// These lookup tables are not necessary: they are intended to make
// startup faster for typical parameters.

struct EvalueParametersByName {
  const char *matrixName;
  int gapOpen;
  int gapEpen;
  Sls::AlignmentEvaluerParameters parameters;
};

struct EvalueParametersByScore {
  int matchScore;
  int mismatchCost;
  int gapOpen;
  int gapEpen;
  Sls::AlignmentEvaluerParameters parameters;
};

struct FrameshiftEvalueParameters {
  const char *geneticCodeName;
  const char *matrixName;
  int gapOpen;
  int gapEpen;
  int frameshiftCost;
  Sls::AlignmentEvaluerParameters parameters;
};

const EvalueParametersByName proteinParameters[] = {
  {"BL62", 11, 1, {0.27553858462416075, 0.052108666891553253,
		   1.5606171794974455, -19.732860493752256,
		   1.5606171794974455, -19.732860493752256,
		   29.210151638988194, -598.91453155494662,
		   29.210151638988194, -598.91453155494662,
		   28.51287191489801, -582.17981817678219}},

  {"BL62", 11, 2, {0.30593548727296388, 0.10240374069870158,
		   0.99050553069382763, -6.5543626660042129,
		   0.99050553069382763, -6.5543626660042129,
		   9.286796977904153, -130.81685466300709,
		   9.286796977904153, -130.81685466300709,
		   9.2266144189146271, -129.25210812927941}},

  {"BL80", 11, 1, {0.32849624141749045, 0.1163738959652578,
		   0.75491225062543932, -6.0768179898445682,
		   0.75491225062543932, -6.0768179898445682,
		   5.5209318716230964, -92.3656298469962,
		   5.5209318716230964, -92.3656298469962,
		   5.2639936937083576, -86.199113577042453}},

  {"BL80", 11, 2, {0.34392164286655347, 0.16475434978940937,
		   0.58112958853087737, -2.0648702745396719,
		   0.58112958853087737, -2.0648702745396719,
		   2.187240038686872, -13.386778011237375,
		   2.187240038686872, -13.386778011237375,
		   2.1552267345409919, -12.554432103444491}},

  {"MIQS", 13, 2, {0.15500512137732353, 0.014722799265496274,
		   2.9058229144393617, -55.393307878090532,
		   2.9058229144393617, -55.393307878090532,
		   133.10966174607341, -3626.8981880862489,
		   133.10966174607341, -3626.8981880862489,
		   132.35440917315739, -3604.2406108987684}},
};

const EvalueParametersByName dnaParametersByName[] = {
  {"AT77", 15, 2, {0.3361723487085515, 0.18977234047431241,
		   0.93917271154892723, -2.8454252194267946,
		   0.93917271154892723, -2.8454252194267946,
		   5.6690708632232027, -53.877468239759928,
		   5.6690708632232027, -53.877468239759928,
		   5.6546212402462572, -53.386181058543784}},

  {"ATMAP", 24, 6, {0.2308433496003553, 0.37475332645251713,
		    0.22571617180589737, -0.015715938682799857,
		    0.22571617180589737, -0.015715938682799857,
		    0.14281472963993982, 2.6440420415859895,
		    0.14281472963993982, 2.6440420415859895,
		    0.1428251000187582, 2.6434198188568869}},

  {"HOXD70", 400, 30, {0.0094463275895916698, 0.095059004086289992,
		       0.039191223120447122, -12.884975655572644,
		       0.039191223120447122, -12.884975655572644,
		       0.42791648613048661, -287.04882906895347,
		       0.42791648613048661, -287.04882906895347,
		       0.41553850600489461, -276.40376616094437}},
};

const EvalueParametersByScore dnaParametersByScore[] = {
  {1, 1, 1, 1, {0.66146689902380096, 0.026071577575191209,
		6.0609090917729898, -16.24362960699618,
		6.0609090917729898, -16.24362960699618,
		89.568020976804803, -334.27201630620215,
		89.568020976804803, -334.27201630620215,
		87.785779979559436, -327.14305231722068}},

  {1, 1, 2, 1, {0.98396641892490544, 0.17109543459934792,
		3.0348127782214962, -6.2088665291853111,
		3.0348127782214962, -6.2088665291853111,
		21.689848628115335, -94.138990367166443,
		21.689848628115335, -94.138990367166443,
		21.480894086337095, -92.885263116497001}},

  {1, 1, 7, 1, {1.0960171987681839, 0.33538787507026158,
		2.0290734315292083, -0.46514786408422282,
		2.0290734315292083, -0.46514786408422282,
		5.0543294182155085, 15.130999712620039,
		5.0543294182155085, 15.130999712620039,
		5.0543962679167036, 15.129930117400917}},

  {6, 18, 21, 9, {0.22852552944644766, 0.43337784178578154,
		  0.17722035780026291, -0.1220983494599942,
		  0.17722035780026291, -0.1220983494599942,
		  0.044639007347921783, -0.44696673676441229,
		  0.044639007347921783, -0.44696673676441229,
		  0.044598546568475124, -0.44453908999761271}},
};

const FrameshiftEvalueParameters frameshiftEvalueParameters[] = {
  {"1", "BL62", 11, 1, 15, {0.31457181182385774, 0.077024909125411836,
			    3.5355057419386005, -39.014329998056937,
			    1.1739847579695837, -12.896364921780187,
			    160.29749789587885, -3200.2716722761552,
			    17.539096792506459, -349.06406999516196,
			    51.79266617536797, -1027.401229133852}},

  // this one is included only to make lest-test.sh faster:
  {"1", "BL62", 11, 2, 12, {0.32704828292493776, 0.10543687626821494,
			    2.7166240938670798, -19.361170444340445,
			    0.89899140520122844, -6.29652445533966,
			    74.744763449386667, -1147.0060455603425,
			    8.3059555754127565, -127.46868078491309,
			    24.78179014970371, -379.14020451790986}},

  {"1", "BL62", 11, 2, 15, {0.33388770870821022, 0.11532516007803961,
			    2.4678058049483518, -14.50532580281522,
			    0.82160372991753583, -4.8091552692419572,
			    55.103072639059761, -731.90592162187147,
			    6.1010321043683131, -80.763060603166991,
			    18.237750047538203, -240.59017890476582}},

  {"1", "BL80", 11, 1, 15, {0.35400649542314511, 0.13270256108942211,
			    1.8960749679829285, -14.061923223904673,
			    0.62940827123451903, -4.6245065070665863,
			    35.18772909081801, -583.19242886423649,
			    3.8260214679558033, -62.789729751450864,
			    11.072568656496113, -178.63729131744145}},

  {"1", "BL80", 11, 2, 15, {0.3652492341706855, 0.16850422398182774,
			    1.5316138005575799, -5.7577598061709985,
			    0.5101720323233776, -1.9097398376324572,
			    17.427364219333899, -170.0223112776693,
			    1.9259860816444827, -18.621287186644096,
			    5.7329546520583801, -54.693768145180513}},
};