777, 80094.267974, 80103.456273, 80112.644675,
   80121.833178, 80131.021784, 80140.210492, 80149.399302, 80158.588215, 80167.777229, 80176.966346, 80186.155565,
   80195.344886, 80204.534309, 80213.723834, 80222.913462, 80232.103191, 80241.293023, 80250.482956, 80259.672992,
   80268.863130, 80278.053369, 80287.243711, 80296.434155, 80305.624700, 80314.815348, 80324.006098, 80333.196950,
   80342.387903, 80351.578959, 80360.770116, 80369.961376, 80379.152737, 80388.344201, 80397.535766, 80406.727433,
   80415.919202, 80425.111073, 80434.303045, 80443.495120, 80452.687296, 80461.879575, 80471.071955, 80480.264437,
   80489.457020, 80498.649706, 80507.842493, 80517.035382, 80526.228373, 80535.421465, 80544.614659, 80553.807955,
   80563.001353, 80572.194852, 80581.388453, 80590.582156, 80599.775960, 80608.969866, 80618.163874, 80627.357984,
   80636.552195, 80645.746507, 80654.940921, 80664.135437, 80673.330055, 80682.524774, 80691.719594, 80700.914516,
   80710.109540, 80719.304665, 80728.499892, 80737.695220, 80746.890650, 80756.086181, 80765.281814, 80774.477548,
   80783.673384, 80792.869321, 80802.065360, 80811.261500, 80820.457741, 80829.654084, 80838.850528, 80848.047074,
   80857.243721, 80866.440469, 80875.637319, 80884.834270, 80894.031323, 80903.228476, 80912.425732, 80921.623088,
   80930.820546, 80940.018105, 80949.215765, 80958.413527, 80967.611390, 80976.809354, 80986.007419, 80995.205586,
   81004.403853, 81013.602222, 81022.800693, 81031.999264, 81041.197937, 81050.396710, 81059.595585, 81068.794561,
   81077.993638, 81087.192817, 81096.392096, 81105.591477, 81114.790958, 81123.990541, 81133.190225, 81142.390010,
   81151.589896, 81160.789883, 81169.989971, 81179.190160, 81188.390450, 81197.590841, 81206.791333, 81215.991926,
   81225.192620, 81234.393415, 81243.594311, 81252.795307, 81261.996405, 81271.197604, 81280.398904, 81289.600304,
   81298.801805, 81308.003408, 81317.205111, 81326.406915, 81335.608820, 81344.810826, 81354.012932, 81363.215140,
   81372.417448, 81381.619857, 81390.822367, 81400.024977, 81409.227689, 81418.430501, 81427.633413, 81436.836427,
   81446.039541, 81455.242756, 81464.446072, 81473.649489, 81482.853006, 81492.056624, 81501.260342, 81510.464161,
   81519.668081, 81528.872102, 81538.076223, 81547.280444, 81556.484767, 81565.689189, 81574.893713, 81584.098337,
   81593.303062, 81602.507887, 81611.712813, 81620.917839, 81630.122966, 81639.328193, 81648.533521, 81657.738949,
   81666.944478, 81676.150107, 81685.355837, 81694.561667, 81703.767598, 81712.973629, 81722.179761, 81731.385992,
   81740.592325, 81749.798758, 81759.005291, 81768.211924, 81777.418658, 81786.625492, 81795.832427, 81805.039462,
   81814.246597, 81823.453833, 81832.661168, 81841.868605, 81851.076141, 81860.283778, 81869.491515, 81878.699352,
   81887.907290, 81897.115327, 81906.323465, 81915.531703, 81924.740042, 81933.948480, 81943.157019, 81952.365658,
   81961.574397, 81970.783236, 81979.992176, 81989.201215, 81998.410355, 82007.619595, 82016.828935, 82026.038374,
   82035.247915, 82044.457555, 82053.667295, 82062.877135, 82072.087075, 82081.297116, 82090.507256, 82099.717496,
   82108.927837
  };
 
