Changeset 582


Ignore:
Timestamp:
06/18/10 20:49:45 (3 months ago)
Author:
reed
Message:

fixed protein models

Location:
current
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • current/src/include/dawg/details/subst_aa.h

    r581 r582  
    128128} 
    129129 
    130  
    131130template<typename It1, typename It2> 
    132131bool subst_model::create_wag(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    133132    static const double s[190] = { 
    134         1.02704, 0.738998, 1.58285, 0.210494, 1.41672, 0.316954, 0.193335, 0.906265,  
    135         0.397915, 0.893496, 0.509848, 1.43855, 0.908598, 0.551571, 3.37079, 2.12111, 
    136         2.00601, 0.113133, 0.240735, 0.0302949, 0.021352, 0.39802, 0.306674, 0.248972, 
    137         0.170135, 0.0740339, 0.384287, 0.390482, 0.265256, 0.109404, 0.0988179, 0.528191, 
    138         1.40766, 0.512984, 1.00214, 0.71707, 0.543833, 6.17416, 0.0467304, 0.865584, 
    139         0.930676, 0.039437, 0.479855, 0.0848047, 0.103754, 5.42942, 0.423984, 0.616783, 
    140         0.147304, 1.07176, 0.374866, 0.152335, 0.129767, 0.325711, 0.0811339, 0.567717, 
    141         0.570025, 0.127395, 2.58443, 0.154263, 0.315124, 0.947198, 0.682355, 5.46947, 
    142         0.439157, 0.704939, 0.822765, 0.588731, 0.156557, 0.196303, 0.049931, 0.679371, 
    143         1.05947, 0.088836, 2.11517, 1.19063, 0.0961621, 0.161444, 0.0999208, 0.102711, 
    144         0.545931, 0.171903, 0.649892, 1.52964, 6.45428, 0.24941, 0.0304501, 0.373558, 
    145         0.0613037, 0.1741, 1.12556, 0.24357, 0.330052, 0.584665, 1.34182, 0.225833, 
    146         0.187247, 0.336983, 0.103604, 0.13819, 0.890432, 0.499462, 0.404141, 3.95629, 
    147         0.696198, 4.29411, 2.13715, 0.740169, 0.473307, 0.118358, 0.262569, 3.87344, 
    148         0.323832, 3.17097, 4.25746, 0.554236, 0.0999288, 0.113917, 0.186979, 0.31944, 
    149         1.45816, 7.8213, 0.212483, 0.42017, 0.257555, 0.934276, 3.01201, 0.556896, 3.8949, 
    150         5.35142, 0.96713, 1.38698, 0.305434, 0.137505, 0.133264, 4.85402, 0.131528, 0.415844, 
    151         0.869489, 0.497671, 0.344739, 0.326622, 1.80034, 0.665309, 0.398618, 0.198221, 
    152         0.171329, 1.54526, 0.683162, 0.493905, 1.51612, 2.05845, 0.515706, 0.428437, 
    153         0.195081, 1.54364, 0.635346, 3.97423, 2.03006, 0.196246, 0.0719167, 1.086, 0.933372, 
    154         0.679489, 1.61328, 0.795384, 0.314887, 0.139405, 0.216046, 3.0355, 1.02887, 0.857928, 
    155         0.301281, 0.215737, 0.22771, 1.22419, 0.554413, 0.251849, 1.16392, 0.381533, 4.37802, 
    156         0.232739, 0.523742, 0.786993, 1.38823, 0.110864, 0.291148, 0.365369, 0.31473, 2.48539 
    157     }; 
    158     static const double p[20] = { 
    159         0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.048466, 
    160         0.0620286, 0.086209, 0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.043972, 0.0695179, 
    161         0.0610127, 0.0708956, 0.0143859, 0.0352742 
     133        1.0270400, 0.7389980, 1.5828500, 0.2104940, 1.4167200, 0.3169540, 0.1933350, 0.9062650, 0.3979150, 0.8934960, 
     134        0.5098480, 1.4385500, 0.9085980, 0.5515710, 3.3707900, 2.1211100, 2.0060100, 0.1131330, 0.2407350, 0.0302949, 
     135        0.0213520, 0.3980200, 0.3066740, 0.2489720, 0.1701350, 0.0740339, 0.3842870, 0.3904820, 0.2652560, 0.1094040, 
     136        0.0988179, 0.5281910, 1.4076600, 0.5129840, 1.0021400, 0.7170700, 0.5438330, 6.1741600, 0.0467304, 0.8655840, 
     137        0.9306760, 0.0394370, 0.4798550, 0.0848047, 0.1037540, 5.4294200, 0.4239840, 0.6167830, 0.1473040, 1.0717600, 
     138        0.3748660, 0.1523350, 0.1297670, 0.3257110, 0.0811339, 0.5677170, 0.5700250, 0.1273950, 2.5844300, 0.1542630, 
     139        0.3151240, 0.9471980, 0.6823550, 5.4694700, 0.4391570, 0.7049390, 0.8227650, 0.5887310, 0.1565570, 0.1963030, 
     140        0.0499310, 0.6793710, 1.0594700, 0.0888360, 2.1151700, 1.1906300, 0.0961621, 0.1614440, 0.0999208, 0.1027110, 
     141        0.5459310, 0.1719030, 0.6498920, 1.5296400, 6.4542800, 0.2494100, 0.0304501, 0.3735580, 0.0613037, 0.1741000, 
     142        1.1255600, 0.2435700, 0.3300520, 0.5846650, 1.3418200, 0.2258330, 0.1872470, 0.3369830, 0.1036040, 0.1381900, 
     143        0.8904320, 0.4994620, 0.4041410, 3.9562900, 0.6961980, 4.2941100, 2.1371500, 0.7401690, 0.4733070, 0.1183580, 
     144        0.2625690, 3.8734400, 0.3238320, 3.1709700, 4.2574600, 0.5542360, 0.0999288, 0.1139170, 0.1869790, 0.3194400, 
     145        1.4581600, 7.8213000, 0.2124830, 0.4201700, 0.2575550, 0.9342760, 3.0120100, 0.5568960, 3.8949000, 5.3514200, 
     146        0.9671300, 1.3869800, 0.3054340, 0.1375050, 0.1332640, 4.8540200, 0.1315280, 0.4158440, 0.8694890, 0.4976710, 
