+++ /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"
-int check_link (CL_node ***G, int S1, int r1, int s2, int r2);
-void light_nodes (CL_node *A, int va, CL_node*B, int vb, CL_node*C,int vc, char *s);
-void print_graph (CL_node *G, Sequence *S);
-Sequence *Seq;
-CL_node *Start;
-static int cycle;
-
-
-
-Alignment * add_constraint2aln ( Alignment *A, int s1, int r1, int s2, int r2)
-{
- /*Note sCL_node ***G;1 and r1 must be numbered from 0 to n-1*/
- CL_node ***G;
-
-
- G=aln2graph(A);
- G=add_constraint2graph_aln (G,s1,r1, s2, r2);
- A=graph2aln (A,G[0][0],aln2seq(A));
- vfree_graph (G[0][0]);
- return A;
-}
-Alignment * graph_aln (Alignment *A, Constraint_list *iCL, Sequence *S)
-{
- CL_node ***G;
- int a,start;
- CLIST_TYPE *entry=NULL;
- Constraint_list *CL;
- Seq=S;
- HERE ("Function graph_aln is deprecated");
- return A;
-
-}
-
-void print_graph (CL_node *G, Sequence *S)
-{
- Alignment *A=NULL;
-
- if (S==NULL) S=Seq;
- A=seq2aln (Seq, A, 1);
- A=graph2aln (A,G, Seq);
- print_aln (A);
-}
-
-Alignment* graph2aln (Alignment *A, CL_node *G, Sequence *S)
-{
- int s, l, a;
- CL_node *Gi;
-
- /*Rewind G*/
- while ( G->p)G=G->p;
- while ( G->l)G=G->l;
-
- l=s=0;
- Gi=G;
- while (Gi){Gi=Gi->r;l++;}
- Gi=G;
- while (Gi){Gi=Gi->c;s++;}
-
- A=realloc_alignment (A, l+1);
-
-
- l=0;
- while (G)
- {
- Gi=G;
- s=0;
- while ( G!=NULL)
- {
-
- if ( G->res==-1)A->seq_al[s][l]='-';
- else if ( G->res==-2)A->seq_al[s][l]='*';
- else if ( G->res==-3)A->seq_al[s][l]='#';
- else if (G->res>=0)A->seq_al[s][l]=S->seq[G->seq][G->res];
-
- G=G->c;
- s++;
- }
- G=Gi->r;
- l++;
- }
-
-
-
- for ( a=0;a<s; a++)
- A->seq_al[a][l]='\0';
- A->len_aln=strlen (A->seq_al[0]);
- A->nseq=s;
-
-
- return A;
-}
-CL_node ***aln2graph (Alignment *A)
-{
- int a=0, b;
- static CL_node ***galn;
- CL_node *N, *iN, *pN;
- int res;
-
- if ( !galn)
- {
- galn=calloc ( A->nseq, sizeof (CL_node**));
- for ( a=0; a< A->nseq; a++)
- {
- galn[a]=calloc (A->len_aln, sizeof (CL_node*));
- }
- }
- pN=iN=NULL;
- N=declare_cl_nodes(-1, a);
-
-
- for ( a=0; a<A->nseq; a++)
- {
- iN=N;
- for (res=A->order[a][1], b=0; b<A->len_aln; b++)
- {
- if (b<A->len_aln-1)
- {
- N->r=declare_cl_nodes(-1, a);
- (N->r)->l=N;
- }
- if ( pN)
- {
- N->p=pN;
- pN->c=N;
- }
-
- N->seq=A->order[a][0];
- N->res=(is_gap(A->seq_al[a][b]))?-1:res++;
-
- if (N->res!=-1)galn[a][res-1]=N;
- if ( pN)
- {
- N->p=pN;
- pN->c=N;
- pN=pN->r;
- }
- N=N->r;
- }
- if ( a<A->nseq-1)iN->c=declare_cl_nodes(-1, a);
- pN=iN;
- N=iN->c;
- }
-
- return galn;
-}
-CL_node ***add_constraint2graph_aln (CL_node ***G, int s1, int r1, int s2, int r2)
-{
- CL_node *S, *E, *B;
- int d;
-
-
- S=G[s1][r1];
- E=G[s2][r2];
-
-
- d=get_node_distance (S,E);
- if (d<0){B=S;S=E;E=B;}
- d=(d<0)?-d:d;
-
-
- insert_gap_columns (E,d);
- shift_segment( S,d+1,d);
