+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-#include "dp_lib_header.h"
-
-Alignment *clean_maln ( Alignment *A, Alignment *I, int T, int n_it)
- {
- Alignment *C=NULL;
- int a, b;
- int in_una, in_aln, in_gap, gap, una, aln;
- int Sstart,Rstate, Sstate;
- int n_segment=0;
- int **segment_list;
-
-
- add_warning ( stderr, "\nWARNING: -clean_aln is not supported anymore [PROGRAM:%s]\n", PROGRAM);
- return A;
-
-
-
- /*Initialization*/
- a=0;
- in_una=a++;in_gap=a++;in_aln=a++; aln=a++;gap=a++;una=a++;
- segment_list=declare_int ( A->len_aln*A->nseq, 3);
-
-
- /*1: Identify the segments*/
- C=copy_aln(A, C);
- for ( a=0; a< A->nseq; a++)
- {
- Sstate=in_aln;
- for ( b=0; b<A->len_aln; b++)
- {
- if (is_gap(A->seq_al[a][b]))Rstate=gap;
- else if ( I->seq_al[a][b]<=T){Rstate=una;}
- else if ( I->seq_al[a][b]==NO_COLOR_RESIDUE)Rstate=una;
- else Rstate=aln;
-
- if (Rstate==una)C->seq_al[a][b]='-';
-
- if (Sstate==in_aln)
- {
- if ( Rstate==gap)
- {Sstate=in_gap;
- Sstart=b;
- }
- else if ( Rstate==una)
- {
- Sstate=in_una;
- Sstart=b;
- }
- else if ( Rstate==aln)
- Sstate=in_aln;
- }
- else if ( Sstate==in_gap)
- {
- if ( Rstate==gap);
- else if ( Rstate==una)Sstate=in_una;
- else if ( Rstate==aln)Sstate=in_aln;
- }
- else if ( Sstate==in_una)
- {
- if ( Rstate==gap);
- else if ( Rstate==una);
- else if ( Rstate==aln)
- {
- segment_list[n_segment][0]=a;
- segment_list[n_segment][1]=Sstart;
- segment_list[n_segment][2]=b-Sstart;
- Sstate=in_aln;
- n_segment++;
- }
- }
- }
- if (Sstate==in_una)
- {
- segment_list[n_segment][0]=a;
- segment_list[n_segment][1]=Sstart;
- segment_list[n_segment][2]=b-Sstart;
- Sstate=in_aln;
- n_segment++;
- }
- }
-
- /*2 Realign the segments*/
-
- for ( b=0; b< n_it; b++)
- {
- for ( a=0; a< n_segment; a++)
- {
- HERE ("1");
- A=realign_segment ( segment_list[a][0], segment_list[a][1], segment_list[a][2], A, C);
-
- }
- }
- free_aln (C);
- free_int ( segment_list, -1);
- make_fast_generic_dp_pair_wise (NULL, NULL, NULL, NULL);
-
- return A;
- }
-Alignment *realign_segment (int seq, int start, int len,Alignment *A, Alignment *C)
- {
- Alignment *S1=NULL, *S2=NULL, *S3=NULL;
- int *ns, **ls;
- int a,b;
- static Constraint_list *CL;
-
-
- /*1 Prepare the Constraint list*/
- if ( !CL)
- {
- CL=vcalloc ( 1, sizeof (Constraint_list));
- CL->extend_jit=0;
- CL->pw_parameters_set=1;
- CL->M=read_matrice ("blosum62mt");
- CL->gop=-20;
- CL->gep=-1;
- CL->evaluate_residue_pair=evaluate_matrix_score;
- sprintf ( CL->dp_mode, "myers_miller_pair_wise");
- }
-
- S1=copy_aln(A,S1);
- S1=extract_aln (S1,0,start);
- S2=copy_aln(A,S2);
- S2=extract_aln (S2, start, start+len);
- S3=copy_aln(A,S3);
- S3=extract_aln (S3, start+len,A->len_aln);
