--- GDE/SUPPORT/CAP2.c 2016-08-22 18:27:49.000000000 +0800 +++ GDE/SUPPORT/CAP2.c 2026-05-22 04:18:04.000000000 +0800 @@ -157,6 +157,8 @@ */ #include +#include +#include int OVERLEN; /* Minimum length of any overlap */ float PERCENT; /* Minimum identity percentage of any overlap */ @@ -273,9 +275,12 @@ } *piece; /* array of segment records */ char *allconsen, *allconpt; /* Storing consensus sequences */ +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wimplicit-int" + main(argc, argv) int argc; char *argv[]; -{ +{ int M; /* Sequence length */ int V[128][128], Q,R; /* Weights */ int V1[128][128], R1; /* Light weights */ @@ -2302,3 +2307,4 @@ return(p); } +#pragma GCC diagnostic pop --- GDE/SUPPORT/count.c 2016-05-02 19:19:08.000000000 +0800 +++ GDE/SUPPORT/count.c 2026-05-22 04:55:29.000000000 +0800 @@ -25,144 +25,8 @@ struct data_format data[10000]; float parta[200], partc[200], partg[200], partu[200], setdist(); -main(ac,av) -int ac; -char **av; -{ - int i,j,k; - extern int ReadFlat(); - FILE *file; - - width = 1; - jump = 1; - if(ac==1) - { - fprintf(stderr, - "usage: %s [-sim] [-case] [-c=] ",av[0]); - fprintf(stderr,"[-t] alignment_flat_file\n"); - exit(1); - } - for(j=1;j] ",av[0]); + fprintf(stderr,"[-t] alignment_flat_file\n"); + exit(1); + } + for(j=1;j */ #include +#include +#include + #define TRUE 1 #define FALSE 0 #define MAX(a,b) ((a)>(b)?(a):(b)) @@ -14,6 +17,8 @@ char type; }; +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wimplicit-int" ErrorOut(code,string) int code; @@ -57,8 +62,6 @@ return(temp); } - - int ReadFlat(file,align,maxseqs) FILE *file; struct data_format align[]; @@ -134,7 +137,6 @@ return(++count); } - Errorout2(string) char *string; { @@ -166,4 +168,4 @@ return 0; } - +#pragma GCC diagnostic pop --- GDE/SUPPORT/lsadt.c 2016-05-02 19:19:08.000000000 +0800 +++ GDE/SUPPORT/lsadt.c 2026-05-22 05:09:04.000000000 +0800 @@ -32,6 +32,8 @@ C----------------------------------------------------------------------- */ #include +#include +#include #include #ifdef DARWIN @@ -45,7 +47,7 @@ #include #include #include - +#include #define BUFLEN 1024 #define MAXLEAVES 256 @@ -149,6 +151,39 @@ } #define gd(i,j) ( (j>>>ERROR:\n>>>>%s\n", message); + exit(0); +} + +show_help() +{ + printf("\nlsadt--options:\n"); + printf(" -f file - write report to 'file'\n"); + printf(" -d - treat data as dissimilarities (default)\n"); + printf(" -s - treat data as similarities\n"); + printf(" -print 0 - don't print out iteration history (default)\n"); + printf(" -print n>0 - print out iteration history every n iterations\n"); + printf(" -print n<0 - print out iteration history every n iterations\n"); + printf(" (including current distance estimates & gradients)\n"); + printf(" -init n - initial parameter estimates (default = 3)\n"); + printf(" n=1 - uniformly distributed random numbers\n"); + printf(" n=2 - error-perturbed data\n"); + printf(" n=3 - original distance data from input matrix\n"); + printf(" -save - save final parameter estimates (default is don't save\n"); + printf(" -seed n - seed for random number generator (default = 12345)\n"); + printf(" -ps1 n - convergence criterion for inner iterations (default = 0.0001)\n"); + printf(" -ps2 n - convergence criterion for major iterations (default = 0.0001)\n"); + printf(" -empty n - missing data indicator (default = 0.0)\n"); + printf(" -help - show this help text\n"); + exit(0); +} + #if 0 double gd(i, j) int i, j; @@ -1280,35 +1315,8 @@ printf("\n);\n"); } -show_help() -{ - printf("\nlsadt--options:\n"); - printf(" -f file - write report to 'file'\n"); - printf(" -d - treat data as dissimilarities (default)\n"); - printf(" -s - treat data as similarities\n"); - printf(" -print 0 - don't print out iteration history (default)\n"); - printf(" -print n>0 - print out iteration history every n iterations\n"); - printf(" -print n<0 - print out iteration history every n iterations\n"); - printf(" (including current distance estimates & gradients)\n"); - printf(" -init n - initial parameter estimates (default = 3)\n"); - printf(" n=1 - uniformly distributed random numbers\n"); - printf(" n=2 - error-perturbed data\n"); - printf(" n=3 - original distance data from input matrix\n"); - printf(" -save - save final parameter estimates (default is don't save\n"); - printf(" -seed n - seed for random number generator (default = 12345)\n"); - printf(" -ps1 n - convergence criterion for inner iterations (default = 0.0001)\n"); - printf(" -ps2 n - convergence criterion for major iterations (default = 0.0001)\n"); - printf(" -empty n - missing data indicator (default = 0.0)\n"); - printf(" -help - show this help text\n"); - exit(0); -} - -show_error(message) - char *message; -{ - printf("\n>>>>ERROR:\n>>>>%s\n", message); - exit(0); -} +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wint-conversion" main(argc, argv) int argc; @@ -1353,3 +1361,6 @@ if(report) close(reportf); } + +#pragma GCC diagnostic pop +#pragma GCC diagnostic pop --- GDE/SUPPORT/Restriction.c 2016-05-02 19:19:08.000000000 +0800 +++ GDE/SUPPORT/Restriction.c 2026-05-22 04:50:51.000000000 +0800 @@ -4,6 +4,70 @@ */ #include "Flatio.c" +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wimplicit-int" + +Comp(a,b) +char a,b; +{ + static int CtoB[128]={ + 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0x00, + 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, + 0x01,0xe,0x02,0x0d,0,0,0x04,0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06, + 0x08,0x08,0x07,0,0x09,0xa,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04, + 0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,0x08,0x08,0x07,0,0x09,0x0a, + 0,0,0,0,0x00,0 + }; + + static int BtoC[128] = + { + '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N', + '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n', + '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N', + '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n', + '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N', + '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n', + '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N', + '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n', + }; + + + return ((CtoB[a]) & (CtoB[b])); +} + +FindNext(target,offset,enzymes,numenzymes,match_len,color) +char *target,enzymes[][80]; +int numenzymes,*match_len,*color; +{ + int i,j,k,closest,len1,dif,flag = FALSE; + closest = strlen(target); + *match_len = 0; + for(k=0;k0) + for(flag = FALSE,j=offset;j0) - for(flag = FALSE,j=offset;j + #include "Flatio.c" + #define MAX(a,b) ((a)>(b)?(a):(b)) /* @@ -12,7 +14,10 @@ * * Copyright 1991/1992 Steven Smith, Harvard Genome lab. * -*/ +*/ + +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wimplicit-int" main(ac,av) int ac; @@ -84,3 +89,5 @@ } exit(0); } + +#pragma GCC diagnostic pop --- GDE/SUPPORT/Zuk_to_gen.c 2016-08-22 18:27:49.000000000 +0800 +++ GDE/SUPPORT/Zuk_to_gen.c 2026-05-22 04:53:03.000000000 +0800 @@ -1,4 +1,6 @@ #include +#include +#include typedef struct Sequence { @@ -8,6 +10,44 @@ char *nuc; } Sequence; +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wimplicit-int" + +WriteGen(seq,file,numseq) +Sequence *seq; +FILE *file; +int numseq; +{ + register i,j; + char temp[14]; + + for(j=0;j