-
- return G;
-
-}
-
-
-CL_node *shift_segment ( CL_node *S, int segL, int shiftL)
-{
- int a;
- CL_node *E, *G;
-
-
- if ( !shiftL)return S;
-
- /*find segment coordinates*/
- for (E=S, a=1; a< segL; a++)E=E->r;
-
- /*Shift the gaps*/
-
- G=swap_gap_in_graph (S, E);
- for (a=1; a< shiftL; a++)swap_gap_in_graph (S, E);
-
- while (G!=E)G=remove_graph_gap_column (G);
- remove_graph_gap_column (E);
-
- return G;
-}
-
-int is_graph_gap_column(CL_node *S)
-{
- while (S->p)S=S->p;
-
- while (S)
- {
- if (S->res>=0)return 0;
- S=S->c;
- }
- return 1;
-}
-CL_node * remove_graph_gap_column (CL_node *S)
-{
- CL_node *R,*L, *P, *RV;
-
- RV=S->r;
- while (S->p)
- {
-
- S=S->p;
- }
-
- if ( !is_graph_gap_column (S))return RV;
-
-
-
- while (S)
- {
-
- R=S->r;
- L=S->l;
- P=S->p;
-
- if (L)L->r=S->r;
- if (R)R->l=S->l;
-
- P=S;
- S=S->c;
- vfree_cl_node (P);
- }
- return RV;
-}
-
-CL_node * swap_gap_in_graph ( CL_node*S, CL_node *E)
-{
- /*Moves gap AFTER End to BEFORE Start
- SxxxE-
- -xxxxx
- straightens the links in between
- */
- CL_node *G, *N, *iE, *iS, *SP, *SC, *SL;
-
-
- /*Preserve the E/S values*/
- iE=E;
- iS=S;
-
-
- /*prepare the parent/child links first*/
-
- SP=S->p;
- SC=S->c;
- SL=S->l;
-
- while ( S!=E->r)
- {
- N=S->r;
-
- S->p=N->p;
- if (N->p)(S->p)->c=S;
-
- S->c=N->c;
- if (N->c)(S->c)->p=S;
-
- S=S->r;
- }
-
- E=iE;
- S=iS;
-
- /*Remove the gap*/
- G=E->r;
- if ( G->res>=0)fprintf ( stderr, "\nERROR: NOT a GAP");
-
- E->r=G->r;
- if (E->r)(E->r)->l=E;
-
- /*insert the gap*/
-
- G->r=S;
- S->l=G;
-
- G->l=SL;
- if (SL)SL->r=G;
-
-
- G->p=SP;
- if (SP)SP->c=G;
-
- G->c=SC;
- if (SC)SC->p=G;
-
- return G;
-
-}
-
-CL_node * declare_cl_nodes ( int len, int seq)
-{
- static CL_node **N;
- CL_node *IN;
- static int Nlen;
- int a;
-
- if (len==-1)
- {
- IN=calloc ( 1, sizeof (CL_node));
- IN->res=-1;
- return IN;
- }
-
-
-
- if ( len>Nlen)
- {
- free (N);
- N=calloc (len, sizeof (CL_node*));
- }
-
- if ( len==0)return NULL;
-
- for (a=0; a<len; a++)N[a]=calloc ( 1, sizeof (CL_node));
- for (a=0; a<len; a++)
- {
- (N[a])->res=-1;
- (N[a])->seq=seq;
- if (a!=0)(N[a])->l=N[a-1];
- if (a!=len-1)(N[a])->r=N[a+1];
- }
-
- (N[0])->l=N[len-1];
- (N[len-1])->r=N[0];
-
- return N[0];
-}
-
-CL_node *insert_gap_columns (CL_node *S, int d)
-{
- CL_node *Gs,*Ge, *pGs, *Gi, *Si;
- int a;
-
- if ( d==0)return S;
-
- pGs=Gi=NULL;
- Si=S;
- while (S->p!=NULL)S=S->p;
-
- while (S!=NULL)
- {
- Gs=declare_cl_nodes(d, S->seq);
- Ge=Gs->l;
-
- Ge->r=S->r;
- if (Ge->r)(Ge->r)->l=Ge;
-
- Gs->l=S;
- S->r=Gs;
-
- if (pGs)
- {
- Gi=Gs;
- for (a=0; a< d; a++)
- {
- Gs->p=pGs;
- pGs->c=Gs;
- Gs=Gs->r;
- pGs=pGs->r;
- }
- pGs=Gi;
- }
- else
- {
- pGs=Gs;
- }
- S=S->c;
- }
- return Si;
-}
-
-int get_node_distance ( CL_node *S, CL_node *E)
-{
- int distance=0;
- CL_node *iS,*B;