     147        0.3447390, 0.3266220, 1.8003400, 0.6653090, 0.3986180, 0.1982210, 0.1713290, 1.5452600, 0.6831620, 0.4939050, 
     148        1.5161200, 2.0584500, 0.5157060, 0.4284370, 0.1950810, 1.5436400, 0.6353460, 3.9742300, 2.0300600, 0.1962460, 
     149        0.0719167, 1.0860000, 0.9333720, 0.6794890, 1.6132800, 0.7953840, 0.3148870, 0.1394050, 0.2160460, 3.0355000, 
     150        1.0288700, 0.8579280, 0.3012810, 0.2157370, 0.2277100, 1.2241900, 0.5544130, 0.2518490, 1.1639200, 0.3815330, 
     151        4.3780200, 0.2327390, 0.5237420, 0.7869930, 1.3882300, 0.1108640, 0.2911480, 0.3653690, 0.3147300, 2.4853900 
     152    }; 
     153    static const double p[20] = { 
     154        0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.0484660, 0.0620286, 0.0862090, 
     155        0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.0439720, 0.0695179, 0.0610127, 0.0708956, 0.0143859, 0.0352742 
    162156    }; 
    163157    if(first2 != last2) { //+F model 
    … …  
    170164bool subst_model::create_wagstar(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    171165    static const double s[190] = { 
    172         1.21324, 0.731152, 0.0379056, 1.55788, 0.0284956, 6.04299, 0.213179, 0.485001, 
    173         0.0458258, 0.0873936, 1.41993, 0.312544, 0.88357, 0.588609, 0.0552962, 0.317684, 
    174         0.341479, 0.958529, 0.599188, 0.631713, 0.279542, 0.214596, 0.198958, 0.0390513, 
    175         0.124553, 1.06458, 0.0310522, 0.162975, 0.881639, 0.0719929, 0.480308, 2.45392, 
    176         0.0832422, 0.381514, 0.854485, 0.320597, 0.400822, 0.451124, 0.0869637, 0.154936, 
    177         2.10414, 0.067443, 0.508952, 3.1554, 0.255092, 0.887458, 0.428648, 0.0992829, 
    178         0.294481, 1.14516, 0.184545, 0.40117, 3.94646, 0.877057, 4.81956, 0.514347, 0.233527, 
    179         5.30821, 1.00122, 0.0848492, 1.12717, 3.9337, 0.527321, 2.88102, 0.144354, 0.198404, 
    180         1.51861, 0.109081, 0.444152, 0.720567, 0.165205, 0.254626, 0.722123, 0.111722, 0.588203, 
    181         0.422851, 0.179858, 0.204905, 1.03344, 0.0999068, 0.657364, 5.6037, 0.109241, 0.346823, 
    182         4.87366, 0.125999, 4.19125, 0.873266, 1.64018, 1.62299, 0.913179, 0.589718, 0.568449, 
    183         0.159054, 0.443685, 0.122792, 0.629768, 2.31211, 0.187262, 5.74119, 0.51821, 0.660816, 
    184         0.67416, 0.711498, 3.02808, 3.52499, 1.35221, 1.09965, 0.822025, 0.563999, 1.33618, 
    185         0.876688, 0.321774, 1.05314, 0.351913, 0.554077, 3.90127, 1.54694, 0.87908, 1.35611, 
    186         2.24161, 0.522957, 0.395176, 0.889765, 0.188237, 0.236489, 0.54992, 1.48876, 1.45173, 
    187         0.351564, 1.56873, 2.06787, 0.802531, 0.829315, 0.594177, 4.02507, 1.92496, 1.10899, 
    188         0.155419, 0.588443, 0.653015, 0.190095, 0.119749, 7.48376, 0.300343, 1.82105, 2.03324, 
    189         0.193323, 0.325745, 0.32893, 0.282892, 0.23769, 1.4088, 0.135395, 0.728065, 0.142159, 
    190         0.176397, 1.58681, 0.366467, 0.261223, 0.259584, 0.159261, 0.706082, 0.565299, 0.0746093, 
    191         0.135024, 0.208163, 1.24086, 0.528249, 0.118584, 0.396884, 0.270321, 0.481954, 0.326191, 
    192         0.209621, 6.49269, 0.108982, 4.31772, 0.44009, 0.155623, 0.427718, 0.437069, 1.05269, 
    193         0.212945, 0.210494, 0.386714, 0.742154, 0.286443, 0.353358, 2.42261 
    194     }; 
    195     static const double p[20] = { 
    196         0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.048466, 
    197         0.0620286, 0.086209, 0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.043972, 0.0695179, 
    198         0.0610127, 0.0708956, 0.0143859, 0.0352742 
     166        1.2132400, 0.7311520, 1.5578800, 0.2131790, 1.4199300, 0.3176840, 0.2145960, 0.8816390, 0.4008220, 0.8874580, 
     167        0.5143470, 1.5186100, 1.0334400, 0.5897180, 3.5249900, 2.2416100, 1.9249600, 0.1353950, 0.2703210, 0.0379056, 
     168        0.0284956, 0.4850010, 0.3125440, 0.3414790, 0.1989580, 0.0719929, 0.4511240, 0.4286480, 0.2335270, 0.1090810, 
     169        0.0999068, 0.5684490, 1.3522100, 0.5229570, 1.1089900, 0.7280650, 0.4819540, 6.0429900, 0.0458258, 0.8835700, 
     170        0.9585290, 0.0390513, 0.4803080, 0.0869637, 0.0992829, 5.3082100, 0.4441520, 0.6573640, 0.1590540, 1.0996500, 
     171        0.3951760, 0.1554190, 0.1421590, 0.3261910, 0.0873936, 0.5886090, 0.5991880, 0.1245530, 2.4539200, 0.1549360, 
     172        0.2944810, 1.0012200, 0.7205670, 5.6037000, 0.4436850, 0.8220250, 0.8897650, 0.5884430, 0.1763970, 0.2096210, 
     173        0.0552962, 0.6317130, 1.0645800, 0.0832422, 2.1041400, 1.1451600, 0.0848492, 0.1652050, 0.1092410, 0.1227920, 
     174        0.5639990, 0.1882370, 0.6530150, 1.5868100, 6.4926900, 0.2795420, 0.0310522, 0.3815140, 0.0674430, 0.1845450, 
