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// $Id: stsmatch.h,v 1.1 2003/03/31 21:08:27 rotmistr Exp $
#ifndef __stsmatch_h__
#define __stsmatch_h__

#include "util.h"

//// Word size
#define ePCR_WDSIZE_MIN       3
#define ePCR_WDSIZE_MAX       8
//// Number of mismatches allowed
#define ePCR_MMATCH_MIN       0
#define ePCR_MMATCH_MAX       10
//// Margin (allowed deviation in product size)
#define ePCR_MARGIN_DEFAULT   50
#define ePCR_MARGIN_MIN       0
#define ePCR_MARGIN_MAX       10000

class STS
      friend class PCRmachine;

      STS  *next;      // pointer to next element in the linked list
      char *pcr_p1;    // left primer
      char *pcr_p2;    // right primer

      unsigned char pcr_p1_len;
      unsigned char pcr_p2_len;
      int   size_lo;   // lower end of PCR amplicon size range
      int   size_hi;   // upper end of PCR amplicon size range
      char  direct;    // 'p' for plus, 'm' for minus

      STS (const char *p1, const char *p2, char d, int lo, int hi, fpos_t fpos);
      ~STS ();

      //int Match (const char *seq, int margin, int &size) const;
      fpos_t  m_fpos;  // offset into STS primer file (beginning of line)


class PCRmachine

      int ReadStsFile (const char *fname);
      int ProcessSeq (const char *seq_label, const char *seq_data);

      void SetWordSize (int wdsize);
      void SetMargin (int margin);
      void SetMismatch (int mmatch);

      // Override the ReportHit() function for customized output of 
      // results.  Return value: FALSE to abort search, TRUE to continue

      virtual int ReportHit (
            const char *seq_label,      // Label for sequence
            int pos1, int pos2,         // STS endpoints, zero-based
            const STS *sts,             // STS that was hit
            fpos_t fpos);               // Offset into STS file

      FILE *m_file;     // STS primer file
      STS **m_sts_table;
      int   m_sts_count;
      int   m_margin;
      int   m_mmatch;
      unsigned int m_wsize;
      unsigned int m_asize;
      unsigned int m_mask;

      void InsertSTS (STS *sts, unsigned hash);
      bool HashValue (const char *primer, unsigned &hash);
      int Match (const char *seq, int seq_len, const STS *sts, int &actual_size);

 * * $Log: stsmatch.h,v $
 * * Revision 1.1  2003/03/31 21:08:27  rotmistr
 * * Imported to CVS
 * * Compilable with gcc
 * *

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