binaries/src/GLProbs-1.0/Defaults.h

   1 /////////////////////////////////////////////////////////////////
   2 // Defaults.h
   3 //
   4 // Default constants for use in MSAPROBS.  The emission
   5 // probabilities were computed using the program used to build
   6 // the BLOSUM62 matrix from the BLOCKS 5.0 dataset.  Transition
   7 // parameters were obtained via unsupervised EM training on the
   8 // BALIBASE 2.0 benchmark alignment database.
   9 /////////////////////////////////////////////////////////////////
  10
  11 #ifndef DEFAULTS_H
  12 #define DEFAULTS_H
  13
  14 #include <string>
  15
  16 using namespace std;
  17
  18 /*
  19  float initDistrib1Default[] = { 0.3202854395, 0.3398572505, 0.3398572505 };
  20  float gapOpen1Default[] = { 0.1375414133, 0.1375414133 };
  21  float gapExtend1Default[] = { 0.7832147479, 0.7832147479 };
  22  */
  23 /*
  24 float initDistrib1Default[] = { 0.6080327034f, 0.1959836632f, 0.1959836632f };
  25 float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f };
  26 float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f };
  27 */
  28
  29 float initDistrib1Default[] = { 0.06188, 0.93812, 0.1959836632f };
  30 float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f };
  31 float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f };
  32
  33 /*
  34 float initDistrib1Default[] = { 0.2031769156f, 0.7968229055f, 0.05529401079f };
  35 float gapOpen1Default[] = { 0.006541831419f, 0.006541831419f };
  36 float gapExtend1Default[] = { 0.3042867482f, 0.3042867482f };
  37 */
  38 /*
  39 float initDistrib1Default[] = { 0.109684445f, 0.8903156519f, 0.01231110841f };
  40 float gapOpen1Default[] = { 0.01968936995f, 0.01968936995f };
  41 float gapExtend1Default[] = { 0.5699355602f, 0.5699355602f };
  42 */
  43 float initDistrib2Default[] = { 0.6814756989f, 8.615339902e-05f,
  44                 0.700645f, 0.1591759622f, 0.1591759622 };
  45 float gapOpen2Default[] = { 0.0119511066f, 0.01993141696f, 0.008008334786f,
  46                 0.008008334786 };
  47 float gapExtend2Default[] = { 0.3965826333f, 0.7943345308f, 0.8988758326f,
  48                 0.8988758326 };
  49
  50 string alphabetDefault = "ARNDCQEGHILKMFPSTWYV";
  51 float emitSingleDefault[20] = { 0.07831005f, 0.05246024f, 0.04433257f,
  52                 0.05130349f, 0.02189704f, 0.03585766f, 0.05615771f, 0.07783433f,
  53                 0.02601093f, 0.06511648f, 0.09716489f, 0.05877077f, 0.02438117f,
  54                 0.04463228f, 0.03940142f, 0.05849916f, 0.05115306f, 0.01203523f,
  55                 0.03124726f, 0.07343426f };
  56
  57 float emitPairsDefault[20][20] = { { 0.02373072f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  58                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  59                 0.0f, 0.0f }, { 0.00244502f, 0.01775118f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  60                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  61                 0.0f }, { 0.00210228f, 0.00207782f, 0.01281864f, 0.0f, 0.0f, 0.0f, 0.0f,
  62                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  63                 0.0f }, { 0.00223549f, 0.00161657f, 0.00353540f, 0.01911178f, 0.0f,
  64                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  65                 0.0f, 0.0f, 0.0f }, { 0.00145515f, 0.00044701f, 0.00042479f,
  66                 0.00036798f, 0.01013470f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  67                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00219102f,
  68                 0.00253532f, 0.00158223f, 0.00176784f, 0.00032102f, 0.00756604f, 0.0f,
  69                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  70                 0.0f }, { 0.00332218f, 0.00268865f, 0.00224738f, 0.00496800f,
  71                 0.00037956f, 0.00345128f, 0.01676565f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  72                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00597898f,
  73                 0.00194865f, 0.00288882f, 0.00235249f, 0.00071206f, 0.00142432f,
  74                 0.00214860f, 0.04062876f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  75                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00114353f, 0.00132105f, 0.00141205f,
