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static char const rcsid[] = "$Id: sim2.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $";
#include <stdio.h>
#include <ncbi.h>
#include <objseq.h>
#include <objloc.h>
#include <seqport.h>
#include <sequtil.h>
#include "simutil.h"
/* SIM2 - calling routine to falign() */
SeqAlignPtr SIM2(SeqLocPtr cslp1, SeqLocPtr cslp2, Int4 k, SimPamPtr a_spp, ValNodePtr PNTR new_list, Uint1 output_type, FilterProc filter)
{
SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC;
Boolean both_strand, is_dna;
CharPtr A, B, compB = NULL;
Int4 w, r, o, e, m, g, h;
FloatHi cut_off;
Int4 Width = -1;
SimPam sp, PNTR spp;
Uint1 m_strand, s_strand;
if(cslp1 == NULL || cslp2 == NULL)
{
Message(MSG_ERROR, "In sufficient input");
return NULL;
}
if(cslp1->choice != SEQLOC_INT || cslp2->choice !=SEQLOC_INT)
{
Message(MSG_ERROR, "Incorrect type of Seq-loc. Only take Seq-int");
return NULL;
}
if(output_type < OUTPUT_ALIGN || output_type > OUTPUT_BOTH)
{
Message(MSG_OK, "Illegal output type");
output_type = OUTPUT_ALIGN;
}
if(new_list !=NULL)
*new_list = NULL;
else
{
if(output_type == OUTPUT_BOTH || output_type == OUTPUT_ENDS)
{
Message(MSG_ERROR, "No space to store the ends");
return NULL;
}
}
both_strand = check_strand_mol(cslp2, &is_dna);
if(!is_dna)
{
Message(MSG_ERROR, "Sorry, Sim2 can only compare two DNA sequences");
return NULL;
}
if(!both_strand)
both_strand = check_strand_mol(cslp1, &is_dna);
if(a_spp == NULL)
{
DefaultSimPam(&sp);
spp = &sp;
}
else
spp = a_spp;
w = spp->word;
r = spp->mismatch;
o = spp->gap_open;
e = spp->gap_ext;
m = spp->mismatch_2;
g = spp->gap_open_2;
h = spp->gap_ext_2;
cut_off = spp->cutoff;
if(both_strand)
{
m_strand = SeqLocStrand(cslp1);
Change_Loc_Strand(cslp1, Seq_strand_plus);
s_strand = SeqLocStrand(cslp2);
Change_Loc_Strand(cslp2, Seq_strand_plus);
}
A= make_sim_seq(cslp1, TRUE, NULL);
if(A == NULL)
{
if(both_strand)
{
Change_Loc_Strand(cslp2, s_strand);
Change_Loc_Strand(cslp1, m_strand);
}
return NULL;
}
B = make_sim_seq(cslp2, TRUE, NULL);
if(B == NULL)
{
if(both_strand)
{
Change_Loc_Strand(cslp2, s_strand);
Change_Loc_Strand(cslp1, m_strand);
}
if(A != NULL)
MemFree(A);
return NULL;
}
sap = NULL;
sap = falign(cslp1, cslp2, A+1, B+1, w, k, r, o, e);
out_sap = Region(sap, cslp1, cslp2, A+1, B+1, m, g, h, Width, new_list, output_type, filter);
sap = free_align_list(sap);/* free sap */
if(both_strand)
{
Change_Loc_Strand(cslp2, (Uint1)2);
B = make_sim_seq(cslp2, TRUE, B);
sap = falign(cslp1, cslp2, A+1, B+1, w, k, r, o, e);
out_sapC = Region(sap, cslp1, cslp2, A+1, B+1, m, g, h, Width, new_list, output_type, filter);
sap = free_align_list(sap); /*free sap */
/* concatenate out_sap and out_sapC */
out_sap = link_align(out_sapC, out_sap);
}
MemFree(A);
MemFree(B);
if(output_type != OUTPUT_ALIGN)
*new_list = get_top_K(*new_list, k);
if(both_strand)
{
Change_Loc_Strand(cslp2, s_strand);
Change_Loc_Strand(cslp1, m_strand);
}
return get_top_K_alignment(out_sap, k, cut_off);
}
/**********************************************************************
*
* SIM2ALN(cslp1, cslp2, K)
* Computes top K alignment beteeen cslp1 and cslp2, return the Seq-align
* object only
*
***********************************************************************/
SeqAlignPtr SIM2ALN (SeqLocPtr cslp1, SeqLocPtr cslp2, Int4 K)
{
return SIM2(cslp1, cslp2, K, NULL, NULL, OUTPUT_ALIGN, NULL);
}
/**********************************************************************
*
* SIM2ENDS(cslp1, csp2, K, filter)
* Computes top K alignment between cslp1, cslp2 and return the
* a linked list (ValNodePtr) of RecordEnds
* filter: filter based on percent identity. set to NULL when
* it is not required
*
**********************************************************************/
ValNodePtr SIM2ENDS (SeqLocPtr cslp1, SeqLocPtr cslp2, Int4 K, FilterProc
filter)
{
ValNodePtr new_list; /*the list for storin the ends*/
SIM2(cslp1, cslp2, K, NULL, &new_list, OUTPUT_ENDS, filter);
return new_list;
}
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