     175        1.1271700, 0.2546260, 0.3468230, 0.6297680, 1.3361800, 0.2364890, 0.1900950, 0.3664670, 0.1089820, 0.1629750, 
     176        0.8544850, 0.5089520, 0.4011700, 3.9337000, 0.7221230, 4.8736600, 2.3121100, 0.8766880, 0.5499200, 0.1197490, 
     177        0.2612230, 4.3177200, 0.3205970, 3.1554000, 3.9464600, 0.5273210, 0.1117220, 0.1259990, 0.1872620, 0.3217740, 
     178        1.4887600, 7.4837600, 0.2595840, 0.4400900, 0.2550920, 0.8770570, 2.8810200, 0.5882030, 4.1912500, 5.7411900, 
     179        1.0531400, 1.4517300, 0.3003430, 0.1592610, 0.1556230, 4.8195600, 0.1443540, 0.4228510, 0.8732660, 0.5182100, 
     180        0.3519130, 0.3515640, 1.8210500, 0.7060820, 0.4277180, 0.1984040, 0.1798580, 1.6401800, 0.6608160, 0.5540770, 
     181        1.5687300, 2.0332400, 0.5652990, 0.4370690, 0.2049050, 1.6229900, 0.6741600, 3.9012700, 2.0678700, 0.1933230, 
     182        0.0746093, 1.0526900, 0.9131790, 0.7114980, 1.5469400, 0.8025310, 0.3257450, 0.1350240, 0.2129450, 3.0280800, 
     183        0.8790800, 0.8293150, 0.3289300, 0.2081630, 0.2104940, 1.3561100, 0.5941770, 0.2828920, 1.2408600, 0.3867140, 
     184        4.0250700, 0.2376900, 0.5282490, 0.7421540, 1.4088000, 0.1185840, 0.2864430, 0.3968840, 0.3533580, 2.4226100 
     185    }; 
     186    static const double p[20] = { 
     187        0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.0484660, 0.0620286, 0.0862090, 
     188        0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.0439720, 0.0695179, 0.0610127, 0.0708956, 0.0143859, 0.0352742 
    199189    }; 
    200190    if(first2 != last2) { //+F model 
    … …  
    207197bool subst_model::create_lg(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    208198    static const double s[190] = { 
    209         2.489084, 0.395144, 0.062556, 1.038545, 0.003499, 5.243870, 0.253701, 1.105251, 0.017416, 0.018811, 
    210         2.066040, 0.569265, 0.844926, 0.348847, 0.089586, 0.358858, 0.640543, 0.927114, 0.423881, 0.682139, 
    211         0.311484, 0.149830, 0.320627, 0.010690, 0.044265, 1.112727, 0.008705, 0.108882, 0.536518, 0.013266, 
    212         0.282959, 1.807177, 0.023918, 0.296636, 0.697264, 0.159069, 0.395337, 0.594007, 0.015076, 0.069673, 
    213         2.592692, 0.044261, 0.366317, 4.145067, 0.137500, 1.124035, 0.893680, 0.025548, 0.173735, 1.798853, 
    214         0.139538, 0.442472, 4.273607, 0.656604, 6.312358, 0.276818, 0.528768, 5.076149, 0.541712, 0.089525, 
    215         1.437645, 4.509238, 0.191503, 2.145078, 0.068427, 0.371004, 1.177651, 0.075382, 0.394456, 0.419409, 
    216         0.094464, 0.196961, 0.508851, 0.078281, 0.390322, 0.249060, 0.099849, 0.161787, 0.969894, 0.084808, 
    217         0.523386, 4.128591, 0.035855, 0.267959, 4.813505, 0.072854, 3.234294, 0.582457, 1.672569, 1.695752, 
    218         0.624294, 0.425093, 0.534551, 0.123954, 0.363970, 0.052722, 0.390192, 2.426601, 0.126991, 6.326067, 
    219         0.301848, 0.484133, 0.751878, 0.332533, 2.807908, 4.727182, 2.784478, 1.240275, 0.611973, 0.361819, 
    220         1.739990, 0.990012, 0.064105, 0.748683, 0.182287, 0.346960, 4.008358, 1.338132, 1.223828, 0.858151, 
    221         2.139501, 1.143480, 0.425860, 0.604545, 0.165001, 0.129836, 0.584262, 1.033739, 1.136863, 0.302936, 
    222         2.020366, 2.000679, 0.571468, 1.080136, 0.578987, 6.472279, 2.547870, 1.959291, 0.037967, 0.245034, 
    223         0.654683, 0.076701, 0.119013,10.649107, 0.185202, 1.702745, 1.898718, 0.083688, 0.296501, 0.210332, 
    224         0.170887, 0.098369, 2.188158, 0.180717, 0.670128, 0.029890, 0.077852, 2.457121, 0.268491, 0.597054, 
    225         0.111660, 0.049906, 0.619632, 0.696175, 0.045376, 0.095131, 0.236199, 0.593607, 0.248862, 0.140825, 
    226         0.189510, 0.218959, 1.165532, 0.135107, 0.120037, 7.803902, 0.054679, 5.306834, 0.232523, 0.131932, 
    227         0.299648, 0.481306, 0.612025, 0.089613, 0.257336, 0.314440, 0.400547, 0.245841, 0.249313, 3.151815 
    228     }; 
    229     static const double p[20] = { 
    230         0.079066, 0.012937, 0.053052, 0.071586, 0.042302, 0.057337, 0.022355, 0.062157, 0.064600, 0.099081, 
    231         0.022951, 0.041977, 0.044040, 0.040767, 0.055941, 0.061197, 0.053287, 0.069147, 0.012066, 0.034155 
     199        2.4890840, 0.3951440, 1.0385450, 0.2537010, 2.0660400, 0.3588580, 0.1498300, 0.5365180, 0.3953370, 1.1240350, 
     200        0.2768180, 1.1776510, 0.9698940, 0.4250930, 4.7271820, 2.1395010, 2.5478700, 0.1807170, 0.2189590, 0.0625560, 
     201        0.0034990, 1.1052510, 0.5692650, 0.6405430, 0.3206270, 0.0132660, 0.5940070, 0.8936800, 0.5287680, 0.0753820, 
     202        0.0848080, 0.5345510, 2.7844780, 1.1434800, 1.9592910, 0.6701280, 1.1655320, 5.2438700, 0.0174160, 0.8449260, 