  76                 0.00097077f, 0.00026421f, 0.00113901f, 0.00131767f, 0.00103704f,
  77                 0.00867996f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  78                 0.0f },
  79                 { 0.00318853f, 0.00138145f, 0.00104273f, 0.00105355f, 0.00094040f,
  80                                 0.00100883f, 0.00124207f, 0.00142520f, 0.00059716f, 0.01778263f,
  81                                 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, {
  82                                 0.00449576f, 0.00246811f, 0.00160275f, 0.00161966f, 0.00138494f,
  83                                 0.00180553f, 0.00222063f, 0.00212853f, 0.00111754f, 0.01071834f,
  84                                 0.03583921f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
  85                                 0.0f }, { 0.00331693f, 0.00595650f, 0.00257310f, 0.00252518f,
  86                                 0.00046951f, 0.00312308f, 0.00428420f, 0.00259311f, 0.00121376f,
  87                                 0.00157852f, 0.00259626f, 0.01612228f, 0.0f, 0.0f, 0.0f, 0.0f,
  88                                 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00148878f, 0.00076734f,
  89                                 0.00063401f, 0.00047808f, 0.00037421f, 0.00075546f, 0.00076105f,
  90                                 0.00066504f, 0.00042237f, 0.00224097f, 0.00461939f, 0.00096120f,
  91                                 0.00409522f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, {
  92                                 0.00165004f, 0.00090768f, 0.00084658f, 0.00069041f, 0.00052274f,
  93                                 0.00059248f, 0.00078814f, 0.00115204f, 0.00072545f, 0.00279948f,
  94                                 0.00533369f, 0.00087222f, 0.00116111f, 0.01661038f, 0.0f, 0.0f,
  95                                 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00230618f, 0.00106268f,
  96                                 0.00100282f, 0.00125381f, 0.00034766f, 0.00090111f, 0.00151550f,
  97                                 0.00155601f, 0.00049078f, 0.00103767f, 0.00157310f, 0.00154836f,
  98                                 0.00046718f, 0.00060701f, 0.01846071f, 0.0f, 0.0f, 0.0f, 0.0f,
  99                                 0.0f }, { 0.00631752f, 0.00224540f, 0.00301397f, 0.00285226f,
 100                                 0.00094867f, 0.00191155f, 0.00293898f, 0.00381962f, 0.00116422f,
 101                                 0.00173565f, 0.00250962f, 0.00312633f, 0.00087787f, 0.00119036f,
 102                                 0.00180037f, 0.01346609f, 0.0f, 0.0f, 0.0f, 0.0f }, {
 103                                 0.00389995f, 0.00186053f, 0.00220144f, 0.00180488f, 0.00073798f,
 104                                 0.00154526f, 0.00216760f, 0.00214841f, 0.00077747f, 0.00248968f,
 105                                 0.00302273f, 0.00250862f, 0.00093371f, 0.00107595f, 0.00147982f,
 106                                 0.00487295f, 0.01299436f, 0.0f, 0.0f, 0.0f }, { 0.00039119f,
 107                                 0.00029139f, 0.00021006f, 0.00016015f, 0.00010666f, 0.00020592f,
 108                                 0.00023815f, 0.00038786f, 0.00019097f, 0.00039549f, 0.00076736f,
 109                                 0.00028448f, 0.00016253f, 0.00085751f, 0.00015674f, 0.00026525f,
 110                                 0.00024961f, 0.00563625f, 0.0f, 0.0f }, { 0.00131840f,
 111                                 0.00099430f, 0.00074960f, 0.00066005f, 0.00036626f, 0.00070192f,
 112                                 0.00092548f, 0.00089301f, 0.00131038f, 0.00127857f, 0.00219713f,
 113                                 0.00100817f, 0.00054105f, 0.00368739f, 0.00047608f, 0.00102648f,
 114                                 0.00094759f, 0.00069226f, 0.00999315f, 0.0f }, { 0.00533241f,
 115                                 0.00169359f, 0.00136609f, 0.00127915f, 0.00119152f, 0.00132844f,
 116                                 0.00178697f, 0.00194579f, 0.00071553f, 0.01117956f, 0.00914460f,
 117                                 0.00210897f, 0.00197461f, 0.00256159f, 0.00135781f, 0.00241601f,
 118                                 0.00343452f, 0.00038538f, 0.00148001f, 0.02075171f } };
 119
 120 #endif