Add GLprobs and MSAprobs to binaries

[jabaws.git] / binaries / src / GLProbs-1.0 / Defaults.h

diff --git a/binaries/src/GLProbs-1.0/Defaults.h b/binaries/src/GLProbs-1.0/Defaults.h
new file mode 100644 (file)
index 0000000..953cdac
--- /dev/null
+++ b/binaries/src/GLProbs-1.0/Defaults.h
@@ -0,0 +1,120 @@
+/////////////////////////////////////////////////////////////////
+// Defaults.h
+//
+// Default constants for use in MSAPROBS.  The emission
+// probabilities were computed using the program used to build
+// the BLOSUM62 matrix from the BLOCKS 5.0 dataset.  Transition
+// parameters were obtained via unsupervised EM training on the
+// BALIBASE 2.0 benchmark alignment database.
+/////////////////////////////////////////////////////////////////
+
+#ifndef DEFAULTS_H
+#define DEFAULTS_H
+
+#include <string>
+
+using namespace std;
+
+/*
+ float initDistrib1Default[] = { 0.3202854395, 0.3398572505, 0.3398572505 };
+ float gapOpen1Default[] = { 0.1375414133, 0.1375414133 };
+ float gapExtend1Default[] = { 0.7832147479, 0.7832147479 };
+ */
+/*
+float initDistrib1Default[] = { 0.6080327034f, 0.1959836632f, 0.1959836632f };
+float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f };
+float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f };
+*/
+
+float initDistrib1Default[] = { 0.06188, 0.93812, 0.1959836632f };
+float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f };
+float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f };
+
+/*
+float initDistrib1Default[] = { 0.2031769156f, 0.7968229055f, 0.05529401079f };
+float gapOpen1Default[] = { 0.006541831419f, 0.006541831419f };
+float gapExtend1Default[] = { 0.3042867482f, 0.3042867482f };
+*/
+/*
+float initDistrib1Default[] = { 0.109684445f, 0.8903156519f, 0.01231110841f };
+float gapOpen1Default[] = { 0.01968936995f, 0.01968936995f };
+float gapExtend1Default[] = { 0.5699355602f, 0.5699355602f };
+*/
+float initDistrib2Default[] = { 0.6814756989f, 8.615339902e-05f,
+               0.700645f, 0.1591759622f, 0.1591759622 };
+float gapOpen2Default[] = { 0.0119511066f, 0.01993141696f, 0.008008334786f,
+               0.008008334786 };
+float gapExtend2Default[] = { 0.3965826333f, 0.7943345308f, 0.8988758326f,
+               0.8988758326 };
+
+string alphabetDefault = "ARNDCQEGHILKMFPSTWYV";
+float emitSingleDefault[20] = { 0.07831005f, 0.05246024f, 0.04433257f,
+               0.05130349f, 0.02189704f, 0.03585766f, 0.05615771f, 0.07783433f,
+               0.02601093f, 0.06511648f, 0.09716489f, 0.05877077f, 0.02438117f,
+               0.04463228f, 0.03940142f, 0.05849916f, 0.05115306f, 0.01203523f,
+               0.03124726f, 0.07343426f };
+
+float emitPairsDefault[20][20] = { { 0.02373072f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f }, { 0.00244502f, 0.01775118f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f }, { 0.00210228f, 0.00207782f, 0.01281864f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f }, { 0.00223549f, 0.00161657f, 0.00353540f, 0.01911178f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f }, { 0.00145515f, 0.00044701f, 0.00042479f,
+               0.00036798f, 0.01013470f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00219102f,
+               0.00253532f, 0.00158223f, 0.00176784f, 0.00032102f, 0.00756604f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f }, { 0.00332218f, 0.00268865f, 0.00224738f, 0.00496800f,
+               0.00037956f, 0.00345128f, 0.01676565f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00597898f,
+               0.00194865f, 0.00288882f, 0.00235249f, 0.00071206f, 0.00142432f,
+               0.00214860f, 0.04062876f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, { 0.00114353f, 0.00132105f, 0.00141205f,
+               0.00097077f, 0.00026421f, 0.00113901f, 0.00131767f, 0.00103704f,
