NCBI C Toolkit Cross Reference

   /* $Id: codon.h,v 6.1 1997/11/06 21:26:11 madden Exp $
   * ===========================================================================
   *
   *                            PUBLIC DOMAIN NOTICE
   *               National Center for Biotechnology Information
   *
   *  This software/database is a "United States Government Work" under the
   *  terms of the United States Copyright Act.  It was written as part of
   *  the author's official duties as a United States Government employee and
  *  thus cannot be copyrighted.  This software/database is freely available
  *  to the public for use. The National Library of Medicine and the U.S.
  *  Government have not placed any restriction on its use or reproduction.
  *
  *  Although all reasonable efforts have been taken to ensure the accuracy
  *  and reliability of the software and data, the NLM and the U.S.
  *  Government do not and cannot warrant the performance or results that
  *  may be obtained by using this software or data. The NLM and the U.S.
  *  Government disclaim all warranties, express or implied, including
  *  warranties of performance, merchantability or fitness for any particular
  *  purpose.
  *
  *  Please cite the author in any work or product based on this material.
  *
  * ===========================================================================
  *
  * File Name:  $RCSfile: codon.h,v $
  *
  * Author:  Jinghui Zhang
  *
  * Initial Version Creation Date: 03/24/97
  *
  * $Revision: 6.1 $
  *
  * File Description:
  *         
  *
  * $Log: codon.h,v $
  * Revision 6.1  1997/11/06 21:26:11  madden
  * Added print_label_to_buffer_all_ex with option to strip semicolons
  *
  * Revision 6.0  1997/08/25 18:05:21  madden
  * Revision changed to 6.0
  *
  * Revision 5.6  1997/07/01 15:15:49  zjing
  * fix the problem of label overflow
  *
  * Revision 5.5  1997/06/19 18:37:28  vakatov
  * [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
  *
  * Revision 5.4  1997/03/24 21:00:07  shavirin
  * Added protection for usage with C++ compiler. Added NCBI header
  * and started logging
  *
  *
  * ==========================================================================
  */
  
  #ifndef _CODON_
  #define _CODON_
  
  #include <ncbi.h>
  #include <objfeat.h>
  #include <seqport.h>
  #include <seqmgr.h>
  #include <jzmisc.h> 
  #include <gather.h>
  #include <satutil.h>
  
  typedef struct codonvector{
          Uint2 exonCount;        /*current count of exons*/
          CharPtr buf[3];
          Int4 dna_pos;           /*position in dna sequence*/
          SeqIdPtr sip;           /*id for the DNA sequence for label*/
          Uint1 strand;           /*orientation of CDs*/
          Uint1 frame;            /*the frame of current exon*/
          Int2 aa_index;          /*0 for partial start , 1 for normal*/
  }CodonVector, PNTR CodonVectorPtr;
  
  
  #undef NLM_EXTERN
  #ifdef NLM_IMPORT
  #define NLM_EXTERN NLM_IMPORT
  #else
  #define NLM_EXTERN extern
  #endif
  
  #ifdef __cplusplus
  extern "C" {
  #endif
  
  /******************************************************************
  *
  *       aa_to_codon(sfp, aa_start, aa_stop)
  *       generate a list of CodonVecotr to show the codons of an
  *       amino acid sequence
  *       sfp: the Seq-feat for cds
  *       aa_start: the start position of protein sequence
  *       aa_stop the stop position of protein sequence
  *
 ******************************************************************/
 NLM_EXTERN ValNodePtr aa_to_codon PROTO((SeqFeatPtr sfp, Int4 aa_start, Int4 aa_stop));
 
 
 /****************************************************************** 
 * 
 *       free_cvp_list(cvp_list)
 *       free a list of CodonVectorPtr 
 * 
 ******************************************************************/ 
 NLM_EXTERN ValNodePtr free_cvp_list PROTO((ValNodePtr cvp_list));
 
