+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-#include <ctype.h>
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-
-#include "dp_lib_header.h"
-
-
-
-
-
-int evaluate_moca_domain ( Alignment *A, Constraint_list *CL)
- {
- /*
- function documentation: start
- int evaluate_moca_domain ( Alignment *A, Constraint_list *CL)
-
- This function evaluates a multiple local alignment
- If the alignmnent is to be accepted, return score
- Else return UNDEFINED
-
- function documentation: end
- */
-
-
- int score=0;
- int start, end, a, b;
- Alignment *B=NULL;
- char alp[200];
-
-
- score=UNDEFINED;
- end=0;
- start=0;
-
- sprintf ( alp, "acefghiklmnpqrstuvwy");
-
- if ( A->len_aln>0)
- {
- score=(int)(output_maln_pval ( "/dev/null", A)*-100);
- return score;
- }
- else
- return 0;
-
-
-
-
- while ((end+1)!=A->len_aln)
- {
- end=get_nol_aln_border (A,start,GO_RIGHT);
- if ( end==start)break;
- fprintf ( stderr, "\n**%d %d (%d)",start, end, A->len_aln);
- B=copy_aln (A, B);
- B=extract_aln (B,start,end);
- for (a=0; a<B->nseq; a++)
- for ( b=0; b<B->len_aln; b++)
- if ( is_gap (B->seq_al[a][b]))B->seq_al[a][b]=alp[(int)rand()%(strlen (alp))];
-
-
- start=end;
- fprintf ( stderr, "==>%d",(int)(output_maln_pval ( "/dev/null", B)*-100) );
- if ( score==UNDEFINED)score=(int)(output_maln_pval ( "/dev/null", B)*-100);
- else
- score=MAX(score,(int)(output_maln_pval ( "/dev/null", B)*-100));
-
-
- }
- free_aln (B);
- return score;
- }
-
-
-int moca_slow_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
- {
- int s;
-
- s=slow_get_dp_cost ( A, pos1, ns1, list1, col1, pos2, ns2, list2, col2, CL);
-
-
- if ( s==UNDEFINED)return UNDEFINED;
- else return s+(CL->moca)->moca_scale;
-
- }
-int moca_evaluate_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
-{
- /*
- function documentation: start
- int moca_residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
-
- THIS FUNCTION RETURNS THE EXTENDED SCORE OF A PAIR OF RESIDUES
- it is meant to work with local aln pair_wise routines, by using (CL->moca)->forbiden_residues
- a constant value is substracted from the extended score.
-
- This function is meant toi be used with omain_dp, therefore, it allows the match of identical residues.
-
- function documentation: end
- */
-
- if (unpack_seq_residues ( &s1, &r1, &s2, &r2, CL->packed_seq_lu)==UNDEFINED)return UNDEFINED;
- else if ( (CL->moca)->forbiden_residues && ((CL->moca)->forbiden_residues[s1][r1]==UNDEFINED ||(CL->moca)->forbiden_residues[s2][r2]==UNDEFINED))return UNDEFINED;
- else if ( s1==s2 && r1 == r2) return UNDEFINED;
- else return evaluate_matrix_score(CL, s1, r1, s2, r2);
- }
-
-
-
-
-int moca_residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
- {
- /*
- function documentation: start
- int moca_residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
-
- THIS FUNCTION RETURNS THE EXTENDED SCORE OF A PAIR OF RESIDUES
- it is meant to work with local aln pair_wise routines, by using (CL->moca)->forbiden_residues
- a constant value is substracted from the extended score.
-
- This function is meant toi be used with omain_dp, therefore, it allows the match of identical residues.
