Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / mafft / core / defs.c

diff --git a/website/archive/binaries/mac/src/mafft/core/defs.c b/website/archive/binaries/mac/src/mafft/core/defs.c
new file mode 100644 (file)
index 0000000..4136bc3
--- /dev/null
+++ b/website/archive/binaries/mac/src/mafft/core/defs.c
@@ -0,0 +1,108 @@
+#include <stdio.h>
+#include "dp.h"
+#include "mltaln.h"
+
+int TLS commonAlloc1 = 0;
+int TLS commonAlloc2 = 0;
+int TLS **commonIP = NULL;
+int TLS **commonJP = NULL;
+int nthread = 1;
+int randomseed = 0;
+int parallelizationstrategy = BAATARI1;
+
+
+char modelname[100];
+int njob, nlenmax;
+int amino_n[0x80];
+char amino_grp[0x80];
+int amino_dis[0x80][0x80];
+int amino_disLN[0x80][0x80];
+double amino_dis_consweight_multi[0x80][0x80];
+int n_dis[26][26];
+int n_disFFT[26][26];
+float n_dis_consweight_multi[26][26];
+char amino[26];
+double polarity[20];
+double volume[20];
+int ribosumdis[37][37];
+
+int ppid;
+double thrinter;
+double fastathreshold;
+int pslocal, ppslocal;
+int constraint;
+int divpairscore;
+int fmodel; // 1-> fmodel 0->default -1->raw
+int nblosum; // 45, 50, 62, 80
+int kobetsubunkatsu;
+int bunkatsu;
+int dorp;
+int niter;
+int contin;
+int calledByXced;
+int devide;
+int scmtd;
+int weight;
+int utree;
+int tbutree;
+int refine;
+int check;
+double cut;
+int cooling;
+int penalty, ppenalty, penaltyLN;
+int RNApenalty, RNAppenalty;
+int RNApenalty_ex, RNAppenalty_ex;
+int penalty_ex, ppenalty_ex, penalty_exLN;
+int penalty_EX, ppenalty_EX;
+int penalty_OP, ppenalty_OP;
+int RNAthr, RNApthr;
+int offset, poffset, offsetLN, offsetFFT;
+int scoremtx;
+int TMorJTT;
+char use_fft;
+char force_fft;
+int nevermemsave;
+int fftscore;
+int fftWinSize;
+int fftThreshold;
+int fftRepeatStop;
+int fftNoAnchStop;
+int divWinSize;
+int divThreshold;
+int disp;
+int outgap = 1;
+char alg;
+int cnst;
+int mix;
+int tbitr;
+int tbweight;
+int tbrweight;
+int disopt;
+int pamN;
+int checkC;
+float geta2;
+int treemethod;
+int kimuraR;
+char *swopt;
+int fftkeika;
+int score_check;
+int makedistmtx;
+char *inputfile;
+char *addfile;
+int addprofile = 1;
+int rnakozo;
+char rnaprediction;
+int scoreout = 0;
+int outnumber = 0;
+
+char *signalSM;
+FILE *prep_g;
+FILE *trap_g;
+char **seq_g;
+char **res_g;
+
+float consweight_multi = 1.0;
+float consweight_rna = 0.0;
+char RNAscoremtx = 'n';
+
+char *newgapstr = "-";