     203        0.9271140, 0.0106900, 0.2829590, 0.0150760, 0.0255480, 5.0761490, 0.3944560, 0.5233860, 0.1239540, 1.2402750, 
     204        0.4258600, 0.0379670, 0.0298900, 0.1351070, 0.0188110, 0.3488470, 0.4238810, 0.0442650, 1.8071770, 0.0696730, 
     205        0.1737350, 0.5417120, 0.4194090, 4.1285910, 0.3639700, 0.6119730, 0.6045450, 0.2450340, 0.0778520, 0.1200370, 
     206        0.0895860, 0.6821390, 1.1127270, 0.0239180, 2.5926920, 1.7988530, 0.0895250, 0.0944640, 0.0358550, 0.0527220, 
     207        0.3618190, 0.1650010, 0.6546830, 2.4571210, 7.8039020, 0.3114840, 0.0087050, 0.2966360, 0.0442610, 0.1395380, 
     208        1.4376450, 0.1969610, 0.2679590, 0.3901920, 1.7399900, 0.1298360, 0.0767010, 0.2684910, 0.0546790, 0.1088820, 
     209        0.6972640, 0.3663170, 0.4424720, 4.5092380, 0.5088510, 4.8135050, 2.4266010, 0.9900120, 0.5842620, 0.1190130, 
     210        0.5970540, 5.3068340, 0.1590690, 4.1450670, 4.2736070, 0.1915030, 0.0782810, 0.0728540, 0.1269910, 0.0641050, 
     211        1.0337390,10.6491070, 0.1116600, 0.2325230, 0.1375000, 0.6566040, 2.1450780, 0.3903220, 3.2342940, 6.3260670, 
     212        0.7486830, 1.1368630, 0.1852020, 0.0499060, 0.1319320, 6.3123580, 0.0684270, 0.2490600, 0.5824570, 0.3018480, 
     213        0.1822870, 0.3029360, 1.7027450, 0.6196320, 0.2996480, 0.3710040, 0.0998490, 1.6725690, 0.4841330, 0.3469600, 
     214        2.0203660, 1.8987180, 0.6961750, 0.4813060, 0.1617870, 1.6957520, 0.7518780, 4.0083580, 2.0006790, 0.0836880, 
     215        0.0453760, 0.6120250, 0.6242940, 0.3325330, 1.3381320, 0.5714680, 0.2965010, 0.0951310, 0.0896130, 2.8079080, 
     216        1.2238280, 1.0801360, 0.2103320, 0.2361990, 0.2573360, 0.8581510, 0.5789870, 0.1708870, 0.5936070, 0.3144400, 
     217        6.4722790, 0.0983690, 0.2488620, 0.4005470, 2.1881580, 0.1408250, 0.2458410, 0.1895100, 0.2493130, 3.1518150 
     218    }; 
     219    static const double p[20] = { 
     220        0.0790660, 0.0129370, 0.0530520, 0.0715860, 0.0423020, 0.0573370, 0.0223550, 0.0621570, 0.0646000, 0.0990810, 
     221        0.0229510, 0.0419770, 0.0440400, 0.0407670, 0.0559410, 0.0611970, 0.0532870, 0.0691470, 0.0120660, 0.0341550 
    232222    }; 
    233223    if(first2 != last2) { //+F model 
    … …  
    240230bool subst_model::create_jtt(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    241231    static const double s[190] = { 
    242         0.574478, 0.827445, 0.105625, 1.066681, 0.053907, 7.766557, 0.138293, 0.678335, 0.032522, 0.043829, 
    243         1.740159, 0.546389, 1.272434, 1.115632, 0.050212, 0.219970, 0.724998, 1.032342, 0.243768, 0.453428, 
    244         0.201696, 0.361684, 0.150559, 0.115968, 0.111773, 0.777090, 0.053769, 0.181788, 0.369437, 0.049009, 
    245         0.282466, 1.731684, 0.024521, 0.269840, 0.525096, 0.202562, 0.310007, 0.164593, 0.061486, 0.097485, 
    246         2.500294, 0.069492, 0.540571, 2.335139, 0.146481, 0.469395, 0.409202, 0.190001, 0.175084, 0.436181, 
    247         0.130379, 0.329660, 4.831666, 0.624581, 3.856906, 0.557967, 0.313311, 5.549530, 0.578115, 0.073481, 
    248         0.773313, 4.025778, 0.491003, 2.529517, 0.137289, 0.330720, 1.959599, 0.123653, 0.127164, 0.191994, 
    249         0.148483, 0.208081, 1.141961, 0.098580, 0.216345, 1.060504, 0.164215, 0.121804, 0.556725, 0.091304, 
    250         0.521646, 3.417706, 0.045683, 0.231294, 5.684080, 0.078270, 2.966732, 0.709004, 0.456901, 0.768834, 
    251         1.608126, 0.531678, 1.019843, 0.154899, 0.318483, 0.065314, 1.359652, 3.210671, 0.239195, 6.529255, 
    252         0.372261, 0.431045, 0.451095, 0.710489, 3.021995, 3.887095, 2.155331, 0.589268, 0.312449, 0.943971, 
    253         1.874296, 0.743458, 0.405119, 0.474478, 0.592511, 0.285564, 5.057964, 2.788406, 0.548807, 1.001551, 
    254         4.582565, 0.469823, 0.425159, 0.331584, 0.138904, 0.316862, 0.477355, 2.553806, 0.965641, 0.272514, 
    255         2.114728, 2.351311, 1.176961, 0.523825, 0.650282, 4.777647, 2.924161, 0.621323, 0.315261, 0.465271, 
    256         0.593478, 0.470140, 0.121827, 9.533943, 0.124066, 1.761439, 3.038533, 0.164525, 0.211561, 0.179771, 
    257         0.171995, 0.408532, 1.143980, 0.084329, 1.104181, 0.057466, 0.114381, 0.537922, 0.544180, 0.128193, 
    258         0.134510, 0.089134, 0.530324, 0.201334, 0.027700, 0.069965, 0.172206, 1.257961, 0.310927, 0.080556, 
    259         0.239697, 0.139492, 2.114852, 0.453952, 0.063452, 5.484236, 0.052500, 5.848400, 0.303445, 0.087904, 
    260         0.241094, 0.189870, 0.700693, 0.113850, 0.254745, 0.235601, 0.628608, 0.201094, 0.165473, 0.747889 
     232        0.5744780, 0.8274450, 1.0666810, 0.1382930, 1.7401590, 0.2199700, 0.3616840, 0.3694370, 0.3100070, 0.4693950, 
