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(-) motif.cc.orig (-4 / +8 lines)
 Lines 49-55    Link Here  
// Background::Background
// Background::Background
// Background constructor for a given fasta file and sequence type (aac or nt)
// Background constructor for a given fasta file and sequence type (aac or nt)
//
//
Background::Background(GFastaFile *F,FILE *outfile,const seqType t,double e=0.0000001)
 
//Background::Background(GFastaFile *F,FILE *outfile,const seqType t,double e=0.0000001)
 

              
Background::Background(GFastaFile *F,FILE *outfile,const seqType t,double e)

            

        
{
{

        
  outf=outfile;
  outf=outfile;

        
  eps=e;
  eps=e;

  

    

    

       Lines 386-392
       
    
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// apply_test_wilcoxon_pair
// apply_test_wilcoxon_pair

        
// applies the wilcoxon pair test on a vector of differences
// applies the wilcoxon pair test on a vector of differences

        
//
//

            

              
void apply_test_wilcoxon_pair(FILE *outf,int diffno, FreqPos *diff,int print=1) 

              
//void apply_test_wilcoxon_pair(FILE *outf,int diffno, FreqPos *diff,int print=1) 

            

            

              

              
void apply_test_wilcoxon_pair(FILE *outf,int diffno, FreqPos *diff,int print) 

            

        
{
{

        
  double *rank;
  double *rank;

        

  

    

    

       Lines 1543-1549
       
    
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// Motif::printMotif
// Motif::printMotif

        
// prints the motif
// prints the motif

        
//
//

            

              
void Motif::printMotif(int printmax,int SignifNo,int print=1)

              
//void Motif::printMotif(int printmax,int SignifNo,int print=1)

            

            

              

              
void Motif::printMotif(int printmax,int SignifNo,int print)

            

        
{
{

        
  fprintf(B->outf,"Motif found:\n\n");
  fprintf(B->outf,"Motif found:\n\n");

        

  

    

    

       Lines 2130-2136
       
    
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// statistical significance after the test sequences have been created; 
// statistical significance after the test sequences have been created; 

        
// can be deterministic (when det=1) or not
// can be deterministic (when det=1) or not

        
//
//

            

              
void Motif::testsignif(int det,char **fkseq, int *posfreqlen,int print=1)

              
//void Motif::testsignif(int det,char **fkseq, int *posfreqlen,int print=1)

            

            

              

              
void Motif::testsignif(int det,char **fkseq, int *posfreqlen,int print)

            

        
{
{

        
  FreqPos diff[B->noseq];
  FreqPos diff[B->noseq];

        
  unsigned long int diffno=0;
  unsigned long int diffno=0;