- int swap=1;
-
- /*project the two points onto one sequence*/
- if (S->seq>E->seq){B=S;S=E;E=B;swap*=-1;}
- while (S->seq!=E->seq)S=S->c;
-
- /*Walk from E to S */
- iS=S;
- while ( iS->res<0 && iS->r!=NULL){iS=iS->r;}
- if (iS->res<0 || iS->res>E->res){B=S; S=E; E=B;swap*=-1;}
-
- while ( S!=E)
- {
- S=S->r;
- distance+=swap;
- }
- return distance;
-}
-
-
-
-
-
-
-
-
-
-int check_graph ( CL_node *S, char *string)
-{
- CL_node *iS;
- static int n;
- int lr;
-
- if ( S==NULL)S=Start;
- fprintf ( stderr, "\n\tGRAPH Check %s #%d\n",string, ++n);
- while ( S->p!=NULL)S=S->p;
- while ( S->l!=NULL)S=S->l;
- while ( S)
- {
- iS=S;
- lr=-1;
- while (iS)
- {
- if (iS->l && (iS->l)->seq!=iS->seq){fprintf ( stderr, "\n\t\tSEq pb");myexit(EXIT_FAILURE);}
- if (iS->free==1){fprintf ( stderr, "\n\t\tFree Node read");myexit(EXIT_FAILURE);}
- if (iS->res>0)
- {
- if (lr!=-1 && iS->res-lr!=1){fprintf ( stderr, "\n\t\tERROR: lost residues");myexit (EXIT_FAILURE);}
- lr=iS->res;
- }
- if ( iS->r && (iS->r)->l!=iS){fprintf ( stderr, "\n\t\tERROR: left != right: [%d %d][%d %d]", iS->seq, iS->res, (iS->l)->seq, (iS->r)->res);myexit (EXIT_FAILURE);}
- if ( iS->p && (iS->p)->c!=iS){fprintf ( stderr, "\n\t\tERROR: parent != child: [%d %d][%d %d]", iS->seq, iS->res, (iS->p)->seq, (iS->p)->res);myexit (EXIT_FAILURE);}
- if ( iS->c && (iS->c)->p!=iS){fprintf ( stderr, "\n\t\tERROR: parent != child: [%d %d][%d %d]", iS->seq, iS->res, (iS->c)->seq, (iS->c)->res);myexit (EXIT_FAILURE);}
- iS=iS->r;
- }
- S=S->c;
- }
- return 1;
-}
-
-CL_node * vfree_graph ( CL_node *S)
-{
- CL_node *Si;
-
- while ( S->p!=NULL)S=S->p;
- while ( S->l!=NULL)S=S->l;
-
- while ( S)
- {
- Si=S->c;
- while ( S)
- {
-
- S=S->r;
- if (S)vfree_cl_node (S->l);
- }
- S=Si;
- }
- return S;
-
-}
-CL_node *vfree_cl_node ( CL_node *N)
-{
- if ( N->free==1)crash("freeing free block");
- N->free=1;
- free (N);
- return N;
-}
-
-
-void light_nodes (CL_node *A, int va, CL_node*B, int vb, CL_node*C,int vc, char *string )
-{
- int ta=0, tb=0, tc=0;
-
- fprintf ( stderr, "\nCycle %d\n LIGHT NODE: %s", cycle,string);
- if ( A){ta=A->res; A->res=va;fprintf ( stderr, "\nA: seq %d res %d", A->seq, A->res);}
- if ( B){tb=B->res; B->res=vb;fprintf ( stderr, "\nB: seq %d res %d", B->seq, B->res);}
- if ( C){tc=C->res; C->res=vc;fprintf ( stderr, "\nC: seq %d res %d", C->seq, C->res);}
- print_graph (A, 0);
- if ( A){A->res=ta;}
- if ( B){B->res=tb;}
- if ( C){C->res=tc;}
-}
-int check_link (CL_node ***G, int s1, int r1, int s2, int r2)
-{
- CL_node *S;
- CL_node *E;
-
- S=G[s1][r1];
- E=G[s2][r2];
- while ( S->p)S=S->p;
- while ( S)
- {
- S=S->c;
- if ( S==E)return 1;
- }
- return 0;
-}
-/******************************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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