/*************************************************
misc.c
P. Clote
Miscellaneous routines for reading in RNA either as
string from command line or FASTA file, etc.

NOTES:
1) I chose a[] to be an array of short int, rather than
   char, since a[0] is the length of the original RNA
   sequence, stored in a[1],...,a[ a[0] ]
   Thus this requires a special irintRNA() function.

*************************************************/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <limits.h>     //for INT_MAX
#include "spectrum.h"   //includes def for DEBUG
#include <ctype.h>   	// character handling, eg toupper()

#define GUbond -1
#define AUbond -2
#define CGbond -3

void printRNA(short *a,short flag){
  //if flag=0 then don't print vertical bars
  int i, len;
  len = a[0];
  //print RNA
  for (i=1;i<=len;i++) printf("%c",a[i]);
  printf("\n");
  //now print separation markers every 10 spaces
  if (flag!=0 && len >= 10){
    for (i=1;i<=len;i++) {
      if (i%10==0) 
        printf("|");
      else
        printf(" ");
      }
    printf("\n");
    }
  }

char * constructString(short *a){
  int i, n;
  char *s; 

  n = a[0];
  s = (char *) calloc(n+1,sizeof(char));

  //print RNA
  for (i=0;i<n;i++) s[i] = (char) a[i+1];
  s[n] = '\0';
  return s;
  }




short *getRNA(char *flag, char *rna){
  //Function to retrieve RNA sequence, either input in command line
  //or as FASTA file
  FILE * infile;
  char ch;
  int i,n,len;
  static short a[NN];  
    //store RNA sequence, static required to retain local variable contents
    //after function call

  /***** retrieve RNA sequence  **/
  if (strcmp("-s",flag) == 0)  {
    len = strlen(rna);
    a[0] = len;
    if (len>=NN-2) {
      fprintf(stderr,"Length of RNA exceeds array size %d\n",NN);
      exit(1);
      }
    for (i=0;i<len;i++) {
      a[i+1] = toupper(rna[i]);
      if (a[i+1] == 'T') a[i+1] = 'U';
      }
    //printRNA(a,1);
    }
  else { //read FASTA format file of RNA
    infile = fopen(rna,"r");
    ch=fgetc(infile);
    if (ch == '>') { //now remove FASTA comment
      while (ch != '\n') ch = fgetc(infile);
      }
      // This only works on Unix, since EOLN marker for DOS is \r\n
      // and of Macintosh is \r
      // At this point, ch is \n, since we have exited while loop
    a[0] = 0; //we'll need to return to set a[0] to be sequence length
    n=1; //current position of insert into RNA string
    while (ch != EOF && n < NN){
      if (ch == '\n') {
        ch = fgetc(infile);
        if (ch == EOF) { a[0]=n-1; break; }
        }
      a[n] = toupper(ch);  n++;
      ch = fgetc(infile); 
      }
    if (n>=NN){
      fprintf(stderr,"Length of RNA exceeds array size %d\n",NN);
      exit(1);
      }
    a[0] = n-1;  //string length is n-1
    a[n+1] = '\0'; //string terminator
    //printRNA(a,1);
    fclose(infile);
    } 
  return a;
} 






void error(char *s){
   fprintf(stderr,"%s\n",s);
   exit(1);
}

int guPair(char x, char y){
   return ( x=='G'&&y=='U' || x=='U'&&y=='G' );
}

int auPair(char x, char y){
   return ( x=='A'&&y=='U' || x=='U'&&y=='A' );
}

int cgPair(char x, char y){
   return ( x=='C'&&y=='G' || x=='G'&&y=='C' );
}


int bondEnergy(int i, int j, char *s) {
  //returns the energy value of the pairing between
  //the ith and jth base in s
  if (i < strlen (s) && j < strlen (s)) {
      if (auPair(s[i],s[j]))
         return AUbond;
      else if (cgPair(s[i],s[j]))
         return CGbond;
      else if (guPair(s[i],s[j]))
         return GUbond;
      else
         return INF;
      }
    else
         error("Indices out of bounds for RNA sequence\n");
}




int basePair(char x, char y){
   return( auPair(x,y) || cgPair(x,y) || guPair(x,y) );
}


int watsonCrick(char x, char y){
   return( auPair(x,y) || cgPair(x,y) );
}


void printMatrix(MatrixType M, int n){
  int i,j,k,s,b;
  for (k=0;k<FF(1,n);k++) {
    printf("k: %d ",k);
    printf("-------------------------------------\n");
    for (i=1;i<=n;i++) {
      for (j=i;j<=n;j++){
        printf("%d,", BP(i,j,k));
        }
      printf("\n");
      }
  }
  printf("\n\n");
}