+               0.00867996f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+               0.0f },
+               { 0.00318853f, 0.00138145f, 0.00104273f, 0.00105355f, 0.00094040f,
+                               0.00100883f, 0.00124207f, 0.00142520f, 0.00059716f, 0.01778263f,
+                               0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, {
+                               0.00449576f, 0.00246811f, 0.00160275f, 0.00161966f, 0.00138494f,
+                               0.00180553f, 0.00222063f, 0.00212853f, 0.00111754f, 0.01071834f,
+                               0.03583921f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
+                               0.0f }, { 0.00331693f, 0.00595650f, 0.00257310f, 0.00252518f,
+                               0.00046951f, 0.00312308f, 0.00428420f, 0.00259311f, 0.00121376f,
+                               0.00157852f, 0.00259626f, 0.01612228f, 0.0f, 0.0f, 0.0f, 0.0f,
+                               0.0f, 0.0f, 0.0f, 0.0f }, { 0.00148878f, 0.00076734f,
+                               0.00063401f, 0.00047808f, 0.00037421f, 0.00075546f, 0.00076105f,
+                               0.00066504f, 0.00042237f, 0.00224097f, 0.00461939f, 0.00096120f,
+                               0.00409522f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }, {
+                               0.00165004f, 0.00090768f, 0.00084658f, 0.00069041f, 0.00052274f,
+                               0.00059248f, 0.00078814f, 0.00115204f, 0.00072545f, 0.00279948f,
+                               0.00533369f, 0.00087222f, 0.00116111f, 0.01661038f, 0.0f, 0.0f,
+                               0.0f, 0.0f, 0.0f, 0.0f }, { 0.00230618f, 0.00106268f,
+                               0.00100282f, 0.00125381f, 0.00034766f, 0.00090111f, 0.00151550f,
+                               0.00155601f, 0.00049078f, 0.00103767f, 0.00157310f, 0.00154836f,
+                               0.00046718f, 0.00060701f, 0.01846071f, 0.0f, 0.0f, 0.0f, 0.0f,
+                               0.0f }, { 0.00631752f, 0.00224540f, 0.00301397f, 0.00285226f,
+                               0.00094867f, 0.00191155f, 0.00293898f, 0.00381962f, 0.00116422f,
+                               0.00173565f, 0.00250962f, 0.00312633f, 0.00087787f, 0.00119036f,
+                               0.00180037f, 0.01346609f, 0.0f, 0.0f, 0.0f, 0.0f }, {
+                               0.00389995f, 0.00186053f, 0.00220144f, 0.00180488f, 0.00073798f,
+                               0.00154526f, 0.00216760f, 0.00214841f, 0.00077747f, 0.00248968f,
+                               0.00302273f, 0.00250862f, 0.00093371f, 0.00107595f, 0.00147982f,
+                               0.00487295f, 0.01299436f, 0.0f, 0.0f, 0.0f }, { 0.00039119f,
+                               0.00029139f, 0.00021006f, 0.00016015f, 0.00010666f, 0.00020592f,
+                               0.00023815f, 0.00038786f, 0.00019097f, 0.00039549f, 0.00076736f,
+                               0.00028448f, 0.00016253f, 0.00085751f, 0.00015674f, 0.00026525f,
+                               0.00024961f, 0.00563625f, 0.0f, 0.0f }, { 0.00131840f,
+                               0.00099430f, 0.00074960f, 0.00066005f, 0.00036626f, 0.00070192f,
+                               0.00092548f, 0.00089301f, 0.00131038f, 0.00127857f, 0.00219713f,
+                               0.00100817f, 0.00054105f, 0.00368739f, 0.00047608f, 0.00102648f,
+                               0.00094759f, 0.00069226f, 0.00999315f, 0.0f }, { 0.00533241f,
+                               0.00169359f, 0.00136609f, 0.00127915f, 0.00119152f, 0.00132844f,
+                               0.00178697f, 0.00194579f, 0.00071553f, 0.01117956f, 0.00914460f,
+                               0.00210897f, 0.00197461f, 0.00256159f, 0.00135781f, 0.00241601f,
+                               0.00343452f, 0.00038538f, 0.00148001f, 0.02075171f } };
+
+#endif