/* Nat log values for 0.1, 0.2, 0.3, etc. */
/* Used instead of repeatedly calculating them. */
double log_win10[] =
{
   0.0, -2.30258509, -1.60943791, -1.203982804, -0.91629073, -0.6931478, -0.510825623, -0.356674944,
   -0.22314355, -0.105360515, 0.0
};
 
 
 
 
const int kProtAlphabet = 2;   /**< identifies protein alphabet (FIXME: needed?). */
 
 
 
/** Information about the alphabet used by seg.
 *  For proteins this version of seg uses ncbistdaa,
 *  This keeps track of those.
 */
typedef struct Alpha
  {
   Int4 alphabet;              /**< which alphabet, kProtAlphabet for proteins. */
   Int4 alphasize;             /**< size of above alphabet. */
   double lnalphasize;         /**< nat. log of size of above alphabet. */
   Int4* alphaindex;           /**< value in ncbistdaa. */
   unsigned char* alphaflag;   /**< array of bools to indicate that letter is (not) valid?? */
  } Alpha;
 
 
/** General sequence information */
typedef struct SSequence
  {
   struct SSequence* parent;   /**< SSequence window that encompasses the current one */
   char* seq;                  /**< sequence in ncbistdaa. */
   Alpha* palpha;              /**< alphabet information */
   Int4 start;                 /**< starting offset to seg. */
   Int4 length;                /**< Length of sequence to be segged. */
   Int4 bogus;                 /**< tracks number of non-allowed residues (e.g., X) */
   Boolean punctuation;        /**< FIXME: always FALSE, never set to TRUE? */
   Int4* composition;          /**< totals number of each type of residue */
   Int4* state;                /**< "state vector as described on pg. 151 of Wootton and Federhen
                                  (Comput. Chem. 17, 149 (1993)).  Tracks number of each residue,
                                  like composition, but without gaps in array. */
   double entropy;             /**< entropy of what this array refers to. */
} SSequence;
 
/** List of sequence segments (hits) */
typedef struct SSeg
  {
   int begin;          /**< beginning of segment (hit). */
   int end;            /**< end of segment (hit). */
   struct SSeg *next;  /**< next object in linked list */
  } SSeg;
 
/** Initializes SSequence structure */
static SSequence*
s_SSequenceNew(void)
{
   SSequence* seq;
 
   seq = (SSequence*) calloc(1, sizeof(SSequence));
   if (seq==NULL)
     {
      /* raise error flag and etc. */
      return(seq);
     }
 
   seq->parent = (SSequence*) NULL;
   seq->seq = (char*) NULL;
   seq->palpha = (Alpha*) NULL;
   seq->start = seq->length = 0;
   seq->bogus = seq->punctuation = FALSE;
   seq->composition = seq->state = (Int4*) NULL;
   seq->entropy = (double) 0.0;
 
   return(seq);
}
 
/*------------------------------------------------------------(AlphaFree)---*/
 
/** Frees the Alpha structure and underlying structures.
 * @param palpha the object to be freed [in]
 */
static void
s_AlphaFree (Alpha* palpha)
 
  {
   if (!palpha) return;
 
   sfree (palpha->alphaindex);
   sfree (palpha->alphaflag);
   sfree (palpha);
 
   return;
 }
 
/*--------------------------------------------------------------(SSequenceFree)---*/
 
/** Frees the SSequence structure and the underlying structure
 * @param seq the object to be freed [in]
 */
static void
s_SSequenceFree(SSequence* seq)
{
   if (seq==NULL) return;
 
   sfree(seq->seq);
   s_AlphaFree(seq->palpha);
   sfree(seq->composition);
   sfree(seq->state);
   sfree(seq);
   return;
}
 
/*--------------------------------------------------------------(SSegFree)---*/
 
/** Frees the SSeg structure
 * @param seg the object to be freed [in]
 */
static void
s_SegFree(SSeg* seg)
{
   SSeg* nextseg;
 
   while (seg)
     {
      nextseg = seg->next;
      sfree(seg);
      seg = nextseg;
     }
 
   return;
}
 
/*--------------------------------------------------------------(hasdash)---*/
 
/** Checks if sequence contains a dash.
 * @param win SSequence structure for a piece of a sequence [in]
 * @return TRUE if dash is found in the sequence, otherwise FALSE [in]
 */
static Boolean
s_HasDash(SSequence* win)
{
    char    *seq, *seqmax;
 
    seq = win->seq;
    seqmax = seq + win->length;
 
    while (seq < seqmax) {
        if (*seq++ == '-')
            return TRUE;
    }
    return FALSE;
}
 
