jpayne@69: #include "tigrinc.hh"
jpayne@69: 
jpayne@69: 
jpayne@69: FILE *  File_Open  (const char * Filename, const char * Mode)
jpayne@69: 
jpayne@69: /* Open  Filename  in  Mode  and return a pointer to its control
jpayne@69: *  block.  If fail, print a message and exit. */
jpayne@69: 
jpayne@69:   {
jpayne@69:    FILE  *  fp;
jpayne@69: 
jpayne@69:    fp = fopen (Filename, Mode);
jpayne@69:    if  (fp == NULL)
jpayne@69:        {
jpayne@69:         fprintf (stderr, "ERROR:  Could not open file  %s \n", Filename);
jpayne@69:         exit (EXIT_FAILURE);
jpayne@69:        }
jpayne@69: 
jpayne@69:    return  fp;
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: void *  Safe_calloc  (size_t N, size_t Len)
jpayne@69: 
jpayne@69: /* Allocate and return a pointer to an array of  N  elements of
jpayne@69: *   Len  bytes each.  All set to 0.  Exit if fail. */
jpayne@69: 
jpayne@69:   {
jpayne@69:    void  * P;
jpayne@69: 
jpayne@69:    P = calloc (N, Len);
jpayne@69:    if  (P == NULL)
jpayne@69:        {
jpayne@69:         fprintf (stderr,
jpayne@69: 		 "ERROR:  calloc failed, there is not enough memory\n");
jpayne@69:         exit (EXIT_FAILURE);
jpayne@69:        }
jpayne@69: 
jpayne@69:    return  P;
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: void *  Safe_malloc  (size_t Len)
jpayne@69: 
jpayne@69: /* Allocate and return a pointer to  Len  bytes of memory.
jpayne@69: *  Exit if fail. */
jpayne@69: 
jpayne@69:   {
jpayne@69:    void  * P;
jpayne@69: 
jpayne@69:    P = malloc (Len);
jpayne@69:    if  (P == NULL)
jpayne@69:        {
jpayne@69:         fprintf (stderr,
jpayne@69: 		 "ERROR:  malloc failed, there is not enough memory\n");
jpayne@69:         exit (EXIT_FAILURE);
jpayne@69:        }
jpayne@69: 
jpayne@69:    return  P;
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: void *  Safe_realloc  (void * Q, size_t Len)
jpayne@69: 
jpayne@69: /* Reallocate memory for  Q  to  Len  bytes and return a
jpayne@69: *  pointer to the new memory.  Exit if fail. */
jpayne@69: 
jpayne@69:   {
jpayne@69:    void  * P;
jpayne@69: 
jpayne@69:    P = realloc (Q, Len);
jpayne@69:    if  (P == NULL)
jpayne@69:        {
jpayne@69:         fprintf (stderr,
jpayne@69: 		 "ERROR:  realloc failed, there is not enough memory\n");
jpayne@69:         exit (EXIT_FAILURE);
jpayne@69:        }
jpayne@69: 
jpayne@69:    return  P;
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: char  Complement  (char Ch)
jpayne@69: 
jpayne@69: /* Returns the DNA complement of  Ch . */
jpayne@69: 
jpayne@69:   {
jpayne@69:    switch  (tolower (Ch))
jpayne@69:      {
jpayne@69:       case  'a' :
jpayne@69:         return  't';
jpayne@69:       case  'c' :
jpayne@69:         return  'g';
jpayne@69:       case  'g' :
jpayne@69:         return  'c';
jpayne@69:       case  't' :
jpayne@69:         return  'a';
jpayne@69:       case  'r' :          // a or g
jpayne@69:         return  'y';
jpayne@69:       case  'y' :          // c or t
jpayne@69:         return  'r';
jpayne@69:       case  's' :          // c or g
jpayne@69:         return  's';
jpayne@69:       case  'w' :          // a or t
jpayne@69:         return  'w';
jpayne@69:       case  'm' :          // a or c
jpayne@69:         return  'k';
jpayne@69:       case  'k' :          // g or t
jpayne@69:         return  'm';
jpayne@69:       case  'b' :          // c, g or t
jpayne@69:         return  'v';
jpayne@69:       case  'd' :          // a, g or t
jpayne@69:         return  'h';
jpayne@69:       case  'h' :          // a, c or t
jpayne@69:         return  'd';
jpayne@69:       case  'v' :          // a, c or g
jpayne@69:         return  'b';
jpayne@69:       default :            // anything
jpayne@69:         return  tolower (Ch);
jpayne@69:      }
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: bool CompareIUPAC (char x, char y)
jpayne@69: {
jpayne@69:   x = tolower(x);
jpayne@69:   y = tolower(y);
jpayne@69: 
jpayne@69:   if ( x == 'n' || x == 'x' || y == 'n' || y == 'x' )
jpayne@69:     return true;
jpayne@69: 
jpayne@69:   switch ( x )
jpayne@69:     {
