Index: arb-6.0.6/GDE/SUPPORT/CAP2.c =================================================================== --- arb-6.0.6.orig/GDE/SUPPORT/CAP2.c +++ arb-6.0.6/GDE/SUPPORT/CAP2.c @@ -284,8 +284,8 @@ char *argv[]; char *sequence; /* Storing all segments */ char *reverse; /* Storing all reverse segments */ int symbol, prev; /* The next character */ - FILE *Ap, *ckopen(); /* For the sequence file */ - char *my_calloc(int); /* space-allocating function */ + FILE *Ap, *ckopen(const char *filename, const char *mode); /* For the sequence file */ + char *my_calloc(int amout); /* space-allocating function */ register int i, j, k; /* index variables */ /* Mod by S.S. */ int jj; @@ -454,7 +454,7 @@ static int *S; /* saving operations /* The following definitions are for function diff() */ -int diff(); +int diff(char *A, char *B, int M, int N, int q1, int q2); static int zero = 0; /* int type zero */ #define gap(k) ((k) <= 0 ? 0 : q+r*(k)) /* k-symbol indel score */ @@ -493,7 +493,7 @@ static int al_len; /* length of ali INIT(M) int M; { register int j; /* row and column indices */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ /* allocate space for all vectors */ j = (M + 1) * sizeof(int ); @@ -514,7 +514,7 @@ MAKE() int size; /* size of a lookup table */ int limit, digit, step; /* temporary variables */ register int i, j, k, p, q; /* index varibles */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ char *A; /* pointer to a sequence */ int M; /* length of a sequence */ @@ -581,14 +581,14 @@ PAIR(V,V1,Q,R,R1) int V[][128],V1[][128 int count, limit; /* temporary variables */ register int i, j, d; /* row and column indices */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ int rl, cl; char *A, *B; int M, N; overptr node1; int total; /* total number of pairs */ int hit; /* number of pairs satisfying cond. */ - int CHECK(); + int CHECK(short int orienti, int i, int j); v = V; q = Q; @@ -633,7 +633,7 @@ PAIR(V,V1,Q,R,R1) int V[][128],V1[][128 if ( no_mat >= al_len * per_cent && ( al_len >= over_len || iscon ) ) { - node1 = ( overptr ) my_calloc( (int ) sizeof(over)); + node1 = ( overptr ) my_calloc( (int) sizeof(over)); if ( iscon ) node1->kind = 0; /* containment */ else @@ -681,8 +681,7 @@ PAIR(V,V1,Q,R,R1) int V[][128],V1[][128 /* Return 1 if two sequences satisfy the necessary condition for overlap, and 0 otherwise. Parameters first and second are the indices of segments, and parameter orient indicates the orientation of segment first. */ -int CHECK(orient,first,second) short orient; -int first, second; +int CHECK(short int orient,int first, int second) { int limit, bound; /* maximum number of jumps */ int small; /* smaller of limit and bound */ @@ -690,10 +689,10 @@ int first, second; float cut; /* cutoff score */ register int i; /* index variable */ int t, q; /* temporary variables */ - int JUMP(); - int RJUMP(); - int JUMPC(); - int RJUMPC(); + int JUMP(int *arr, int first, int second, int orient); + int RJUMP(int *arr, int first, int second, int orient); + int JUMPC(int *arr, int first, int second); + int RJUMPC(int *arr, int first, int second); delta = DELTA; if ( orient ) @@ -730,8 +729,7 @@ int first, second; } /* Compute a vector of lengths of jumps */ -int JUMP(H,one,two,orient) int H[], one, two; -short orient; +int JUMP(int H[], int one, int two, short int orient) { char *A, *B; /* pointers to two sequences */ int M, N; /* lengths of two sequences */ @@ -781,7 +779,7 @@ short orient; } /* Compute a vector of lengths of jumps for reverse complement of one */ -int JUMPC(H,one,two) int H[], one, two; +int JUMPC(int H[], int one, int two) { char *A, *B; /* pointers to two sequences */ int M, N; /* lengths of two sequences */ @@ -831,8 +829,7 @@ int JUMPC(H,one,two) int H[], one, two } /* Compute a vector of lengths of reverse jumps */ -int RJUMP(H,one,two,orient) int H[], one, two; -short orient; +int RJUMP(int H[], int one, int two, short int orient) { char *A, *B; /* pointers to two sequences */ int N; /* length of a sequence */ @@ -881,7 +878,7 @@ short orient; } /* Compute a vector of lengths of reverse jumps for reverse complement */ -int RJUMPC(H,one,two) int H[], one, two; +int RJUMPC(int H[], int one, int two) { char *A, *B; /* pointers to two sequences */ int M, N; /* lengths of two sequences */ @@ -934,7 +931,8 @@ int RJUMPC(H,one,two) int H[], one, tw /* Construct contigs */ ASSEM() { - char *my_calloc(); /* space-allocating function */ + + char *my_calloc(int amount); /* space-allocating function */ register int i, j, k; /* index variables */ overptr node1, x, y; /* temporary pointer */ int five, three; /* indices of 5' and 3' segments */ @@ -1045,7 +1043,7 @@ REPAIR() short isconi, isconj; /* containment condition */ int score; /* the max score */ int i, j, f, d, e; /* row and column indices */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ char *A, *B; int M, N; overptr node1; @@ -1135,9 +1133,9 @@ REPAIR() } /* Construct contigs */ -REASSEM(piece_num, number) int piece_num, number; +REASSEM(int piece_num, int number) { - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ int i, j, k, d; /* index variables */ overptr node1, x, y; /* temporary pointer */ int five, three; /* indices of 5' and 3' segments */ @@ -1233,13 +1231,12 @@ REASSEM(piece_num, number) int piece_nu } } -RECONCILE(y, pp,nn) overptr y; -int *pp,*nn; +RECONCILE(overptr y, int *pp, int *nn) { short orienti, orientj; /* orientation of segments */ short orientk, orientd; /* orientation of segments */ int i, j, k, d, f; /* row and column indices */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ char *A, *B; int M, N; overptr node1; @@ -1344,7 +1341,7 @@ int *pp,*nn; FORM_TREE() { register int i, j, k; /* index variables */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ overptr node1; /* temporary pointer */ short orient; /* orientation of segment */ int group; /* serial number of contigs */ @@ -1422,7 +1419,7 @@ SORT(seg, ort) int seg; short ort; { register int i, j, k; /* index variables */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ overptr node1; /* temporary pointer */ short orient; /* orientation of segment */ char *A, *B; /* pointers to segment sequences */ @@ -1495,7 +1492,7 @@ short ort; SHOW() { register int i, j, k; /* index variables */ - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ int n; /* number of working segments */ int limit; /* number of slots in work */ int col; /* number of output columns prepared */ @@ -1697,7 +1694,7 @@ SHOW() /* allocate more space for output fragment */ ALOC_SEQ(t) rowptr t; { - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ char *start, *end, *p; t->linesize *= 2; start = t->line; @@ -1714,7 +1711,7 @@ ENTER(b, d, id, pos, par) int *b, *d, i rowptr par; { int i; - char *my_calloc(); /* space-allocating function */ + char *my_calloc(int amount); /* space-allocating function */ rowptr t; if ( *b <= *d ) @@ -2110,10 +2107,7 @@ S.S. A[1..M] and B[1..N] that begins(ends) with a delete if tb(te) is zero and appends such a conversion to the current script. */ -int diff(A,B,M,N,tb,te) char *A, *B; -int M, N; -int tb, te; - +int diff(char *A, char *B, int M, int N, int tb, int te) { int midi, midj, type; /* Midpoint, type, and cost */ int midc; @@ -2122,7 +2116,7 @@ int tb, te; register int i, j; register int c, e, d, s; int t, *va; - char *my_calloc(); + char *my_calloc(int amount); /* Boundary cases: M <= 1 or N == 0 */ @@ -2281,10 +2275,9 @@ char *msg, *val; } /* ckopen - open file; check for success */ -FILE *ckopen(name, mode) -char *name, *mode; +FILE *ckopen(char *name, char *mode) { - FILE *fopen(), *fp; + FILE *fp; if ((fp = fopen(name, mode)) == NULL) fatalf("Cannot open %s.", name); @@ -2292,13 +2285,13 @@ char *name, *mode; } /* my_calloc - allocate space; check for success */ -char *my_calloc(amount) -int amount; +char *my_calloc(int amount) { - char *malloc(), *p; + char *malloc(int),*p; - if ((p = malloc( (unsigned) amount)) == NULL) + if ((p =(char *) malloc( (unsigned) amount)) == NULL) fatal("Ran out of memory."); return(p); } +