/*------------------------------------------------------------(state_cmp)---*/
 
/** State comparison function */
static int
s_StateCmp(const void* s1, const void* s2)
{
    int *np1, *np2;
 
    np1 = (int *) s1;
    np2 = (int *) s2;
 
    return (*np2 - *np1);
}
 
/*---------------------------------------------------------------(compon)---*/
 
/** Calculates sequence composition array values.
 * @param win the object to be analyzed [in]
 */
static void
s_CompOn(SSequence* win)
 
{
    Int4* comp;
    Int4 letter;
    char* seq,* seqmax;
        Int4* alphaindex;
        unsigned char* alphaflag;
        Int4 alphasize;
 
        alphasize = win->palpha->alphasize;
        alphaindex = win->palpha->alphaindex;
        alphaflag = win->palpha->alphaflag;
 
    win->composition = comp =
                (Int4*) calloc(alphasize, sizeof(Int4));
    seq = win->seq;
    seqmax = seq + win->length;
 
    while (seq < seqmax) {
        letter = *seq++;
        if (!alphaflag[letter])
            comp[alphaindex[letter]]++;
                else
                        win->bogus++;
    }
 
    return;
}
 
/*--------------------------------------------------------------(stateon)---*/
 
/** Calculates state array values
 * @param win the object to be analyzed [in]
 */
static void
s_StateOn(SSequence* win)
 
{
    Int4 letter, nel, c;
        Int4 alphasize;
 
        alphasize = win->palpha->alphasize;
 
    if (win->composition == NULL)
        s_CompOn(win);
 
    win->state = (Int4*) calloc((alphasize+1), sizeof(win->state[0]));
 
    for (letter = nel = 0; letter < alphasize; ++letter) {
        if ((c = win->composition[letter]) == 0)
            continue;
        win->state[nel++] = c;
    }
    for (letter = nel; letter < alphasize+1; ++letter)
        win->state[letter] = 0;
 
    qsort(win->state, nel, sizeof(win->state[0]), s_StateCmp);
 
    return;
}
 
/*--------------------------------------------------------------(s_OpenWin)---*/
 
/** Initializes an SSequence structure for part of sequence contained in a
 * window.
 * @param parent Parent (whole) sequence [in]
 * @param start Window start in parent [in]
 * @param length Window length in parent [in]
 * @return Pointer to the resulting SSequence structure.
 */
static SSequence*
s_OpenWin(SSequence* parent, Int4 start, Int4 length)
{
   SSequence* win;
 
   if (start<0 || length<0 || start+length>parent->length)
     {
      return((SSequence*) NULL);
     }
 
      win = (SSequence*) calloc(1, sizeof(SSequence));
 
/*---                                          ---[set links, up and down]---*/
 
      win->parent = parent;
      win->palpha = parent->palpha;
 
/*---                          ---[install the local copy of the sequence]---*/
 
      win->start = start;
      win->length = length;
    win->seq = parent->seq + start;
 
        win->bogus = 0;
    win->punctuation = FALSE;
 
    win->entropy = -2.;
    win->state = (Int4*) NULL;
    win->composition = (Int4*) NULL;
 
    s_StateOn(win);
 
    return win;
}
 
/*--------------------------------------------------------------(s_Entropy)---*/
 
/** Calculates entropy of an integer array
 * @param sv array to be analyzed [in]
 * @return the entropy
 */
static double
s_Entropy(Int4* sv)
{
   double ent;
   Int4 i, total;
 
   total = 0;
   for (i=0; sv[i]!=0; i++)
     {
      total += sv[i];
     }
   if (total==0) return(0.);
 
   ent = 0.0;
   if (total == 10)
   { /* Use precomputed table. */
    for (i=0; sv[i]!=0; i++)
        {
            ent += ((double)sv[i])*log_win10[sv[i]]/NCBIMATH_LN2;
        }
 