jpayne@69:     case 'a' :
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'a':
jpayne@69:         case 'r':
jpayne@69:         case 'w':
jpayne@69:         case 'm':
jpayne@69:         case 'd':
jpayne@69:         case 'h':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'c' :
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'c':
jpayne@69:         case 'y':
jpayne@69:         case 's':
jpayne@69:         case 'm':
jpayne@69:         case 'b':
jpayne@69:         case 'h':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'g' :
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'g':
jpayne@69:         case 'r':
jpayne@69:         case 's':
jpayne@69:         case 'k':
jpayne@69:         case 'b':
jpayne@69:         case 'd':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 't' :
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 't':
jpayne@69:         case 'y':
jpayne@69:         case 'w':
jpayne@69:         case 'k':
jpayne@69:         case 'b':
jpayne@69:         case 'd':
jpayne@69:         case 'h':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'r' :          // a or g
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'r':
jpayne@69:         case 'a':
jpayne@69:         case 'g':
jpayne@69:         case 'd':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'y' :          // c or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'y':
jpayne@69:         case 'c':
jpayne@69:         case 't':
jpayne@69:         case 'b':
jpayne@69:         case 'h':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 's' :          // c or g
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 's':
jpayne@69:         case 'c':
jpayne@69:         case 'g':
jpayne@69:         case 'b':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'w' :          // a or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'w':
jpayne@69:         case 'a':
jpayne@69:         case 't':
jpayne@69:         case 'd':
jpayne@69:         case 'h':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'm' :          // a or c
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'm':
jpayne@69:         case 'a':
jpayne@69:         case 'c':
jpayne@69:         case 'h':
jpayne@69:         case 'v':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'k' :          // g or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'k':
jpayne@69:         case 'g':
jpayne@69:         case 't':
jpayne@69:         case 'b':
jpayne@69:         case 'd':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'b' :          // c, g or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'b':
jpayne@69:         case 'c':
jpayne@69:         case 'g':
jpayne@69:         case 't':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'd' :          // a, g or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'd':
jpayne@69:         case 'a':
jpayne@69:         case 'g':
jpayne@69:         case 't':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'h' :          // a, c or t
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'h':
jpayne@69:         case 'a':
jpayne@69:         case 'c':
jpayne@69:         case 't':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69: 
jpayne@69:     case 'v' :          // a, c or g
jpayne@69:       switch ( y )
jpayne@69:         {
jpayne@69:         case 'v':
jpayne@69:         case 'a':
jpayne@69:         case 'c':
jpayne@69:         case 'g':
jpayne@69:           return true;
jpayne@69:         }
jpayne@69:       return false;
jpayne@69:     }
jpayne@69:   return false;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: int Read_String  (FILE * fp, char * & T, long int & Size, char Name [],
jpayne@69: 		  int Partial)
jpayne@69: 
jpayne@69: /* Read next string from  fp  (assuming FASTA format) into  T [1 ..]
jpayne@69: *  which has  Size  characters.  Allocate extra memory if needed
jpayne@69: *  and adjust  Size  accordingly.  Return  TRUE  if successful,  FALSE
jpayne@69: *  otherwise (e.g., EOF).  Partial indicates if first line has
jpayne@69: *  numbers indicating a subrange of characters to read.