     233        0.5579670, 1.9595990, 0.5567250, 0.5316780, 3.8870950, 4.5825650, 2.9241610, 0.0843290, 0.1394920, 0.1056250, 
     234        0.0539070, 0.6783350, 0.5463890, 0.7249980, 0.1505590, 0.0490090, 0.1645930, 0.4092020, 0.3133110, 0.1236530, 
     235        0.0913040, 1.0198430, 2.1553310, 0.4698230, 0.6213230, 1.1041810, 2.1148520, 7.7665570, 0.0325220, 1.2724340, 
     236        1.0323420, 0.1159680, 0.2824660, 0.0614860, 0.1900010, 5.5495300, 0.1271640, 0.5216460, 0.1548990, 0.5892680, 
     237        0.4251590, 0.3152610, 0.0574660, 0.4539520, 0.0438290, 1.1156320, 0.2437680, 0.1117730, 1.7316840, 0.0974850, 
     238        0.1750840, 0.5781150, 0.1919940, 3.4177060, 0.3184830, 0.3124490, 0.3315840, 0.4652710, 0.1143810, 0.0634520, 
     239        0.0502120, 0.4534280, 0.7770900, 0.0245210, 2.5002940, 0.4361810, 0.0734810, 0.1484830, 0.0456830, 0.0653140, 
     240        0.9439710, 0.1389040, 0.5934780, 0.5379220, 5.4842360, 0.2016960, 0.0537690, 0.2698400, 0.0694920, 0.1303790, 
     241        0.7733130, 0.2080810, 0.2312940, 1.3596520, 1.8742960, 0.3168620, 0.4701400, 0.5441800, 0.0525000, 0.1817880, 
     242        0.5250960, 0.5405710, 0.3296600, 4.0257780, 1.1419610, 5.6840800, 3.2106710, 0.7434580, 0.4773550, 0.1218270, 
     243        0.1281930, 5.8484000, 0.2025620, 2.3351390, 4.8316660, 0.4910030, 0.0985800, 0.0782700, 0.2391950, 0.4051190, 
     244        2.5538060, 9.5339430, 0.1345100, 0.3034450, 0.1464810, 0.6245810, 2.5295170, 0.2163450, 2.9667320, 6.5292550, 
     245        0.4744780, 0.9656410, 0.1240660, 0.0891340, 0.0879040, 3.8569060, 0.1372890, 1.0605040, 0.7090040, 0.3722610, 
     246        0.5925110, 0.2725140, 1.7614390, 0.5303240, 0.2410940, 0.3307200, 0.1642150, 0.4569010, 0.4310450, 0.2855640, 
     247        2.1147280, 3.0385330, 0.2013340, 0.1898700, 0.1218040, 0.7688340, 0.4510950, 5.0579640, 2.3513110, 0.1645250, 
     248        0.0277000, 0.7006930, 1.6081260, 0.7104890, 2.7884060, 1.1769610, 0.2115610, 0.0699650, 0.1138500, 3.0219950, 
     249        0.5488070, 0.5238250, 0.1797710, 0.1722060, 0.2547450, 1.0015510, 0.6502820, 0.1719950, 1.2579610, 0.2356010, 
     250        4.7776470, 0.4085320, 0.3109270, 0.6286080, 1.1439800, 0.0805560, 0.2010940, 0.2396970, 0.1654730, 0.7478890 
    261251    };  
    262252    static const double p[20] = { 
    263         0.076862, 0.020279, 0.051269, 0.061820, 0.040530, 0.074714, 0.022983, 0.052569, 0.059498, 0.091111, 
    264         0.023414, 0.042546, 0.050532, 0.041061, 0.051057, 0.068225, 0.058518, 0.066374, 0.014336, 0.032303 
     253        0.0768620, 0.0202790, 0.0512690, 0.0618200, 0.0405300, 0.0747140, 0.0229830, 0.0525690, 0.0594980, 0.0911110, 
     254        0.0234140, 0.0425460, 0.0505320, 0.0410610, 0.0510570, 0.0682250, 0.0585180, 0.0663740, 0.0143360, 0.0323030 
    265255    }; 
    266256    if(first2 != last2) { //+F model 
    … …  
    273263bool subst_model::create_dayhoff(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    274264    static const double s[190] = { 
    275         0.360016, 1.199805, 0.0,      1.961167, 0.0,     11.388659, 0.183641, 0.0,      0.0,      0.0, 
    276         2.386111, 0.107278, 1.240981, 0.811907, 0.153478, 0.228116, 0.282729, 0.868241, 0.439469, 0.475927, 
    277         0.106802, 0.653416, 0.438074, 0.239248, 0.609526, 1.951951, 0.0,      0.076981, 0.258635, 0.0, 
    278         0.716913, 0.830078, 0.0,      0.267683, 0.270475, 0.460857, 0.406431, 0.0,      0.0,      0.11288, 
    279         1.565160, 0.071514, 0.443504, 2.556685, 0.180629, 0.717840, 0.0,      0.0,      0.304803, 0.92186, 
    280         0.170372, 0.0,      3.332732, 2.411739, 5.230115, 0.984474, 0.0,      8.931515, 1.493409, 0.138503, 
    281         1.385352, 5.290024, 0.768024, 3.148371, 0.341113, 0.0,      2.48592,  0.18755,  0.13394,  0.507003, 
    282         0.110506, 0.347153, 0.933709, 0.119152, 0.335419, 0.316258, 0.170205, 0.419244, 0.887753, 0.0, 
    283         1.348551, 7.086022, 0.0,      0.281581, 6.011613, 0.180393, 1.519078, 0.730772, 1.127499, 1.028509, 
    284         1.526188, 0.267828, 0.232374, 0.0,      0.0,      0.136906, 0.087791, 2.383148, 0.632629, 4.610124, 
    285         0.154924, 0.896321, 0.327059, 1.028313, 2.439939, 4.05187,  1.598356, 0.956097, 0.793999, 0.459901, 
    286         2.322243, 0.353643, 0.247955, 0.954557, 0.171432, 0.619951, 4.885892, 2.427202, 0.561828, 1.53159, 
    287         3.680365, 0.162366, 0.66093,  0.340156, 0.136655, 0.306662, 0.226333, 1.900739, 1.350599, 0.33109, 
    288         1.031534, 2.271697, 0.782857, 0.525651, 0.265745, 5.436674, 2.059564, 0.484678, 0.178316, 0.36725, 
    289         0.123606, 0.538165, 0.438715, 8.810038, 0.10385,  1.745156, 2.565955, 0.158067, 0.485026, 0.346983, 