   }
   else
   {
    for (i=0; sv[i]!=0; i++)
        {
            ent += ((double)sv[i])*log(((double)sv[i])/(double)total)/NCBIMATH_LN2;
        }
   }
   ent = fabs(ent/(double)total);
 
   return(ent);
}
 
/*----------------------------------------------------------(decrementsv)---*/
 
 
 
/** Decrements the value in the Int4 array for every element that matches class.
 * There is also another criteria that the next element must have a vlaue
 * less than class.
 * @param sv the array to be examined and decremented [in|out]
 * @param class criteria for decrementing an element [in]
 */
static void
s_DecrementSV(Int4* sv, Int4 class)
 
{
    Int4    svi;
 
    while ((svi = *sv++) != 0) {
        if (svi == class && *sv < class) {
            sv[-1] = svi - 1;
            break;
        }
    }
}
 
/** Increments the value in the Int4 array for every element that matches class.
 * @param sv the array to be examined and incremented [in|out]
 * @param class criteria for incrementing an element [in]
 */
static void
s_IncrementSV(Int4* sv, Int4 class)
 
{
    for (;;) {
        if (*sv++ == class) {
            sv[-1]++;
            break;
        }
    }
}
 
/** Moves over the "window" of sequence seg is currently working on.
 *
 * @param win object to be operated on [in]
 * @return FALSE if nothing done, TRUE otherwise
 */
 
static Boolean
s_ShiftWin1(SSequence* win)
{
    Uint4 j, length;
    Int4* comp;
    Int4* alphaindex;
    unsigned char* alphaflag;
 
    length = (Uint4) win->length;
    comp = win->composition;
    alphaindex = win->palpha->alphaindex;
    alphaflag = win->palpha->alphaflag;
 
    if ((Uint1) win->seq[length] == FENCE_SENTRY) {
        return FALSE;
    }
    if ((++win->start + length) > win->parent->length) {
        --win->start;
        return FALSE;
    }
 
    j = (Uint1) win->seq[0];        /* prevent sign-extension */
 
    if (!alphaflag[j])
        s_DecrementSV(win->state, comp[alphaindex[j]]--);
    else win->bogus--;
 
    j = (Uint1) win->seq[length];   /* prevent sign-extension */
    ++win->seq;
 
    if (!alphaflag[j])
        s_IncrementSV(win->state, comp[alphaindex[j]]++);
    else win->bogus++;
 
    if (win->entropy > -2.)
        win->entropy = s_Entropy(win->state);
 
    return TRUE;
}
 
/*-------------------------------------------------------------(closewin)---*/
 
/** Frees the SSequence structure corresponding to a sequence window
 * Does not free palpha like s_SSequenceFree (two functions needed?).
 * @param win object to be freed
 */
static void
s_CloseWin(SSequence* win)
{
   if (win==NULL) return;
 
   if (win->state!=NULL)       sfree(win->state);
   if (win->composition!=NULL) sfree(win->composition);
 
   sfree(win);
   return;
}
 
/*----------------------------------------------------------------(enton)---*/
 
/** Calculates entropy of a sequence window
 * @param win object to be analyzed [in]
 */
static void
s_EntropyOn(SSequence* win)
 
  {
   if (win->state==NULL) {s_StateOn(win);}
 
   win->entropy = s_Entropy(win->state);
 
   return;
  }
 
/** Calculates entropy for a given sequence and window
 *
 * @param seq Sequence to examine [in]
 * @param window amount of sequence to examine at once [in]
 * @param maxbogus limit on non-allowed (e.g., X) characters [in]
 * @return calculated entropy
 */
static double*
s_SeqEntropy(SSequence* seq, Int4 window, Int4 maxbogus)
{
   SSequence* win;
   double* H;
   Int4 i, first, last, downset, upset;
 
   downset = (window+1)/2 - 1;
   upset = window - downset;
 
   if (window>seq->length)
     {
      return((double*) NULL);
     }
 
   H = (double*) calloc(seq->length, sizeof(double));
 
