+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*All rights reserved. */
+/*This file is part of T-COFFEE. */
+/* */
+/* T-COFFEE is free software; you can redistribute it and/or modify */
+/* it under the terms of the GNU General Public License as published by */
+/* the Free Software Foundation; either version 2 of the License, or */
+/* (at your option) any later version. */
+/* */
+/* T-COFFEE is distributed in the hope that it will be useful, */
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of */
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */
+/* GNU General Public License for more details. */
+/* */
+/* You should have received a copy of the GNU General Public License */
+/* along with Foobar; if not, write to the Free Software */
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
+/*............................................... */
+/* If you need some more information */
+/* cedric.notredame@europe.com */
+/*............................................... */
+/******************************COPYRIGHT NOTICE*******************************/
+#ifndef MATRICES_H
+#define MATRICES_H
+
char *amino_acid_order = "ABCDEFGHIKLMNPQRSTVWXYZ";
0,
0, 0,
0, 0, 0,
- 0, 0, 0, 6,
- 0, 0, 0, 1, 6,
- 0, 0, 0, 2, 2, 5,
+ 0, 0, 0, 5,
+ 0, 0, 0, 4, 6,
+ 0, 0, 0, 5, 7, 5,
0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 2, 2, 1, 0, 6,
- 0, 0, 0, 1, -1, -1, 0, -2, 6,
- 0, 0, 0, -3, 1, -2, 0, -3, 1, 6,
- 0, 0, 0, -2, -1, 2, 0, -2, 2, 1, 6,
- 0, 0, 0, -1, -1, -1, 0, 1, 2, 2, 2, 6,
- 0, 0, 0, 1, -1, 0, 0, -2, 1, -2, -1, -1, 6,
- 0, 0, 0, -2, 2, -1, 0, -2, -2, 1, -2, -1, 2, 6,
- 0, 0, 0, -3, -3, 2, 0, -4, -3, -3, 0, -3, 1, 0, 4,
- 0, 0, 0, -2, -1, -2, 0, 2, -2, -2, -2, 2, 1, 2, 0, 6,
- 0, 0, 0, 1, -1, -1, 0, -1, 1, -2, -2, -1, 1, -2, -3, -1, 6,
+ 0, 0, 0, 5, 5, 5, 0, 5,
+ 0, 0, 0, -7, -3, -3, 0, -6, 6,
+ 0, 0, 0, -7, -6, -2, 0, -7, 3, 5,
+ 0, 0, 0, -4, -2, -2, 0, -4, 5, 5, 7,
+ 0, 0, 0, -3, -2, -1, 0, -5, 6, 6, 7, 6,
+ 0, 0, 0, -7, -3, 0, 0, -5, -7, -5, -2, -3, 5,
+ 0, 0, 0, -5, -5, -2, 0, -5, -4, -7, -3, -3, 7, 4,
+ 0, 0, 0, -5, -6, -4, 0, -9, -7, -6, -7, -6, 4, 2, 3,
+ 0, 0, 0, -5, -3, -2, 0, -5, -5, -6, -4, -4, 4, 5, 3, 4,
+ 0, 0, 0, -6, -3, -2, 0, -3, -6, -4, -4, -2, -7, -5, -8, -2, 6,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, -2, 2, -2, 0, -2, -1, 2, -2, 0, -2, 1, -3, -1, 1, 0, 6,
- 0, 0, 0, -2, -2, 2, 0, -2, -2, -2, 2, -1, -1, -2, 0, -1, 2, 0, 1, 5,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, -1, -2, -2, 0, 2, -2, -2, -2, 2, -2, -3, -4, 1, 2, 0, 2, 1, 0, 6,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, -5, -5, -2, 0, -4, -3, -5, -2, -1, -4, -6, -6, -2, 4, 0, 6,
+ 0, 0, 0, -4, -3, -3, 0, -2, -4, -3, -3, 0, -2, -4, -7, 0, 6, 0, 6, 6,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1,
+ 0, 0, 0, -4, -5, -2, 0, -4, -4, -5, -4, -4, -6, -7, -9, -6, 5, 0, 4, 5, 0, 5,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
};
int blosumR[]={
0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, -1, -2, -2, 0, 2, -2, -2, -2, 2, -2, -3, -4, 1, 2, 0, 2, 1, 0, 6,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,};
-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
+
+
+
+//matrix in alphabetic format
+
+double strikeP_mat[][26] ={
+ {-0.744055875823878, 0, -0.302714763884203, -8.18065408358324, -9.43250108594488, 4.0024319077819, 0, -3.44290454108591, 3.85786863942911, 0, -7.48891663653909, 2.85310469061013, 1.44275947475201, -6.88728722453311, 0, -4.60033702306021, -5.07604456146783, -4.07450237434039, -6.01162469424305, -3.79684159474661, 0, 3.68503771993837, 3.77629309202085, 0, 2.30547732746785, 0},
