+++ /dev/null
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-/*********************************************************************/
-/* */
-/* MASKING LIST FUNCTIONS */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list * mask_list_with_aln (Alignment *A,int start, int len,Constraint_list *CL, int new_value)
- {
- int a, c,d;
- static int *entry;
- int s1, s2, r1, r2;
- int **pos;
- int **cache;
- int max_nseq;
- int max_len;
-
-
-
- if ( A==NULL || A->len_aln==0 || A->nseq<=1)return CL;
- if ( entry==NULL) entry=vcalloc (CL->entry_len , CL->el_size);
-
- cache=declare_int (return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),0)+1,return_max_int (A->order,read_size_int ( A->order,sizeof (int)),1)+A->len_aln+1);
-
- max_nseq=return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),0)+1;
- max_len =return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),1)+A->len_aln+1;
-
- pos=aln2pos_simple(A, A->nseq);
-
- for (a=0; a< A->nseq; a++)
- for (c=start; c< (start+len); c++)
- if ( pos[a][c]>0)cache[A->order[a][0]][pos[a][c]]=1;
-
-
- if (!CL->M)
- {
- for ( d=0; d<CL->ne; d++)
- {
- s1=vread_clist(CL, d, SEQ1);
- s2=vread_clist(CL, d, SEQ2);
- r1=vread_clist(CL, d, R1);
- r2=vread_clist(CL, d, R2);
- if ( s1>=max_nseq);
- else if (r1>=max_len);
- else if ( cache[s1][r1]==1)
- {
- mask_entry(CL,d,new_value);
- }
-
- if ( s2>=max_nseq);
- else if (r2>=max_len);
- else if ( cache[s2][r2]==1)
- {
- mask_entry(CL,d,new_value);
- }
- }
-
- sort_constraint_list_inv (CL,0, CL->ne);
- sort_constraint_list (CL,0, CL->ne);
- free_int ( cache, -1);
- }
- else if ( CL->M)
- {
-
- for (a=0; a< A->nseq; a++)
- for (c=start; c< (start+len); c++)
- if ( pos[a][c]>0)
- {
- vwrite_clist(CL,30+A->order[a][0],pos[a][c],UNDEFINED);
- }
- }
- free_int (pos, -1);
- return CL;
- }
-Constraint_list* mask_list_with_aln_pair (Alignment *A,int start, int len ,Constraint_list *CL,int new_value)
- {
- int a, b, p;
- int *entry;
-
-
- int l1, l2, r1, r2, s1, s2;
- int x, y;
-
- if ( A==NULL || A->len_aln==0 || A->nseq<=1)return CL;
-
- if (CL->M)
- {
- fprintf ( stderr, "\nERROR: AA matrix cannot be masked with mask_list_with_aln_pair");
- myexit (EXIT_SUCCESS);
- }
-
-
- entry=vcalloc (CL->entry_len, sizeof (int));
-
- for ( a=0; a< A->nseq-1; a++)
- {
- for (l1=A->order[a][1]+1,p=0 ; p<start ; p++)l1+=!is_gap(A->seq_al[a][p]);
- for (r1=l1-1 ,p=start; p<(start+len) ; p++)r1+=!is_gap(A->seq_al[a][p]);
- s1=A->order[a][0];
-
- for ( b=a+1; b< A->nseq; b++)
- {
- for (l2=A->order[b][1]+1,p=0 ; p<start; p++)l2+=!is_gap(A->seq_al[b][p]);
- for (r2=l2-1 ,p=start; p<(start+len) ; p++)r2+=!is_gap(A->seq_al[b][p]);
- s2=A->order[b][0];
-
-
- for ( x=l1; x<=r1; x++)
- {
-
- for ( y=l2; y<=r2; y++)
- {
-
- set_int(entry,4,x,R1,y,R2,s1,SEQ1,s2,SEQ2);
- if ( (main_search_in_list_constraint ( entry,&p,4,CL))!=NULL)
- {
- mask_entry(CL,p,new_value);
- }
- set_int(entry,4,y,R1,x,R2,s2,SEQ1,s1,SEQ2);
- if ( (main_search_in_list_constraint ( entry,&p,4,CL))!=NULL)
- {
-
- mask_entry(CL,p,new_value);
- }
- }
- }
- }
- }
-
-
- vfree(entry);
-
- return CL;
- }
-
-Constraint_list *mask_entry( Constraint_list *CL, int p, int new_value)
- {
- vwrite_clist(CL, p, WE, new_value);
- vwrite_clist(CL, p, CONS, new_value);
- vwrite_clist(CL, p, MISC, new_value);
- return CL;
- }
-/*********************************************************************/
-/* */
-/* SEQUENCE CONCATENATION */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list *prepare_list_and_seq4sw(Constraint_list *I, int n_seq, char **seq_name)
- {
- int a, b;
- int len,l;
- char **long_seq=NULL;
- int **translation;
- char **name;
- int s1, s2;
- Constraint_list *Out=NULL;
- Sequence *S_Out;
-
- translation=declare_int ( (I->S)->nseq,2);
- name=declare_char (1,STRING);
- long_seq=declare_char(1, STRING);
-
- for (len=0,a=0; a< (I->S)->nseq; a++)
- {
- if((b=name_is_in_list ((I->S)->name[a],seq_name, n_seq, 100))!=-1)
- {
- l=strlen((I->S)->seq[a])+1;
- long_seq[0]=vrealloc(long_seq[0],(len+l+1)*sizeof(char));
- long_seq[0]=strcat(long_seq[0], (I->S)->seq[a]);
- long_seq[0]=strcat(long_seq[0], "O");
-
- translation[a][0]=b;
- translation[a][1]=len;
- len+=l;
- }
- else translation[a][0]=-1;
- }
-
- long_seq[0][len-1]='\0';
- len--;
- sprintf ( name[0], "concatenat");
- S_Out=fill_sequence_struc(1, long_seq, name);
- free_char(name, -1);
- free_char(long_seq, -1);
-
-
- if (!I->M)
- {
- if ( I->fp) Out=declare_constraint_list(S_Out, NULL, NULL, 0, vtmpfile(),NULL);
- else if ( I->L)Out=declare_constraint_list(S_Out, NULL, NULL, 0, NULL ,NULL);
-
- for (a=0; a<I->ne; a++)
- {
- s1=vread_clist(I,a,SEQ1);
- s2=vread_clist(I,a,SEQ2);
-
- if ( translation[s1][0]!=-1 && translation[s2][0]!=-1)
- Out=add_list_entry2list(Out, Out->entry_len, SEQ1, 0, SEQ2, 0, R1,vread_clist(I,a,R1)+translation[s1][1], R2,vread_clist(I,a,R2)+translation[s2][1], WE,vread_clist(I,a,WE),CONS, vread_clist(I,a,CONS), MISC, vread_clist(I,a,MISC));
- }
-
- for ( a=0; a<(I->S)->nseq; a++)
- {
- if (translation[a][0]!=-1 && translation[a][1]!=0)
- {
- for (b=1; b<=len; b++)
- {
- add_list_entry2list(Out,Out->entry_len, SEQ1, 0, SEQ2, 0, R1, translation[a][1], R2, b, WE, UNDEFINED, CONS, 0,MISC, vread_clist(I,a,MISC));
- }
- }
- }
- sort_constraint_list (Out, 0, Out->ne);
- }
- else if (I->M)
- {
- Out=declare_constraint_list(S_Out, NULL, NULL, 0, vtmpfile(),I->M);
- vfree((Out->M)[30]);
- (Out->M)[30]=vcalloc ( len+1, sizeof (int));
- for ( a=0; a<len; a++)
- {
- if ( long_seq[0][a]=='O')vwrite_clist(Out, 30, a+1,UNDEFINED);
- }
- Out->ne=SIZEOF_AA_MAT;
- }
- free_int (translation,-1);
- return Out;
- }
-/*********************************************************************/
-/* */
-/* MISCEANELLOUS */
-/* */
-/* */
-/*********************************************************************/
-int ** get_undefined_list (Constraint_list *CL)
- {
- int **list;
- int a;
- CLIST_TYPE x;
-