   for (i=0; i<seq->length; i++)
     {
      H[i] = -1.;
     }
 
   win = s_OpenWin(seq, 0, window);
   s_EntropyOn(win);
 
   first = downset;
   last = seq->length - upset;
 
   for (i=first; i<=last; i++)
     {
      if (seq->punctuation && s_HasDash(win))
        {
         H[i] = -1.;
         s_ShiftWin1(win);
         continue;
        }
      if (win->bogus > maxbogus)
        {
         H[i] = -1.;
         s_ShiftWin1(win);
         continue;
        }
      H[i] = win->entropy;
      s_ShiftWin1(win);
     }
 
   s_CloseWin(win);
   return(H);
}
 
/*---------------------------------------------------------------(s_FindLow)---*/
 
/** Finds the first element above hicut, looks from i to limit.
 * @param i first element to check [in]
 * @param limit last element to check [in]
 * @param hicut value to check for [in]
 * @param H the array to check.
 * @return index of last element with value below hicut
 */
 
static Int4 s_FindLow(Int4 i, Int4 limit, double hicut, double* H)
 
  {
   Int4 j;
 
   for (j=i; j>=limit; j--)
     {
      if (H[j]==-1.0) break;
      if (H[j]>hicut) break;
     }
 
   return(j+1);
  }
 
/*---------------------------------------------------------------(s_FindHigh)---*/
 
/** Finds the last element below hicut, looks from i to limit.
 * @param i first element to check [in]
 * @param limit last element to check [in]
 * @param hicut value to check for [in]
 * @param H the array to check.
 * @return index of last element with value below hicut
 */
static Int4 s_FindHigh(Int4 i, Int4 limit, double hicut, double* H)
 
  {
   Int4 j;
 
   for (j=i; j<=limit; j++)
     {
      if (H[j]==-1.0) break;
      if (H[j]>hicut) break;
     }
 
   return(j-1);
  }
 
/** calculate log(n!) using either tabulated data or Sterling's formula
 * @param n [in]
 * @return log(n!)
 */
static double
s_lnfact(Int4 n) {
  if (n < sizeof(lnfact)/sizeof(*lnfact))
     return lnfact[n];
  else return ((n+0.5)*log(n) - n + 0.9189385332);
}
 
/** calculate "K2" entropy per equation 3 of Wootton and Federhen
 * (Comput. Chem. 17, 149 (1993).
 * @param sv state vector [in]
 * @param window_length length of window being examined
 * @return K2
 */
static double
s_LnPerm(const Int4* sv, Int4 window_length)
 
  {
   double ans;
   Int4 i;
 
   ans = s_lnfact(window_length);
 
   for (i=0; sv[i]!=0; i++)
     {
      ans -= s_lnfact(sv[i]);
     }
 
   return(ans);
  }
 
 
/** Calculates natural log of "Farben" which is the number of compositions
 * in any complexity state.  See equation 1 of Wootton and Federhen
 * (Comput. Chem. 17, 149 (1993)).
 * @param sv state vector [in]
 * @param alphasize total letters in alphabet [in]
 * @return number of compositions as described above
 */
static double
s_LnAss(const Int4* sv, Int4 alphasize)
 
{
    double  ans;
    int svi, svim1;
    int class, total;
    int    i;
 
    ans = lnfact[alphasize];
    if (sv[0] == 0)
        return ans;
 
    total = alphasize;
    class = 1;
    svi = *sv;
    svim1 = sv[0];
    for (i=0;; svim1 = svi) {
            if (++i==alphasize) {
                ans -= s_lnfact(class);
            break;
              }
        else if ((svi = *++sv) == svim1) {
            class++;
            continue;
        }
        else {
            total -= class;
            ans -= s_lnfact(class);
            if (svi == 0) {
                ans -= s_lnfact(total);
                break;
            }
            else {
                class = 1;
                continue;
            }
        }
    }
 
    return ans;
}
 
 
/** This function calculates the natural log of the value P sub 0 from
 * equation 3 of Wootton and Federhen (Methods Enzymol. 1996;266:554-71).
 * @param sv state vector [in]
 * @param total window length of area examined [in]
 * @param palpha structure for alphabet information [in]
 * @return log of P sub 0 as mentioned above
 */
static double
s_GetProb(const Int4* sv, Int4 total, const Alpha* palpha)
 