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {0.563429964483508, 0, 23.216631475072, -2.46542154563067, -6.72154030935699, 8.8817354132774, 0, 3.20305900859143, 6.45432849214352, 0, -2.50078977078133, 6.00125028548607, 6.25869831131468, 0.378437968143603, 0, 2.11768974544946, -1.70881749866372, 1.18009003408374, 0.334810553015332, 0.225137748719709, 0, 7.82014196956194, 9.577338158519, 0, 7.06811548677035, 0 },
+ {-8.35163406201817, 0, -2.18731267859346, -0.218002408932713, -8.83887440995716, -0.686016175955611, 0, 2.17660681512101, -3.79113118180437, 0, 1.24650083684101, -4.94895524022016, -4.55988908963644, -1.43633017659302, 0, -5.01220415079131, -4.41848441506915, 5.19967117328199, -4.08551959944597, -3.41215924689882, 0, -2.41681947053046, 3.31679259913042, 0, 2.13215246195462, 0 },
+ {-9.950903462798, 0, -6.97835976568042, -9.40741613874478, -6.66818887034316, -2.69010742926591, 0, -0.687100811252813, -4.88018555189452, 0, 0.292533478461261, -5.24591068348682, -5.17566558598087, -5.80533065701881, 0, -5.93230821405525, -5.77566569026334, 3.26563880412349, -6.87847328766169, -5.5200043098517, 0, -5.43781499307001, 1.84918821122744, 0, 0.279569067093439, 0 },
+ {3.67725126351843, 0, 8.7710002220826, -0.722240808041252, -2.70505671128115, 13.9923883824675, 0, 4.37388335008561, 11.2292913417867, 0, -0.52331140390248, 10.96968518683, 9.93735965253691, 0.0458151874604124, 0, 2.38227895696109, 1.32385179829162, 3.82598885660533, 0.208057460461618, 2.67049207079983, 0, 10.5250957740446, 12.0412570276562, 0, 10.0146608775621, 0, },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {-3.10216149835793, 0, 3.82529448538273, 2.16612463386772, 0.052029486982624, 4.21102831437299, 0, 9.49792354772278, 1.50771884705347, 0, -3.02740642811791, 1.63224047570807, 3.74464198050375, 0.267892937193302, 0, -0.0299429064730965, 0.269787234259044, 2.44541786827413, -0.293416316686081, 0.786792285904228, 0, 1.02531084556973, 7.63235746651112, 0, 6.29901500153958, 0 },
+ {3.74349355722008, 0, 6.25610916712523, -3.60785220179623, -4.79560653063696, 11.5185741110095, 0, 1.55950262214948, 12.9089012970287, 0, -2.95219382759794, 10.9023524846628, 8.32655707815868, -2.59234288581899, 0, -0.218850768824713, -0.803227535434448, 0.322674298350308, -1.86999228038304, 1.85308807950936, 0, 10.7707377068528, 9.65650468156088, 0, 8.53229371552018, 0 },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {-7.68623245516504, 0, -4.23985336946803, 1.1443213113889, 0.723436662981594, -0.199066191408116, 0, -3.29238310043893, -2.99256826306329, 0, -0.105272837432747, -3.25622060503402, -3.83965951581705, -2.47727008479023, 0, -4.11844544680173, -3.97775804984858, -2.45558345362291, -5.05503682868254, -2.7681567364425, 0, -1.6618422965417, 1.79130594754075, 0, 1.85937593327484, 0 },
+ {2.70234583828839, 0, 5.82777438871162, -5.00631677417541, -5.13794578445595, 11.3210694876418, 0, 1.23953643741971, 11.018661110017, 0, -3.37810839296511, 11.9418737408998, 7.59430180722096, -3.27745738962111, 0, -0.178941058608256, -1.48112963358673, 0.904958024861746, -2.74428197881832, 1.14236626008265, 0, 10.2043435797671, 10.1601656618937, 0, 7.67592505167412, 0 },
+ {1.55938642840778, 0, 6.29019440034364, -4.04763002291339, -3.78753190045664, 10.5636744337802, 0, 2.62760208470374, 8.77182329713585, 0, -3.15186915228681, 7.84254150450822, 11.711539124619, -1.66160274002826, 0, 0.616594251751747, -0.484055295747724, 0.914603692262962, -1.95969917087105, 0.758184360747387, 0, 6.89809969641056, 10.1468295187994, 0, 7.67787773603446, 0 },