jpayne@69: */
jpayne@69: 
jpayne@69:   {
jpayne@69:    char  * P, Line [MAX_LINE];
jpayne@69:    long int  Len, Lo, Hi;
jpayne@69:    int  Ch, Ct;
jpayne@69: 
jpayne@69:    while  ((Ch = fgetc (fp)) != EOF && Ch != '>')
jpayne@69:      ;
jpayne@69: 
jpayne@69:    if  (Ch == EOF)
jpayne@69:        return  FALSE;
jpayne@69: 
jpayne@69:    fgets (Line, MAX_LINE, fp);
jpayne@69:    Len = strlen (Line);
jpayne@69:    assert (Len > 0 && Line [Len - 1] == '\n');
jpayne@69:    P = strtok (Line, " \t\n");
jpayne@69:    if  (P != NULL)
jpayne@69:        strcpy (Name, P);
jpayne@69:      else
jpayne@69:        Name [0] = '\0';
jpayne@69:    Lo = 0;  Hi = LONG_MAX;
jpayne@69:    if  (Partial)
jpayne@69:        {
jpayne@69:         P = strtok (NULL, " \t\n");
jpayne@69:         if  (P != NULL)
jpayne@69:             {
jpayne@69:              Lo = strtol (P, NULL, 10);
jpayne@69:              P = strtok (NULL, " \t\n");
jpayne@69:              if  (P != NULL)
jpayne@69:                  Hi = strtol (P, NULL, 10);
jpayne@69:             }
jpayne@69:         assert (Lo <= Hi);
jpayne@69:        }
jpayne@69: 
jpayne@69:    Ct = 0;
jpayne@69:    T [0] = '\0';
jpayne@69:    Len = 1;
jpayne@69:    while  ((Ch = fgetc (fp)) != EOF && Ch != '>')
jpayne@69:      {
jpayne@69:       if  (isspace (Ch))
jpayne@69:           continue;
jpayne@69: 
jpayne@69:       Ct ++;
jpayne@69:       if  (Ct < Lo || Ct > Hi)
jpayne@69:           continue;
jpayne@69: 
jpayne@69:       if  (Len >= Size)
jpayne@69:           {
jpayne@69:            Size += INCR_SIZE;
jpayne@69:            T = (char *) Safe_realloc (T, Size);
jpayne@69:           }
jpayne@69:       Ch = tolower (Ch);
jpayne@69: 
jpayne@69:       if  (! isalpha (Ch) && Ch != '*')
jpayne@69:           {
jpayne@69:            fprintf (stderr, "Unexpected character `%c\' in string %s\n",
jpayne@69:                                  Ch, Name);
jpayne@69:            Ch = 'x';
jpayne@69:           }
jpayne@69: 
jpayne@69:       T [Len ++] = Ch;
jpayne@69:      }
jpayne@69: 
jpayne@69:    T [Len] = '\0';
jpayne@69:    if  (Ch == '>')
jpayne@69:        ungetc (Ch, fp);
jpayne@69: 
jpayne@69:    return  TRUE;
jpayne@69:   }
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: void  Reverse_Complement
jpayne@69:     (char S [], long int Lo, long int Hi)
jpayne@69: 
jpayne@69: //  Convert substring  S [Lo .. Hi]  to its Watson-Crick reverse
jpayne@69: //  complement
jpayne@69: 
jpayne@69:   {
jpayne@69:    char  Ch;
jpayne@69: 
jpayne@69:    while  (Lo <= Hi)
jpayne@69:      {
jpayne@69:       Ch = S [Hi];
jpayne@69:       S [Hi] = Complement (S [Lo]);
jpayne@69:       S [Lo] = Complement (Ch);
jpayne@69:       Lo ++;
jpayne@69:       Hi --;
jpayne@69:      }
jpayne@69: 
jpayne@69:    return;
jpayne@69:   }
jpayne@69: