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/***********************************************************************
*
* Header file for satutil.c (for copy Seq-feat based on sequence
* alignment
*
************************************************************************/
#ifndef _SATUTIL_
#define _SATUTIL_
#include <ncbi.h>
#include <objfeat.h>
#include <objseq.h>
#include <objloc.h>
#include <objalign.h>
#include <sequtil.h>
#include <edutil.h>
#include <seqport.h>
#include <seqmgr.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#define DEFAULT_GAP_CHOICE 0
#define IGNORE_GAP_CHOICE 1
#define TAKE_GAP_CHOICE 2
#define MAX_GAP_LEN_BY_DEFAULT 10 /*the maximum allowd length of gap*/
/******************************************************************
*
* CopyFeatureFromAlign(source_sfp, target_id, source_id, align,
* gap_choice, check_trunc
*
* Copy the source_sfp to the target sequence based on their
* alignment
* source_sfp: Seq-feat of the source
* target_id: Seq-id of the target
* source_id: Seq-id of the source in the alignment. This is
* neccessary when the source_sfp may composed from different
* segment of a Bioseq-set
* align: The Seq-align that contains alignment of the source
* and the target
* gap_choice: choice to select to map the gap to the new feature
* can have default, ignore or take
* check_trunc: load the fuzziness of the new Seq-feat
*
******************************************************************/
NLM_EXTERN SeqFeatPtr CopyFeatureFromAlign PROTO((SeqFeatPtr source_sfp, SeqIdPtr target_id, SeqIdPtr source_id, SeqAlignPtr align, Uint1 gap_choice, Boolean check_trunc));
/***************************************************************
*
* Load a protein Bioseq to replace the Bogo product
* sfp: the coding region feature
* new_prot_id: if NULL a new default will be generated
*
***************************************************************/
NLM_EXTERN Boolean LoadProteinForCdRegion PROTO((SeqFeatPtr sfp, SeqIdPtr new_prot_id));
/********************************************************
*
* functions related to the Bogo product
*
*********************************************************/
/*make the bogo product UserObject and link it to the chain*/
NLM_EXTERN void make_bogo_product PROTO((UserObjectPtr PNTR head));
/*************************************************************
*
* check if the UserObject contains the identifyer for the
* BOGO product
*
**************************************************************/
NLM_EXTERN Boolean IS_BOGO_Product PROTO((UserObjectPtr uop));
/************************************************************
*
* DeleteBogoProduct(head)
* Delete the UserObject of Bogo Product from the chain
*
**************************************************************/
NLM_EXTERN void DeleteBogoProduct PROTO((UserObjectPtr PNTR head));
/**********************************************************************
*
* map_one_location()
* map the source_loc to the target by the Sequence alignment
* source_loc: the source Seq-loc
* align: the alignment between the source and the target
* target_sip: the Seq-id for the target
* gap_choice: choice for mapping the gaps
* r_start, r_stop: the real start, stop value in the source
* sequence during the mapping. This value allows
* the mapping of truncation info for the results
* return NULL for failure
*
*********************************************************************/
NLM_EXTERN SeqLocPtr map_one_location PROTO((SeqLocPtr source_loc, SeqAlignPtr align, SeqIdPtr target_sip, Uint1 gap_choice, Int4Ptr r_start, Int4Ptr r_stop));
/********************************************************************
*
* SeqAlignReplaceId ()
* replaces a Seq-Id (oldId) in a Seq-Id list in a Seq-Align (salp)
* with a new Seq-Id (newId)
*
*********************************************************************/
NLM_EXTERN SeqAlignPtr SeqAlignReplaceId (SeqIdPtr oldId, SeqIdPtr newId, SeqAlignPtr salp);
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
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