+ {-6.97360408439622, 0, 0.536794404756985, -1.64213332435025, -5.84176056980382, 0.492930553149589, 0, 0.421102324936293, -2.52766425574413, 0, -2.28331611375334, -3.33373215827839, -1.49458424384894, 3.54042853933437, 0, -2.24045763023172, -2.32632019925434, 0.47610050074255, -3.61872525748528, -2.05790633052002, 0, -2.53122932744671, 3.5154572067431, 0, 2.17461479980675, 0 },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {-4.02589696574941, 0, 1.8004002990208, -4.4451438758483, -5.59156841071773, 2.71835194380965, 0, 0.530800872441051, 0.17981113130917, 0, -3.94978191425315, 0.349175798604766, 1.14329322630196, -1.74901312668558, 0, 1.88011666965195, -2.31939347590581, 0.665304173903774, -4.68774787500018, -1.24691703239316, 0, 0.647276956486846, 6.67939336538368, 0, 5.81506379335207, 0 },
+ {-5.43452385328595, 0, -2.01187099361701, -5.18273328165406, -5.6978190434846, 1.19759088657582, 0, -0.0759779585919578, -0.836130032802324, 0, -3.97135804963012, -1.22326002187265, -0.787220842424092, -2.30419629642493, 0, -2.73547549822475, 2.38902737633693, 0.569428466580743, -3.81699410796334, -1.51550803986253, 0, -1.39939693070244, 4.70924146078409, 0, 2.5523347016674, 0 },
+ {-4.29460695368328, 0, 0.486680636965371, 4.97864298162259, 3.73792347220258, 4.120405016859, 0, 2.07793813286723, 0.484656930029987, 0, -2.14886974285032, 0.918037330907308, -0.139001464315301, -0.0719262273602284, 0, 0.255314473807657, 0.721341602266994, 4.56708300380649, -1.89726669816384, -0.302663528339019, 0, 0.811421867579365, 6.98019169754308, 0, 4.13430458624569, 0 },
+ {-5.97434915125163, 0, 0.37000120516729, -3.84227496633226, -6.2868731804832, 0.916830441207946, 0, -0.245650958044545, -1.61275897569608, 0, -4.52756656046882, -2.34350770176258, -1.14582876794365, -3.06224276480934, 0, -4.54673183595703, -3.29087890173511, -1.18020888354511, -1.26690806529519, -2.32693632188832, 0, -1.3342050295879, 3.38185822875439, 0, 1.31315196123521, 0 },
+ {-3.11731389780309, 0, 0.777086537192059, -3.61720275969269, -5.634874749723, 3.44217523582176, 0, 0.773750223409985, 2.51516697324763, 0, -2.31731371405645, 1.77235516403156, 1.22299484344795, -1.48552401197085, 0, -0.822581048247189, -0.939216911496162, 0.287544821379587, -2.26940290177121, 1.98280130317421, 0, 2.37061530829648, 4.64228021321104, 0, 3.39402873869243, 0 },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {3.47525983750936, 0, 7.67451376582157, -2.43297021428344, -5.56834852431571, 10.9380813232173, 0, 0.977222270090444, 10.6672101743659, 0, -1.6592912761197, 10.0381020190232, 6.52573994231515, -3.03191596981711, 0, 0.325204390252507, -1.70803866377506, 0.568752061815176, -1.82358388525935, 1.8427638669967, 0, 12.2107146432932, 8.7060924695392, 0, 8.01050059154028, 0 },
+ {2.65030580535629, 0, 9.89656271080995, 2.75539108474302, 1.10985791384256, 11.850117069215, 0, 6.63670372488712, 9.77104878522572, 0, 1.49073687321265, 9.87838725652592, 9.76942623897098, 3.07444085903699, 0, 5.46732812430464, 4.42312207819857, 6.86845869156183, 1.82444154072241, 3.58113522413606, 0, 8.75438014272746, 16.5887015359961, 0, 10.6389300440303, 0 },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
+ {2.1101256430652, 0, 6.39719325710416, 2.01253588448169, 0.126949825672711, 10.1489062237833, 0, 5.55441616678257, 8.07070277474075, 0, 1.46586436884238, 7.13299422800749, 7.20287205512148, 1.60724349375672, 0, 4.9235805791322, 2.32699599640634, 4.17964145146598, 0.513201790334874, 1.75557819027692, 0, 7.53688784559063, 10.8105318880362, 0, 10.3916984190201, 0 },
+ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
+ };
+
+#endif // MATRICES_H
git://source.jalview.org / jabaws.git / blobdiff