    290         0.240368, 0.303836, 1.561997, 0.0,      0.0,      0.0,      0.0,      0.762354, 0.0,      0.270564, 
    291         0.0,      0.0,      0.461776, 0.0,      0.224968, 0.0,      0.0,      2.001375, 0.740819, 0.0, 
    292         0.0,      0.244139, 0.953164, 0.0,      0.214717, 6.952629, 0.0,      1.2654,   0.374834, 0.132142, 
    293         0.286572, 0.0,      0.94694,  0.0,      0.0,      0.078012, 0.336289, 0.417839, 0.279379, 0.60807 
    294     }; 
    295     static const double p[20] = { 
    296         0.087127, 0.033474, 0.046872, 0.04953, 0.039772, 0.088612, 0.033619, 0.036886, 0.080481, 0.085357, 
    297         0.014753, 0.040432, 0.05068, 0.038255, 0.040904, 0.069577, 0.058542, 0.064718, 0.010494, 0.029916 
     265        0.3600160, 1.1998050, 1.9611670, 0.1836410, 2.3861110, 0.2281160, 0.6534160, 0.2586350, 0.4064310, 0.7178400, 
     266        0.9844740, 2.4859200, 0.8877530, 0.2678280, 4.0518700, 3.6803650, 2.0595640, 0.0000000, 0.2441390, 0.0000000, 
     267        0.0000000, 0.0000000, 0.1072780, 0.2827290, 0.4380740, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.1875500, 
     268        0.0000000, 0.2323740, 1.5983560, 0.1623660, 0.4846780, 0.0000000, 0.9531640,11.3886590, 0.0000000, 1.2409810, 
     269        0.8682410, 0.2392480, 0.7169130, 0.0000000, 0.0000000, 8.9315150, 0.1339400, 1.3485510, 0.0000000, 0.9560970, 
     270        0.6609300, 0.1783160, 0.0000000, 0.0000000, 0.0000000, 0.8119070, 0.4394690, 0.6095260, 0.8300780, 0.1128800, 
     271        0.3048030, 1.4934090, 0.5070030, 7.0860220, 0.0000000, 0.7939990, 0.3401560, 0.3672500, 0.0000000, 0.2147170, 
     272        0.1534780, 0.4759270, 1.9519510, 0.0000000, 1.5651600, 0.9218600, 0.1385030, 0.1105060, 0.0000000, 0.1369060, 
     273        0.4599010, 0.1366550, 0.1236060, 0.7623540, 6.9526290, 0.1068020, 0.0000000, 0.2676830, 0.0715140, 0.1703720, 
     274        1.3853520, 0.3471530, 0.2815810, 0.0877910, 2.3222430, 0.3066620, 0.5381650, 0.0000000, 0.0000000, 0.0769810, 
     275        0.2704750, 0.4435040, 0.0000000, 5.2900240, 0.9337090, 6.0116130, 2.3831480, 0.3536430, 0.2263330, 0.4387150, 
     276        0.2705640, 1.2654000, 0.4608570, 2.5566850, 3.3327320, 0.7680240, 0.1191520, 0.1803930, 0.6326290, 0.2479550, 
     277        1.9007390, 8.8100380, 0.0000000, 0.3748340, 0.1806290, 2.4117390, 3.1483710, 0.3354190, 1.5190780, 4.6101240, 
     278        0.9545570, 1.3505990, 0.1038500, 0.0000000, 0.1321420, 5.2301150, 0.3411130, 0.3162580, 0.7307720, 0.1549240, 
     279        0.1714320, 0.3310900, 1.7451560, 0.4617760, 0.2865720, 0.0000000, 0.1702050, 1.1274990, 0.8963210, 0.6199510, 
     280        1.0315340, 2.5659550, 0.0000000, 0.0000000, 0.4192440, 1.0285090, 0.3270590, 4.8858920, 2.2716970, 0.1580670, 
     281        0.2249680, 0.9469400, 1.5261880, 1.0283130, 2.4272020, 0.7828570, 0.4850260, 0.0000000, 0.0000000, 2.4399390, 
     282        0.5618280, 0.5256510, 0.3469830, 0.0000000, 0.0000000, 1.5315900, 0.2657450, 0.2403680, 2.0013750, 0.0780120, 
     283        5.4366740, 0.3038360, 0.7408190, 0.3362890, 1.5619970, 0.0000000, 0.4178390, 0.0000000, 0.2793790, 0.6080700 
     284    }; 
     285    static const double p[20] = { 
     286        0.0871270, 0.0334740, 0.0468720, 0.0495300, 0.0397720, 0.0886120, 0.0336190, 0.0368860, 0.0804810, 0.0853570, 
     287        0.0147530, 0.0404320, 0.0506800, 0.0382550, 0.0409040, 0.0695770, 0.0585420, 0.0647180, 0.0104940, 0.0299160 
    298288    }; 
    299289    if(first2 != last2) { //+F model 
    … …  
    306296bool subst_model::create_molphy(const char *, It1 first1, It1 last1, It2 first2, It2 last2) { 
    307297    static const double s[190] = { 
    308         0.365255, 1.196794, 0.007072, 1.943156, 0.004083,11.236928, 0.182627, 0.024074, 0.003597, 0.005491, 
    309         2.376209, 0.108197, 1.230667, 0.799778, 0.151745, 0.225596, 0.283222, 0.855075, 0.429931, 0.467311, 
    310         0.105015, 0.651534, 0.442435, 0.237558, 0.601184, 1.932390, 0.006405, 0.075779, 0.260244, 0.002234, 
    311         0.718366, 0.826204, 0.001843, 0.267785, 0.268704, 0.461627, 0.408223, 0.010824, 0.007180, 0.112160, 
    312         1.560815, 0.071409, 0.439814, 2.556320, 0.182251, 0.706162, 0.039211, 0.032318, 0.296582, 0.900346, 
    313         0.166619, 0.034749, 3.263592, 2.383284, 5.159102, 0.995319, 0.020464, 8.992246, 1.493525, 0.139025, 
    314         1.392474, 5.280613, 0.772963, 3.197574, 0.345815, 0.052957, 2.470839, 0.188814, 0.132571, 0.498468, 
    315         0.109043, 0.343043, 0.916303, 0.117884, 0.334907, 0.315206, 0.166172, 0.420586, 0.893910, 0.006067, 
    316         1.352218, 7.057870, 0.005001, 0.281880, 5.976661, 0.180812, 1.536592, 0.737865, 1.114993, 1.045293, 
    317         1.524901, 0.267257, 0.234872, 0.016493, 0.015501, 0.135634, 0.087085, 2.347959, 0.628428, 4.621249, 