- list=declare_int ( (CL->S)->nseq+1, (CL->S)->max_len+1);
-
- for ( a=0; a< CL->ne; a++)
- {
- x=vread_clist(CL, a, WE);
- list[vread_clist(CL, a, SEQ1)][vread_clist(CL, a, R1)]=(x==UNDEFINED);
- list[vread_clist(CL, a, SEQ2)][vread_clist(CL, a, R2)]=(x==UNDEFINED);
- }
- return list;
- }
-int is_never_undefined (Constraint_list *CL,int r)
- {
- int a;
- for ( a=0; a< CL->ne; a++)
- {
- if ( (vread_clist(CL,a,R1)==r || vread_clist(CL,a,R2)==r) && vread_clist(CL,a,WE)==UNDEFINED)return 0;
- }
- return 1;
- }
-
-int* do_analyse_list ( Constraint_list *CL)
- {
- int **seq_score;
- int **seq_score2;
- int *pos_L;
- int a;
- int n_res;
-
-
- int n_it=4;
-
- double sum, sum2, tot;
- int field=2;
- double z;
- int r1, r2;
- int max_we=0;
-
-
-
- fprintf ( stderr, "\nDO ANALYSE");
-
- n_res=(CL->S)->max_len;
-
- pos_L =vcalloc (n_res+2, sizeof (int));
- pos_L++;
- pos_L[-1]=n_res;
- seq_score=declare_int (n_res+1,n_it+1);
- seq_score2=declare_int(n_res+1,n_it+1);
-
-
-
- for ( a=0; a< CL->ne; a++)
- {
- r1=vread_clist(CL, a, R1);
- r2=vread_clist(CL, a, R2);
-
- seq_score[r1][0]+=vread_clist(CL, a, WE);
- seq_score[r2][0]+=vread_clist(CL, a, WE);
-
-
- seq_score[r1][1]+=vread_clist(CL, a, CONS);
- seq_score[r2][1]+=vread_clist(CL, a, CONS);
-
-
- seq_score[r1][2]+=vread_clist(CL, a, MISC);
- seq_score[r2][2]+=vread_clist(CL, a, MISC);
-
- }
- for ( a=1; a<=n_res; a++)max_we=MAX(seq_score[a][0],max_we);
- for ( a=1; a<=n_res; a++)
- {
- if ( a!=n_res && seq_score[a][0]> seq_score[a-1][0]) fprintf ( stderr, "\n%4d %s", a, num2plot(seq_score[a][0],max_we,40));
- else fprintf ( stderr, "\n");
- }
-
- for ( a=0; a< CL->ne; a++)if ( vread_clist(CL, a, MISC)>1000)fprintf ( stderr, "\n%4d %4d %4d", vread_clist(CL, a,R1), vread_clist(CL, a, R2), vread_clist(CL, a, MISC));
- myexit (EXIT_SUCCESS);
-
- for ( a=0; a<CL->ne; a++)
- {
- if ( vread_clist(CL, a, WE)!=UNDEFINED &&vread_clist(CL, a, MISC)>=1 )
- {
- seq_score[vread_clist(CL, a, R1)][0]+=vread_clist(CL, a, CONS);
- seq_score[vread_clist(CL, a, R1)][1]+=vread_clist(CL, a, WE);
- seq_score[vread_clist(CL, a, R1)][2]+=vread_clist(CL, a, MISC);
-
- seq_score[vread_clist(CL, a, R2)][0]+=vread_clist(CL, a, CONS);
- seq_score[vread_clist(CL, a, R2)][1]+=vread_clist(CL, a, WE);
- seq_score[vread_clist(CL, a, R2)][2]+=vread_clist(CL, a, MISC);
- }
- }
-
- for (a=1, tot=0,sum=0, sum2=0; a<= n_res ; a++)
- {
- if ( seq_score[a][2]>0)
- {
- sum +=seq_score[a][field];
- sum2+=seq_score[a][field]*seq_score[a][field];
- tot++;
- }
- }
-
- fprintf ( stderr, "\n");
-
-
-
- for (a=1; a<= n_res ; a++)
- {
- z=return_z_score (seq_score[a][field],sum, sum2, tot );
- if ( seq_score[a][2]>0)
- {
-
- pos_L[a]=(int)(z*10);
- pos_L[0]++;
-
- }
- }
-
-
- free_int (seq_score2,-1);
- free_int (seq_score,-1);
- return pos_L;
- }
-/*********************************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**********************************/
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