  {
   double ans, ans1, ans2 = 0, totseq;
 
   totseq = ((double) total) * palpha->lnalphasize;
 
   ans1 = s_LnAss(sv, palpha->alphasize);
   if (ans1 > -100000.0 && sv[0] != INT4_MIN)
   {
    ans2 = s_LnPerm(sv, total);
   }
   else
   {
#ifdef ERR_POST_EX_DEFINED
        ErrPostEx (SEV_ERROR, 0, 0, "Illegal value returned by s_LnAss");
#endif
   }
   ans = ans1 + ans2 - totseq;
 
   return ans;
  }
 
/** Trims view of sequence so as to minimize the probability returned by s_GetProb
 * @param seq the part of sequence to be examined [in]
 * @param leftend left-most end of sequence [in|out]
 * @param rightend right-most end of sequence [in|out]
 * @param sparamsp the SEG parameters [in]
 */
static Int2
s_Trim(SSequence* seq, Int4* leftend, Int4* rightend, const SegParameters* sparamsp)
 
{
   double prob, minprob;
   Int4 len;
   Int4 lend, rend;
   Int4 minlen;
   Int4 maxtrim;
   Int2 status = 0;
 
   lend = 0;
   rend = seq->length - 1;
   minlen = 1;
   maxtrim = sparamsp->maxtrim;
   if ((seq->length-maxtrim)>minlen)
        minlen = seq->length-maxtrim;
 
   minprob = 1.;
   for (len=seq->length; len>minlen; len--)
   {
      Boolean shift = TRUE;
      Int4 i = 0;
      SSequence* win = s_OpenWin(seq, 0, len);
 
      while (shift)
      {
         prob = s_GetProb(win->state, len, win->palpha);
         if (prob<minprob)
         {
            minprob = prob;
            lend = i;
            rend = len + i - 1;
         }
         shift = s_ShiftWin1(win);
         i++;
      }
      s_CloseWin(win);
   }
 
   *leftend = *leftend + lend;
   *rightend = *rightend - (seq->length - rend - 1);
 
   s_CloseWin(seq);
   return status;
}
 
/** High-level function to perform calculations to find
 * low-complexity segments.  Thi function calls itself
 * recursively
 *
 * @param seq sequence to be checked [in]
 * @param sparamsp seg parameters [in]
 * @param segs low-complexity segments found [out]
 * @param offset offset of sequence passed in [in]
 */
static Int2
s_SegSeq(SSequence* seq, SegParameters* sparamsp, SSeg **segs,
                   Int4 offset)
{
   SSeg* seg = (SSeg*) NULL;
   Int4 window;
   double locut, hicut;
   Int4 downset, upset;
   Int4 first, last, lowlim;
   Int4 i;
   Int4 leftend, rightend;
   double* H;
   Int2 status = 0;
 
   if (sparamsp->window<=0) return status;
   if (sparamsp->locut<=0.) sparamsp->locut = 0.;
   if (sparamsp->hicut<=0.) sparamsp->hicut = 0.;
 
   window = sparamsp->window;
   locut = sparamsp->locut;
   hicut = sparamsp->hicut;
   downset = (window+1)/2 - 1;
   upset = window - downset;
 
   H = s_SeqEntropy(seq, window, sparamsp->maxbogus);
 
   if (H == NULL)
      return status;
 
   first = downset;
   last = seq->length - upset;
   lowlim = first;
 
   for (i=first; i<=last; i++)
   {
      if (H[i] <= locut && H[i] != -1.0)
        {
         Int4 loi = s_FindLow(i, lowlim, hicut, H);
         Int4 hii = s_FindHigh(i, last, hicut, H);
         SSequence* temp_seq = NULL;
 
         leftend = loi - downset;
         rightend = hii + upset - 1;
 
         temp_seq = s_OpenWin(seq, leftend, rightend-leftend+1);
         status = s_Trim(temp_seq, &leftend, &rightend, sparamsp);
 
         if (status < 0) {
             s_CloseWin(temp_seq);
             break;
         }
 
         if (i+upset-1<leftend)   /* check for trigger window in left trim */
         {
            Int4 lend = loi - downset;
            Int4 rend = leftend - 1;
 