 /*********************************************************************
 *
 *       make_cds_paragraph(sfp, aa_start, aa_stop)
 *       return a buffer for the display of 3-codon under one amino 
 *       acid format. It also includes the new line characters 
 *       This is what Jonathan K. desires to have for the sequin 
 *       doc object
 *       aa_start, aa_stop: start and stop in the amino acid sequence
 *
 *********************************************************************/
 NLM_EXTERN CharPtr make_cds_paragraph PROTO((SeqFeatPtr sfp, Int4 aa_start, Int4 aa_stop));
 
 
 
 
 /******************************************************************
 *
 *       aa_to_dnaloc(sfp, aa_start, aa_stop)
 *       map the amino acid sequence to a list of Seq-locs in the 
 *       DNA sequence
 *
 ******************************************************************/
 NLM_EXTERN SeqLocPtr aa_to_dnaloc PROTO((SeqFeatPtr sfp, Int4 aa_start, Int4 aa_stop));
 
 NLM_EXTERN Int4 print_protein_for_cds PROTO((SeqFeatPtr sfp, CharPtr buf, SeqLocPtr loc, Boolean reverse_minus));
 
 #define POS_SPACE 10    /*empty space used to write the position*/
 #define STRAND_SPACE 3  /*empty space used to laod the orientation*/
 #define B_SPACE 10
 
 /******************************************************************** 
 * 
 *       print_label_to_buffer(buf, label, pos, strand, extra_space) 
 *
 *       print a label (with label_name=label, position=pos, 
 *       orientation = strand, extra_space = extra_space for partial start) 
 *       into the current buffer 
 *       return the offset of the buffer pointer to the current buffer 
 * 
 *********************************************************************/
  
 NLM_EXTERN Int4 print_label_to_buffer PROTO((CharPtr buf, CharPtr label, Int4 pos, 
         Uint1 strand, Boolean extra_space, Boolean is_html, Int4 label_space, 
         Int4 num_space));
 
 NLM_EXTERN void print_label PROTO((FILE *fp, CharPtr label, Int4 pos, Uint1 strand, Boolean extra_space));
 
 /********************************************************************
 *
 *       print_label_to_buffer(buf, label, pos, strand, extra_space)
 *
 *       print a label (with label_name=label, position=pos, 
 *       orientation = strand, extra_space = extra_space for partial start)
 *       into the current buffer
 *       return the offset of the buffer pointer to the current buffer
 *
 *********************************************************************/
 NLM_EXTERN Int4 print_label_to_buffer_all PROTO((CharPtr buf, CharPtr label, 
                 Int4 pos, Uint1 strand, Boolean extra_space, Boolean is_html, 
                 Int4 label_space, Int4 num_space, Boolean show_strand));
 
 /********************************************************************
 *
 *       print_label_to_buffer_all_ex(buf, label, pos, strand, extra_space)
 *
 *       print a label (with label_name=label, position=pos, 
 *       orientation = strand, extra_space = extra_space for partial start)
 *       into the current buffer
 *       return the offset of the buffer pointer to the current buffer
 *       Has an option to strip/not-strip semicolons for hardline old blast
 *       users.
 *
 *********************************************************************/
 NLM_EXTERN Int4 print_label_to_buffer_all_ex PROTO((CharPtr buf, CharPtr label, 
                 Int4 pos, Uint1 strand, Boolean extra_space, Boolean is_html, 
                 Int4 label_space, Int4 num_space, Boolean show_strand, 
                 Boolean strip_semicolon));
 
 NLM_EXTERN Boolean make_scale_bar_str PROTO((CharPtr PNTR bar, CharPtr PNTR num_str, 
                 Int4 num_empty, Int4 line_len));
 
 #ifdef __cplusplus
 }
 #endif
 
 #undef NLM_EXTERN
 #ifdef NLM_EXPORT
 #define NLM_EXTERN NLM_EXPORT
 #else
 #define NLM_EXTERN
 #endif
 
 #endif