-
-
- /*for (a=0; a<S2->nseq; a++){S2->order[a][1]=0;S2->order[a][0]=a;}*/
-
-
- ungap ( S2->seq_al[seq]);
- CL->S=A->S;/*aln2seq(S2);*/
- /*3 Prepare Sequence Presentation*/
- ns=vcalloc (2, sizeof (int));
- ls=declare_int (2,S2->nseq);
-
- ns[0]=A->nseq-1;
- for ( a=0,b=0; a< S2->nseq; a++)if (a!=seq)ls[0][b++]=a;
- ns[1]=1;
- ls[1][0]=seq;
-
- pair_wise (S2, ns, ls, CL);
-
- A=realloc_aln (A, strlen (S1->seq_al[0])+ strlen (S2->seq_al[0])+ strlen (S3->seq_al[0])+1);
- for ( a=0; a< A->nseq; a++)
- {
- sprintf ( A->seq_al[a], "%s%s%s", S1->seq_al[a], S2->seq_al[a], S3->seq_al[a]);
- }
-
- free_aln (S1);
- free_aln (S2);
- free_aln (S3);
- vfree(ns);free_int(ls, -1);
-
- return A;
- }
-Alignment *realign_segment_old (int seq, int start, int len,Alignment *A, Alignment *C)
- {
- Alignment *S=NULL;
- int *ns, **ls;
- char *sub_seq;
- static Dp_Model *M=NULL;
- static Constraint_list *CL=NULL;
- Dp_Result *R=NULL;
- int a,b, c;
-
-
- /*1 Prepare the Constraint list*/
- if ( !CL)
- {
- CL=vcalloc ( 1, sizeof (Constraint_list));
- CL->extend_jit=0;
- CL->pw_parameters_set=1;
- CL->M=read_matrice ("blosum62mt");
- CL->gop=-20;
- CL->gep=-1;
- CL->evaluate_residue_pair=evaluate_matrix_score;
-
- }
- S=copy_aln(C,S);
- S=extract_aln (S, start, start+len);
- S->len_aln=strlen(S->seq_al[0]);
- sub_seq=extract_char (A->seq_al[seq], start, len);
-
- ungap(sub_seq);
-
- sprintf ( S->seq_al[seq],"%s", sub_seq);
- CL->S=aln2seq(S);
-
-
-
- /*2 Prepare the Model*/
- M=initialize_seg2prf_model((start==0)?2:0,(start+len==A->len_aln)?2:0,CL);
- M->diag=vcalloc ( 2*len+1, sizeof (int));
- M->diag[0]=len+strlen (sub_seq)-1;
- for ( a=1; a<=M->diag[0]; a++)M->diag[a]=a;
-
- /*3 Prepare Sequence Presentation*/
- ns=vcalloc (2, sizeof (int));
- ls=declare_int (2,A->nseq);
-
- ns[0]=A->nseq-1;
- for ( a=0,b=0; a< A->nseq; a++)if (a!=seq)ls[0][b++]=a;
- ns[1]=1;
- ls[1][0]=seq;
-
- if ( strlen (sub_seq)!=len)
- {
-
-
- R=make_fast_generic_dp_pair_wise(S, ns, ls, M);
-
- for (c=0, b=1,a=start; a< start+len; b++,a++)
- {
- if (R->traceback[b]==0)
- {
- A->seq_al[seq][a]=sub_seq[c];
- C->seq_al[seq][a]=sub_seq[c];
- c++;
- }
- else
- {
- A->seq_al[seq][a]='-';
- C->seq_al[seq][a]='-';
- }
- }
- }
-
- free_dp_model (M);
- free_aln (S);
- free_dp_result (R);
- vfree(sub_seq);
- vfree(ns);
- free_int (ls, -1);
- free_sequence (CL->S, (CL->S)->nseq);
-
-
- return A;
- }
-
-Dp_Model * initialize_seg2prf_model(int left_tg_mode, int right_tg_mode, Constraint_list *CL)
- {
-
- Dp_Model *M;
- int a, b, c,d;
-
- M=vcalloc ( 1, sizeof (Dp_Model));
- M->nstate=2;
- M->START=M->nstate++;
- M->END =M->nstate++;
-
- M->TG_MODE=1;
- M->F_TG_MODE=0;
- M->gop=CL->gop*SCORE_K;
- M->gep=CL->gep*SCORE_K;