            SSequence* leftseq = s_OpenWin(seq, lend, rend-lend+1);
            SSeg *leftsegs = (SSeg*) NULL;
            status = s_SegSeq(leftseq, sparamsp, &leftsegs, offset+lend);
            if (status < 0)
        {
        sfree(H);
                return status;
        }
 
            /* prepend here, order will be restored in s_SegToSeqLoc */
            if (leftsegs!=NULL)
            {
               leftsegs->next = *segs;
               *segs = leftsegs;
            }
            s_CloseWin(leftseq);
 
         }
 
         seg = (SSeg*) calloc(1, sizeof(SSeg));
         seg->begin = leftend + offset;
         seg->end = rightend + offset;
         seg->next = *segs;
         *segs = seg;
         i = MIN(hii, rightend+downset);
         lowlim = i + 1;
        }
   }
   sfree(H);
   return status;
}
 
/*------------------------------------------------------------(mergesegs)---*/
/** merge together overlapping segments,
 * hilenmin also does something, but we need to ask Scott Federhen what?
 * @param seq information about sequence [in]
 * @param segs segment information [in]
*/
static void
s_MergeSegs(SSequence* seq, SSeg* segs)
{
   SSeg* seg,* nextseg;
   Int4 hilenmin;              /* hilenmin yet unset */
 
   hilenmin = 0;               /* hilenmin - temporary default */
 
   if (segs==NULL) return;
 
   if (seq->length -1 - segs->end < hilenmin)
       segs->end = seq->length -1;
 
   seg = segs;
   nextseg = seg->next;
 
   while (nextseg!=NULL) {
      if (seg->begin - nextseg->end - 1 < hilenmin) {
         if (seg->end < nextseg->end) seg->end = nextseg->end;
         if (seg->begin > nextseg->begin) seg->begin = nextseg->begin;
         seg->next = nextseg->next;
         sfree(nextseg);
      } else {
         seg = nextseg;
      }
      nextseg = seg->next;
   }
 
   if (seg->begin < hilenmin) seg->begin = 0;
 
   return;
}
 
/** Converts the internal representation used by seg to that used by BLAST
 *
 * @param segs internal representation [in]
 * @param offset fixed value to add to offsets [in]
 * @param seg_locs the new BLAST specific representation [out]
 * @return 0 on success, -1 if memory allocation failed.
 */
static Int2
s_SegsToBlastSeqLoc(SSeg* segs, Int4 offset, BlastSeqLoc** seg_locs)
{
   for ( ; segs; segs = segs->next) {
      BlastSeqLoc *loc = (BlastSeqLoc*) calloc(1, sizeof(BlastSeqLoc));
      loc->ssr = (SSeqRange*) calloc(1,sizeof(SSeqRange));
      loc->ssr->left = segs->begin + offset;
      loc->ssr->right = segs->end  + offset;
      loc->next = *seg_locs;
      *seg_locs = loc;
   }
   /* If not all segs have been processed, it means that memory allocation
      failed, hence return error status. */
   if (segs) {
       *seg_locs = BlastSeqLocFree(*seg_locs);
       return -1;
   }
 
   return 0;
}
 
/** Creats the Alphabet structure for standard protein alphabet.
 * @return pointer to the alphabet structure.
 */
static Alpha*
s_AA20alphaStd (void)
{
   Alpha* palpha;
   Int4* alphaindex;
   unsigned char* alphaflag;
   Uint1 c, i;
   const int kCharSet = 128;
   const double kLn20 = 2.9957322735539909;
 
   palpha = (Alpha*) calloc(1, sizeof(Alpha));
 
   palpha->alphabet = kProtAlphabet;
   palpha->alphasize = 20;
   palpha->lnalphasize = kLn20;
 
