78,80c78
< int **LoadScores(filename, Tipo, AlfabX,Alfab2, lAlfaX,lAlfa2)
<     char *filename, *AlfabX, *Alfab2;
<     int Tipo, *lAlfaX, *lAlfa2;
---
> int **LoadScores(char *filename, int Tipo, char *AlfabX, char *Alfab2, int *lAlfaX, int *lAlfa2)
164,165c162
< void impreseq(s)
<   char *s;
---
> void impreseq(char *s)
178c175
< int IdentityScore(numX, n0, numY, n1)
---
> int IdentityScore(char *numX, int n0, char *numY, int n1)
180,181d176
<  char *numX,*numY;
<  int n0,n1;
231,240c226,235
< int NWsoma(P, S, lp, fp, ls , iG, eG,Pam,F,LaX,flagA)
<   float **P;   /* profile            */
<   char *S;     /* sequence           */
<   int lp;      /* profile len        */
<   int fp;      /* profile rows       */
<   int ls;      /* seq len            */
<   int iG,eG;   /* init and extend gap penalty */
<   int **Pam;   /* PAM  */
<   int flagA;   /* 0: do not align seq/profile   1: insert gaps */
<   struct fragP *F;
---
> int NWsoma(float **P, char *S, int lp, int fp, int ls, int iG, int eG, int **Pam, struct fragP *F, int LaX, int flagA)
> //  float **P;   /* profile            */
> //  char *S;     /* sequence           */
> //  int lp;      /* profile len        */
> //  int fp;      /* profile rows       */
> //  int ls;      /* seq len            */
> //  int iG,eG;   /* init and extend gap penalty */
> //  int **Pam;   /* PAM  */
> //  int flagA;   /* 0: do not align seq/profile   1: insert gaps */
> //  struct fragP *F;
286c281
<         aux_x = MCx[j-1];
---
>         aux_x = (int)MCx[j-1];
498,500c493
< int LeeSeqDB_BOSA(f, sX)
<   FILE *f;
<   struct Sequence *sX;
---
> int LeeSeqDB_BOSA(FILE *f, struct Sequence *sX)
529,532c522
< int LeeSeqDBoffset(f, sX, offset)
<   FILE *f;
<   struct Sequence *sX;
<   int offset;
---
> int LeeSeqDBoffset(FILE *f, struct Sequence *sX, int offset)
539,542c529
< int ScoreMaximo(aa0,n0,PAM)
<   char *aa0;
<   int n0;
<   int **PAM;
---
> int ScoreMaximo(char *aa0, int n0, int **PAM)
545c532
<   int sco=0.;
---
>   int sco=0;
550,552c537
< int ScoreBestDiag(aa0,aa1,n0,Pint)
<     char 	*aa0, *aa1;
<     int 	n0,**Pint;
---
> int ScoreBestDiag(char *aa0, char *aa1, int n0, int **Pint)
561,563c546
< int *IniMaxScoreFast(seq, Pam, slen)
<    char *seq;
<    int **Pam, slen;
---
> int *IniMaxScoreFast(char *seq, int **Pam, unsigned int slen) // was int **slen
574,575c557
< int MaxScoreFast(Vsco, iniP,endP)
<     int *Vsco, iniP,endP;
---
> int MaxScoreFast(int *Vsco, int iniP, int endP)
577c559,560
<     if (iniP) return Vsco[endP];
---
>     if (iniP)
>          return Vsco[endP];
587c570
< int AllUnGappedFrags(numX, n0, numY, n1, PAM, Frag, StartPoints, Lmin,Ts,flagM,FD)
---
> int AllUnGappedFrags(char *numX, int n0, char *numY, int n1, int **PAM, struct frags *Frag, int *StartPoints, int Lmin, int *Ts, int flagM, long **FD)
589,596d571
<  char *numX,*numY;
<  int n0,n1;
<  int **PAM;
<  struct frags *Frag;
<  int *StartPoints, Lmin;
<  int *Ts;
<  int flagM;
<  long **FD;