-
- M->bounded_model=declare_int (M->nstate+1, M->nstate+1);
- M->model=declare_int (M->nstate+1, M->nstate+1);
- for ( a=0; a<=M->nstate; a++)
- for ( b=0; b<= M->nstate; b++)
- M->model[a][b]=UNDEFINED;
-
- a=0;
- M->TYPE=a++;M->LEN_I=a++; M->LEN_J=a++; M->DELTA_I=a++;M->DELTA_J=a++; M->CODING0=a++;M->DELETION=a++;
- M->model_properties=declare_int ( M->nstate, 10);
-
- a=0;
- M->EMISSION=a++;M->TERM_EMISSION=a++;M->START_EMISSION=a++;
- M->model_emission_function=vcalloc(M->nstate, sizeof (int (**)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *)));
- for ( a=0; a< M->nstate; a++)
- M->model_emission_function[a]=vcalloc(3, sizeof (int (*)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *)));
-
-
- /*Substitution*/
- M->model_properties[0][M->TYPE]=M->CODING0;
- M->model_properties[0][M->LEN_I]=1;
- M->model_properties[0][M->LEN_J]=1;
- M->model_properties[0][M->DELTA_I]=-1;
- M->model_properties[0][M->DELTA_J]= 0;
-
- M->model_emission_function[0][M->EMISSION] =cw_profile_get_dp_cost;
- M->model_emission_function[0][M->START_EMISSION]=get_start_gep_cost;
- M->model_emission_function[0][M->TERM_EMISSION] =get_start_gep_cost;
-
- /*Deletions*/
- M->model_properties[1][M->TYPE]=M->DELETION;
- M->model_properties[1][M->LEN_I]=1;
- M->model_properties[1][M->LEN_J]=0;
- M->model_properties[1][M->DELTA_I]=-1;
- M->model_properties[1][M->DELTA_J]=+1;
- M->model_emission_function[1][M->EMISSION]=get_gep_cost;
-
- if (left_tg_mode ==2)
- M->model_emission_function[1][M->START_EMISSION]=get_start_gep_cost;
- else M->model_emission_function[1][M->START_EMISSION]=get_gep_cost;
-
- if (right_tg_mode ==2)
- M->model_emission_function[1][M->TERM_EMISSION]=get_term_gep_cost;
- else M->model_emission_function[1][M->TERM_EMISSION]=get_gep_cost;
-
- /*Transitions*/
- M->model[0][M->END]=M->model[M->START][0]=ALLOWED;
- M->model[0][1]=M->gop;
- M->model[0][0]=ALLOWED;
-
- M->model[1][M->END]= (right_tg_mode==0)?0:-M->gop;
- M->model[M->START][1]=( left_tg_mode==0)?M->gop:0;
- M->model[1][1]=ALLOWED;
- M->model[1][0]=ALLOWED;
-
-
-
-
- /*Prune the model*/
-
- for (c=0,a=0, d=0; a< M->START; a++)
- for ( b=0; b<M->START; b++, d++)
- {
- if (M->model[a][b]!=UNDEFINED)
- {
- M->bounded_model[b][1+M->bounded_model[b][0]++]=a;
- c++;
- }
- }
- M->CL=CL;
-
- return M;
- }
-
-int get_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
-{
- return CL->gep*SCORE_K;
-}
-
-int get_start_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
-{
- return 0;
-}
-int get_term_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
-{
- return CL->gep*SCORE_K*-1;
-}
-
-
-
-
-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
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