    318         0.155010, 0.878398, 0.329397, 1.018202, 2.447538, 4.028242, 1.609487, 0.946552, 0.780814, 0.453952, 
    319         2.295303, 0.347137, 0.245388, 0.953314, 0.170901, 0.605287, 4.902751, 2.394418, 0.561469, 1.516886, 
    320         3.715525, 0.166031, 0.664453, 0.339684, 0.136975, 0.307796, 0.225599, 1.910180, 1.369705, 0.335177, 
    321         1.022709, 2.314805, 0.784224, 0.533471, 0.267254, 5.447514, 2.051045, 0.488888, 0.176829, 0.361776, 
    322         0.122215, 0.532821, 0.431365, 8.733750, 0.103887, 1.742707, 2.509573, 0.158886, 0.479300, 0.347358, 
    323         0.238484, 0.300312, 1.567787, 0.010673, 0.096295, 0.008979, 0.020261, 0.794428, 0.035705, 0.280386, 
    324         0.027380, 0.009493, 0.486002, 0.044996, 0.238328, 0.009932, 0.026659, 2.092641, 0.771731, 0.011637, 
    325         0.035082, 0.243501, 0.962946, 0.022541, 0.211851, 6.885035, 0.004742, 1.246168, 0.372170, 0.132407, 
    326         0.286614, 0.031862, 0.953314, 0.012138, 0.027880, 0.077505, 0.332907, 0.420039, 0.277033, 0.635541 
     298        0.3652550, 1.1967940, 1.9431560, 0.1826270, 2.3762090, 0.2255960, 0.6515340, 0.2602440, 0.4082230, 0.7061620, 
     299        0.9953190, 2.4708390, 0.8939100, 0.2672570, 4.0282420, 3.7155250, 2.0510450, 0.0106730, 0.2435010, 0.0070720, 
     300        0.0040830, 0.0240740, 0.1081970, 0.2832220, 0.4424350, 0.0022340, 0.0108240, 0.0392110, 0.0204640, 0.1888140, 
     301        0.0060670, 0.2348720, 1.6094870, 0.1660310, 0.4888880, 0.0962950, 0.9629460,11.2369280, 0.0035970, 1.2306670, 
     302        0.8550750, 0.2375580, 0.7183660, 0.0071800, 0.0323180, 8.9922460, 0.1325710, 1.3522180, 0.0164930, 0.9465520, 
     303        0.6644530, 0.1768290, 0.0089790, 0.0225410, 0.0054910, 0.7997780, 0.4299310, 0.6011840, 0.8262040, 0.1121600, 
     304        0.2965820, 1.4935250, 0.4984680, 7.0578700, 0.0155010, 0.7808140, 0.3396840, 0.3617760, 0.0202610, 0.2118510, 
     305        0.1517450, 0.4673110, 1.9323900, 0.0018430, 1.5608150, 0.9003460, 0.1390250, 0.1090430, 0.0050010, 0.1356340, 
     306        0.4539520, 0.1369750, 0.1222150, 0.7944280, 6.8850350, 0.1050150, 0.0064050, 0.2677850, 0.0714090, 0.1666190, 
     307        1.3924740, 0.3430430, 0.2818800, 0.0870850, 2.2953030, 0.3077960, 0.5328210, 0.0357050, 0.0047420, 0.0757790, 
     308        0.2687040, 0.4398140, 0.0347490, 5.2806130, 0.9163030, 5.9766610, 2.3479590, 0.3471370, 0.2255990, 0.4313650, 
     309        0.2803860, 1.2461680, 0.4616270, 2.5563200, 3.2635920, 0.7729630, 0.1178840, 0.1808120, 0.6284280, 0.2453880, 
     310        1.9101800, 8.7337500, 0.0273800, 0.3721700, 0.1822510, 2.3832840, 3.1975740, 0.3349070, 1.5365920, 4.6212490, 
     311        0.9533140, 1.3697050, 0.1038870, 0.0094930, 0.1324070, 5.1591020, 0.3458150, 0.3152060, 0.7378650, 0.1550100, 
     312        0.1709010, 0.3351770, 1.7427070, 0.4860020, 0.2866140, 0.0529570, 0.1661720, 1.1149930, 0.8783980, 0.6052870, 
     313        1.0227090, 2.5095730, 0.0449960, 0.0318620, 0.4205860, 1.0452930, 0.3293970, 4.9027510, 2.3148050, 0.1588860, 
     314        0.2383280, 0.9533140, 1.5249010, 1.0182020, 2.3944180, 0.7842240, 0.4793000, 0.0099320, 0.0121380, 2.4475380, 
     315        0.5614690, 0.5334710, 0.3473580, 0.0266590, 0.0278800, 1.5168860, 0.2672540, 0.2384840, 2.0926410, 0.0775050, 
     316        5.4475140, 0.3003120, 0.7717310, 0.3329070, 1.5677870, 0.0116370, 0.4200390, 0.0350820, 0.2770330, 0.6355410 
    327317    }; 
    328318    static double p[20] = { 
    329         0.087, 0.033, 0.047, 0.050, 0.040, 0.089, 0.034, 0.037, 0.08, 0.085, 
    330         0.015, 0.040, 0.051, 0.038, 0.041, 0.070, 0.058, 0.065, 0.01, 0.030 
     319        0.0870000, 0.0330000, 0.0470000, 0.0500000, 0.0400000, 0.0890000, 0.0340000, 0.0370000, 0.0800000, 0.0850000, 
     320        0.0150000, 0.0400000, 0.0510000, 0.0380000, 0.0410000, 0.0700000, 0.0580000, 0.0650000, 0.0100000, 0.0300000 
    331321    }; 
    332322    if(first2 != last2) { //+F model 

  • current/utils/paml2dawg/paml2dawg.R

    r578 r582  
    11aa <- "A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V" 
    22aa <- strsplit(aa, "\\s+")[[1]] 
    3 m <- scan("in.txt") 
     3m <- scan("wag.txt") 
    44ss <- m[1:190] 
    55p <- m[191:210] 
    … …  
    1313s <- s[o,][,o] 
    1414 
    15 ss.new <- s[upper.tri(s)] 
     15ss.new <- s[lower.tri(s)] 
    1616 
    1717p.new <- p[o] 
    1818 
    19 cat(paste(ss.new, collapse=", ")) 
    20 cat("\n") 
    21 cat(paste(p.new, collapse=", ")) 
    22 cat("\n") 
     19m <- matrix(sprintf("%.7f", ss.new),nrow=10) 
     20m <- apply(m,2,paste, collapse=", ") 
     21m <- paste(m, collapse=",\n") 
     22cat(m); cat("\n\n") 
    2323 
    24 p2 <- p.new/sum(p.new) 
    25 s2 <- t(p2*s)*p2 