   alphaindex = (Int4*) calloc(kCharSet , sizeof(Int4));
   alphaflag = (unsigned char*) calloc(kCharSet , sizeof(unsigned char));
 
   for (c=0, i=0; c<kCharSet; c++)
     {
        if (c == 1 || (c >= 3 && c <= 20) || c == 22) {
           alphaflag[c] = FALSE;
           alphaindex[c] = i;
           ++i;
        } else {
           alphaflag[c] = TRUE; alphaindex[c] = 20;
        }
     }
 
   palpha->alphaindex = alphaindex;
   palpha->alphaflag = alphaflag;
 
   return (palpha);
}
 
/* Comments in blast_seg.h */
SegParameters* SegParametersNewAa (void)
{
   SegParameters* sparamsp;
 
   sparamsp = (SegParameters*) calloc(1, sizeof(SegParameters));
 
   sparamsp->window = kSegWindow;
   sparamsp->locut = kSegLocut;
   sparamsp->hicut = kSegHicut;
   sparamsp->period = 1;
   sparamsp->hilenmin = 0;
   sparamsp->overlaps = FALSE;
   sparamsp->maxtrim = 50;
   sparamsp->maxbogus = 2;
 
   return (sparamsp);
}
 
/** Checks SeqParameter struct for proteins, sets default values if not set.
 * @param sparamsp parameters to check [in]
 */
static void
s_SegParametersCheck (SegParameters* sparamsp)
{
   if (!sparamsp) return;
 
   if (sparamsp->window <= 0) sparamsp->window = 12;
 
   if (sparamsp->locut < 0.0) sparamsp->locut = 0.0;
 
   if (sparamsp->hicut < 0.0) sparamsp->hicut = 0.0;
 
   if (sparamsp->locut > sparamsp->hicut)
       sparamsp->hicut = sparamsp->locut;
 
   if (sparamsp->maxbogus < 0)
       sparamsp->maxbogus = 0;
   if (sparamsp->maxbogus > sparamsp->window)
       sparamsp->maxbogus = sparamsp->window;
 
   if (sparamsp->period <= 0) sparamsp->period = 1;
   if (sparamsp->maxtrim < 0) sparamsp->maxtrim = 0;
 
   return;
}
 
/* Comments in blast_seg.h */
void SegParametersFree(SegParameters* sparamsp)
{
   if (!sparamsp)
      return;
   sfree(sparamsp);
   return;
}
 
/* comments in blast_seg.h */
Int2 SeqBufferSeg (Uint1* sequence, Int4 length, Int4 offset,
                     SegParameters* sparamsp, BlastSeqLoc** seg_locs)
{
   SSequence* seqwin;
   SSeg* segs;
   Boolean params_allocated = FALSE;
   Int2 status = 0;
 
   s_SegParametersCheck (sparamsp);
 
   /* check seg parameters */
   if (!sparamsp) {
      params_allocated = TRUE;
      sparamsp = SegParametersNewAa();
      s_SegParametersCheck (sparamsp);
      if (!sparamsp)
         return -1;
   }
 
   /* make an old-style genwin sequence window object */
 
   seqwin = s_SSequenceNew();
   seqwin->seq = (char*) sequence;
   seqwin->length = length;
   seqwin->palpha = s_AA20alphaStd();
 
   *seg_locs = NULL;
 
   /* seg the sequence */
 
   segs = (SSeg*) NULL;
   status = s_SegSeq (seqwin, sparamsp, &segs, 0);
   if (status < 0)
   {
     seqwin->seq = NULL;
     s_SSequenceFree (seqwin);
     return status;
   }
 
   /* merge the segment if desired. */
   if (sparamsp->overlaps)
      s_MergeSegs(seqwin, segs);
 
   /* convert segs to seqlocs */
   s_SegsToBlastSeqLoc(segs, offset, seg_locs);
 
   /* clean up & return */
   seqwin->seq = NULL;
   s_SSequenceFree (seqwin);
   s_SegFree (segs);
 
   if(params_allocated)
       SegParametersFree(sparamsp);
 
   return 0;
}