-
- function documentation: end
- */
-
- if (unpack_seq_residues ( &s1, &r1, &s2, &r2, CL->packed_seq_lu)==UNDEFINED)return UNDEFINED;
- else if ( (CL->moca)->forbiden_residues && ((CL->moca)->forbiden_residues[s1][r1]==UNDEFINED ||(CL->moca)->forbiden_residues[s2][r2]==UNDEFINED))return UNDEFINED;
- else if ( s1==s2 && r1 == r2) return UNDEFINED;
- else return residue_pair_extended_list (CL, s1, r1, s2, r2);
-
-
- }
-
-int **cache_cl_with_moca_domain (Alignment *A, Constraint_list *CL)
- {
- /*
- function documentation: start
- int **cache_cl_with_moca_domain (Alignment *A, Constraint_list *CL)
-
- Read a multiple alignmnent
- Given all the residues (CL->S)->seq[x][y] contained in the maln
- Set (CL->moca)->forbiden_residues[x][y] to UNDEFINED
- return (CL->moca)->forbiden_residues
-
- WARNING
- You must make sure that the evalation strategy uses (CL->moca)->forbiden_residues
- (CL->moca)->forbiden_residues[0][1]->first residue(1) of First sequence(0)
- function documentation: end
- */
-
- int **pos;
- int a, b;
-
- pos=aln2pos_simple(A, A->nseq);
-
- if ( !(CL->moca)->forbiden_residues)(CL->moca)->forbiden_residues=declare_int ((CL->S)->nseq, strlen ((CL->S)->seq[0])+1);
-
- for ( a=0; a<A->nseq;a++)
- for ( b=0; b< A->len_aln; b++)
- (CL->moca)->forbiden_residues[A->order[a][0]][pos[a][b]]=UNDEFINED;
-
- free_int (pos, -1);
- return (CL->moca)->forbiden_residues;
- }
-Alignment *make_moca_nol_aln ( Alignment *A, Constraint_list *CL)
-{
-
- return A;
-}
-
-/*********************************************************************************************/
-/* */
-/* DOMAIN Z SCORE EVALUATION */
-/* */
-/*********************************************************************************************/
-
-int evaluate_domain_aln_z_score (Alignment *A, int start, int end,Constraint_list *CL, char *alphabet)
- {
- int a;
- static Alignment *B;
- double score, ref_score;
- double N_EVAL=1000;
- double sum=0, sum2=0;
-
-
- if ( A==NULL || A->nseq==0 || A->len_aln==0)return 0;
- ref_score=(double)evaluate_domain_aln (A,start, end,CL);
- for (sum=0, sum2=0,a=0;a<N_EVAL; a++)
- {
- B=make_random_aln ( B, A->nseq, end-start, alphabet);
- score=(double)evaluate_domain_aln (B,0,B->len_aln,CL);
- sum+=score;
- sum2+=score*score;
- }
- score=(return_z_score(ref_score, sum, sum2, N_EVAL)*100)/A->len_aln;
-
- return(int) score;
- }
-
-int evaluate_domain_aln ( Alignment *A, int start, int end,Constraint_list *CL)
- {
- int a, b, c;
- int score, c1, c2;
- static int **mat;
-
- /*
- function documentation: start
-
- This function uses a pam250 to evaluate the sum of pairs score of A,
- between position start(included) to position end (exluded),
-
- the numbering starts 0
- function documentation: end
- */
-
- if ( !mat)mat=read_matrice ( "pam250mt");
-
- for ( c=start, score=0; c<end; c++)
- {
- for ( a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq; b++)
- {
- c1=tolower(A->seq_al[a][c]);
- c2=tolower(A->seq_al[b][c]);
-
- if ( !is_gap (c1) && !is_gap(c2))score+=mat[c1-'A'][c2-'A'];
- }
- }
- return score;
- }
-
-int unpack_seq_residues ( int *s1, int *r1, int *s2, int *r2, int **packed_seq_lu)
- {
- /* Given a series of sequences concatenated (packed), and the coordinates of two residues
- This function translates the coordinates into the real ones and allows evaluation
- Note for this function residues go from [1->N], sequences from [0->N[
- This is true for in and out comming residues number
- NOTE: The sequence cannot be guessed when the residues r1 or r2 are GAPS, therefore UNDEFINED is returned
- NOTE: Concatenated sequences are separated with X, such residues cause an UNDEFINED to be returned
- */
-
- if ( packed_seq_lu==NULL)return 1;
- else if ( s1[0]!=s2[0])return 1;
- else if ( r1[0]<=0 || r2[0]<=0)return UNDEFINED;
- else if ( packed_seq_lu[r1[0]][0]==UNDEFINED || packed_seq_lu[r2[0]][0]==UNDEFINED)return UNDEFINED;
- else
- {
- s1[0]=packed_seq_lu[r1[0]][0];
- r1[0]=packed_seq_lu[r1[0]][1];
-
- s2[0]=packed_seq_lu[r2[0]][0];
- r2[0]=packed_seq_lu[r2[0]][1];
- }
- return 1;
- }
-
-Alignment * unpack_seq_aln ( Alignment *A,Constraint_list *CL)
- {
- int a, b, r_seq, r_start, r_len;
-
-
- if (!CL->packed_seq_lu) return A;
-
- for (a=0; a< A->nseq; a++)
- {
- r_seq =CL->packed_seq_lu[A->order[a][1]+1][0];
- r_start=CL->packed_seq_lu[A->order[a][1]+1][1];
-
- A->order[a][0]=r_seq;
- A->order[a][1]=r_start-1;
-
- for ( r_len=0,b=0; b< A->len_aln; b++)r_len+=!is_gap(A->seq_al[a][b]);
- sprintf ( A->name[a],"%s_%d_%d", (A->S)->name[r_seq], r_start, r_start+r_len-1);
- }
-
- return A;
- }
-
-
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/
git://source.jalview.org / jabaws.git / blobdiff