    26 s2 <- s2/sum(s2) 
    27 s2 <- s2/p2 
    28 r2 <- rowSums(s2) 
    29 r3 <- max(r2) 
    30 diag(s2) <- r3-r2 
    31 s2 <- s2/rowSums(s2) 
     24m <- matrix(sprintf("%.7f", p.new),nrow=10) 
     25m <- apply(m,2,paste, collapse=", ") 
     26m <- paste(m, collapse=",\n") 
     27cat(m); cat("\n\n") 
    3228 
    33 ## WAG 
    34 # 1.02704, 0.738998, 0.0302949, 1.58285, 0.021352, 6.17416, 0.210494, 0.39802, 0.0467304, 0.0811339, 1.41672, 0.306674, 0.865584, 0.567717, 0.049931, 0.316954, 0.248972, 0.930676, 0.570025, 0.679371, 0.24941, 0.193335, 0.170135, 0.039437, 0.127395, 1.05947, 0.0304501, 0.13819, 0.906265, 0.0740339, 0.479855, 2.58443, 0.088836, 0.373558, 0.890432, 0.323832, 0.397915, 0.384287, 0.0848047, 0.154263, 2.11517, 0.0613037, 0.499462, 3.17097, 0.257555, 0.893496, 0.390482, 0.103754, 0.315124, 1.19063, 0.1741, 0.404141, 4.25746, 0.934276, 4.85402, 0.509848, 0.265256, 5.42942, 0.947198, 0.0961621, 1.12556, 3.95629, 0.554236, 3.01201, 0.131528, 0.198221, 1.43855, 0.109404, 0.423984, 0.682355, 0.161444, 0.24357, 0.696198, 0.0999288, 0.556896, 0.415844, 0.171329, 0.195081, 0.908598, 0.0988179, 0.616783, 5.46947, 0.0999208, 0.330052, 4.29411, 0.113917, 3.8949, 0.869489, 1.54526, 1.54364, 0.933372, 0.551571, 0.528191, 0.147304, 0.439157, 0.102711, 0.584665, 2.13715, 0.186979, 5.35142, 0.497671, 0.683162, 0.635346, 0.679489, 3.0355, 3.37079, 1.40766, 1.07176, 0.704939, 0.545931, 1.34182, 0.740169, 0.31944, 0.96713, 0.344739, 0.493905, 3.97423, 1.61328, 1.02887, 1.22419, 2.12111, 0.512984, 0.374866, 0.822765, 0.171903, 0.225833, 0.473307, 1.45816, 1.38698, 0.326622, 1.51612, 2.03006, 0.795384, 0.857928, 0.554413, 4.37802, 2.00601, 1.00214, 0.152335, 0.588731, 0.649892, 0.187247, 0.118358, 7.8213, 0.305434, 1.80034, 2.05845, 0.196246, 0.314887, 0.301281, 0.251849, 0.232739, 1.38823, 0.113133, 0.71707, 0.129767, 0.156557, 1.52964, 0.336983, 0.262569, 0.212483, 0.137505, 0.665309, 0.515706, 0.0719167, 0.139405, 0.215737, 1.16392, 0.523742, 0.110864, 0.365369, 0.240735, 0.543833, 0.325711, 0.196303, 6.45428, 0.103604, 3.87344, 0.42017, 0.133264, 0.398618, 0.428437, 1.086, 0.216046, 0.22771, 0.381533, 0.786993, 0.291148, 0.31473, 2.48539 
    35 # 
    36 # 0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.048466, 0.0620286, 0.086209, 0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.043972, 0.0695179, 0.0610127, 0.0708956, 0.0143859, 0.0352742 
    37  
    38 ## WAG* 
    39 # 1.21324, 0.731152, 0.0379056, 1.55788, 0.0284956, 6.04299, 0.213179, 0.485001, 0.0458258, 0.0873936, 1.41993, 0.312544, 0.88357, 0.588609, 0.0552962, 0.317684, 0.341479, 0.958529, 0.599188, 0.631713, 0.279542, 0.214596, 0.198958, 0.0390513, 0.124553, 1.06458, 0.0310522, 0.162975, 0.881639, 0.0719929, 0.480308, 2.45392, 0.0832422, 0.381514, 0.854485, 0.320597, 0.400822, 0.451124, 0.0869637, 0.154936, 2.10414, 0.067443, 0.508952, 3.1554, 0.255092, 0.887458, 0.428648, 0.0992829, 0.294481, 1.14516, 0.184545, 0.40117, 3.94646, 0.877057, 4.81956, 0.514347, 0.233527, 5.30821, 1.00122, 0.0848492, 1.12717, 3.9337, 0.527321, 2.88102, 0.144354, 0.198404, 1.51861, 0.109081, 0.444152, 0.720567, 0.165205, 0.254626, 0.722123, 0.111722, 0.588203, 0.422851, 0.179858, 0.204905, 1.03344, 0.0999068, 0.657364, 5.6037, 0.109241, 0.346823, 4.87366, 0.125999, 4.19125, 0.873266, 1.64018, 1.62299, 0.913179, 0.589718, 0.568449, 0.159054, 0.443685, 0.122792, 0.629768, 2.31211, 0.187262, 5.74119, 0.51821, 0.660816, 0.67416, 0.711498, 3.02808, 3.52499, 1.35221, 1.09965, 0.822025, 0.563999, 1.33618, 0.876688, 0.321774, 1.05314, 0.351913, 0.554077, 3.90127, 1.54694, 0.87908, 1.35611, 2.24161, 0.522957, 0.395176, 0.889765, 0.188237, 0.236489, 0.54992, 1.48876, 1.45173, 0.351564, 1.56873, 2.06787, 0.802531, 0.829315, 0.594177, 4.02507, 1.92496, 1.10899, 0.155419, 0.588443, 0.653015, 0.190095, 0.119749, 7.48376, 0.300343, 1.82105, 2.03324, 0.193323, 0.325745, 0.32893, 0.282892, 0.23769, 1.4088, 0.135395, 0.728065, 0.142159, 0.176397, 1.58681, 0.366467, 0.261223, 0.259584, 0.159261, 0.706082, 0.565299, 0.0746093, 0.135024, 0.208163, 1.24086, 0.528249, 0.118584, 0.396884, 0.270321, 0.481954, 0.326191, 0.209621, 6.49269, 0.108982, 4.31772, 0.44009, 0.155623, 0.427718, 0.437069, 1.05269, 0.212945, 0.210494, 0.386714, 0.742154, 0.286443, 0.353358, 2.42261 
    40 # 
    41 # 0.0866279, 0.0193078, 0.0570451, 0.0580589, 0.0384319, 0.0832518, 0.0244313, 0.048466, 0.0620286, 0.086209, 0.0195027, 0.0390894, 0.0457631, 0.0367281, 0.043972, 0.0695179, 0.0610127, 0.0708956, 0.0143859, 0.0352742 
     29# p2 <- p.new/sum(p.new) 
     30# s2 <- t(p2*s)*p2 
     31# s2 <- s2/sum(s2) 
     32# s2 <- s2/p2 
     33# r2 <- rowSums(s2) 
     34# r3 <- max(r2) 
     35# diag(s2) <- r3-r2 
     36# s2 <- s2/rowSums(s2) 
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