JWS-112 Bumping version of Mafft to version 7.310.

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

diff --git a/binaries/src/mafft/core/defs.c b/binaries/src/mafft/core/defs.c
index 4136bc3..7a50555 100644 (file)
--- a/binaries/src/mafft/core/defs.c
+++ b/binaries/src/mafft/core/defs.c
@@ -11,19 +11,21 @@ int randomseed = 0;
 int parallelizationstrategy = BAATARI1;
 
 
-char modelname[100];
+char modelname[500];
 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 amino_n[0x100];
+char amino_grp[0x100];
+//int amino_dis[0x100][0x100];
+int **amino_dis = NULL;
+double **n_disLN = NULL;
+//double amino_dis_consweight_multi[0x100][0x100];
+double **amino_dis_consweight_multi = NULL;
+int **n_dis = NULL;
+int **n_disFFT = NULL;
+double **n_dis_consweight_multi = NULL;
+unsigned char amino[0x100];
+double polarity[0x100];
+double volume[0x100];
 int ribosumdis[37][37];
 
 int ppid;
@@ -36,7 +38,7 @@ int fmodel; // 1-> fmodel 0->default -1->raw
 int nblosum; // 45, 50, 62, 80
 int kobetsubunkatsu;
 int bunkatsu;
-int dorp;
+int dorp = NOTSPECIFIED; // arguments de shitei suruto, tbfast -> pairlocalalign no yobidashi de futsugou
 int niter;
 int contin;
 int calledByXced;
@@ -49,12 +51,16 @@ int refine;
 int check;
 double cut;
 int cooling;
+int trywarp = 0;
 int penalty, ppenalty, penaltyLN;
+int penalty_dist, ppenalty_dist;
 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 penalty_shift, ppenalty_shift;
+double penalty_shift_factor = 100.0;
 int RNAthr, RNApthr;
 int offset, poffset, offsetLN, offsetFFT;
 int scoremtx;
@@ -80,7 +86,7 @@ int tbrweight;
 int disopt;
 int pamN;
 int checkC;
-float geta2;
+double geta2;
 int treemethod;
 int kimuraR;
 char *swopt;
@@ -93,7 +99,11 @@ int addprofile = 1;
 int rnakozo;
 char rnaprediction;
 int scoreout = 0;
+int spscoreout = 0;
 int outnumber = 0;
+int legacygapcost = 0;
+double minimumweight = 0.0005;
+int nwildcard = 0;
 
 char *signalSM;
 FILE *prep_g;
@@ -101,8 +111,55 @@ FILE *trap_g;
 char **seq_g;
 char **res_g;
 
-float consweight_multi = 1.0;
-float consweight_rna = 0.0;
+double consweight_multi = 1.0;
+double consweight_rna = 0.0;
 char RNAscoremtx = 'n';
 
-char *newgapstr = "-";
+char TLS *newgapstr = "-";
+
+int nalphabets = 26;
+int nscoredalphabets = 20;
+
+double specificityconsideration = 0.0;
+int ndistclass = 10;
+int maxdistclass = -1;
+
+int gmsg = 0;
+
+double sueff_global = SUEFF;
+
+double lenfaca, lenfacb, lenfacc, lenfacd;
+int maxl, tsize;
+
+void initglobalvariables()
+{
+       commonAlloc1 = 0;
+       commonAlloc2 = 0;
+       commonIP = NULL;
+       commonJP = NULL;
+       nthread = 1;
+       randomseed = 0;
+       parallelizationstrategy = BAATARI1;
+
+       trywarp = 0;
+       penalty_shift_factor = 100.0;
+       outgap = 1;
+       addprofile = 1;
+       scoreout = 0;
+       outnumber = 0;
+       legacygapcost = 0;
+       consweight_multi = 1.0;
+       consweight_rna = 0.0;
+       RNAscoremtx = 'n';
+
+       newgapstr = "-";
+
+       nalphabets = 26;
+       nscoredalphabets = 20;
+
+       specificityconsideration = 0.0;
+       ndistclass = 10;
+       maxdistclass = -1;
+       
+       gmsg = 0;
+}