+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <strings.h>
-#include <string.h>
-#include <limits.h>
-#include <float.h>
-#include <assert.h>
-#include <math.h>
-#include <stdarg.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-#include "dp_lib_header.h"
-
-void free_pair_wise()
-{
- //Free static allocated memory
- free_proba_pair_wise();
-}
-
-/************************************************************************/
-/* */
-/* CONSTRAINT_LIST */
-/* */
-/* */
-/************************************************************************/
-int *** duplicate_residue_index (int ***r)
-{
- int a,b,c;
- int d1,d2,d3;
-
- int ***nr;
-
- d1=read_array_size_new(r);
- nr=vcalloc ( d1, sizeof (int**));
- for (a=0; a<d1; a++)
- {
- d2=read_array_size_new (r[a])-1;
- nr[a]=vcalloc ( d2+1, sizeof (int*));
- for (b=0; b<d2; b++)
- {
- d3=read_array_size_new (r[a][b]);
- for (c=0; c<d3; c++)nr[a][b][c]=r[a][b][c];
- }
- }
- return nr;
-}
-int *** declare_residue_index (Sequence *S)
-{
- int ***r;
- int a,b,c;
-
- if ( !S)return NULL;
- r=vcalloc ( S->nseq, sizeof (int**));
- for ( a=0; a<S->nseq; a++)
- {
- r[a]=vcalloc (S->len[a]+2, sizeof (int*));//The empty terminator makes a scan possible without knowing len
- for ( b=0; b<=S->len[a]; b++)
- {
- r[a][b]=vcalloc ( 1, sizeof (int));
- r[a][b][0]=1;
- }
- }
- return r;
-}
-
-Constraint_list * declare_constraint_list_simple ( Sequence *S)
-{
- return declare_constraint_list (S, NULL, NULL, 0, NULL, NULL);
-}
-
-Constraint_list * declare_constraint_list ( Sequence *S, char *name, int *L, int ne,FILE *fp, int **M)
- {
- Constraint_list *CL;
-
- CL=vcalloc (1, sizeof ( Constraint_list));
-
-
- CL->S=S;
- CL->M=M;
-
- if ( name!=NULL)
- {
- sprintf ( CL->list_name, "%s", name);
-
- }
- CL->cpu=1;
- CL->fp=fp;
- if (L)
- {
- HERE ("The USE of L is now Deprecated with Constraint Lists");
- exit (0);
- }
- CL->ne=ne;
- CL->entry_len=LIST_N_FIELDS;
- CL->el_size=sizeof (CLIST_TYPE);
- CL->matrices_list=declare_char(20,20);
-
-
- CL->weight_field=WE;
- if ( S)CL->seq_for_quadruplet=vcalloc ( S->nseq, sizeof (int));
- CL->Prot_Blast=vcalloc ( 1, sizeof ( Blast_param));
- CL->DNA_Blast=vcalloc ( 1, sizeof ( Blast_param));
- CL->Pdb_Blast=vcalloc ( 1, sizeof ( Blast_param));
- CL->TC=vcalloc (1, sizeof (TC_param));
-
- //New data structure
- CL->residue_index=declare_residue_index (S);
-
-
-
- return CL;
- }
-
-Constraint_list *free_constraint_list4lib_computation (Constraint_list *CL)
-{
- if (!CL)return NULL;
-
- free_arrayN(CL->residue_index, 3);
- free_int (CL->M, -1);
-
- vfree (CL);
- return CL;
-}
-Constraint_list *duplicate_constraint_list4lib_computation (Constraint_list *CL)
-{
- Constraint_list *SCL;
- SCL=vcalloc (1, sizeof ( Constraint_list));
- SCL[0]=CL[0];
- SCL->S=CL->S;
- SCL->RunName=CL->RunName;
-
- SCL->max_L_len=0;
- SCL->M=NULL;
- SCL->ne=0;
-
- return SCL;
-}
-Constraint_list *duplicate_constraint_list_soft (Constraint_list *CL)
-{
- /*Duplication that does not copy the long lists*/
- return copy_constraint_list (CL,SOFT_COPY);
-}
-Constraint_list *duplicate_constraint_list (Constraint_list *CL)
- {
- /*Duplicate everything in the constraint_list*/
- return copy_constraint_list (CL,HARD_COPY);
- }
-Constraint_list *copy_constraint_list (Constraint_list *CL, int mode)
- {
- Constraint_list *NCL;
- Sequence *S;
- int a, b;
-
-
-
- /*Sequences*/
-
-
- S=(mode==HARD_COPY)?duplicate_sequence (CL->S):CL->S;
-
-
- if (mode==HARD_COPY)
- NCL=declare_constraint_list (S, NULL, NULL,0, NULL, NULL);
- else
- {
- NCL=vcalloc ( 1, sizeof (Constraint_list));
- NCL[0]=CL[0];
- }
-
-
- NCL->copy_mode=mode;
- if (mode==SOFT_COPY)NCL->pCL=CL;
- NCL->S=S;
- /*master*/
- if (mode==HARD_COPY && CL->master)
- {NCL->master=vcalloc ( S->nseq, sizeof(int));
- for ( a=0; a< S->nseq; a++)
- NCL->master[a]=CL->master[a];
- }
- else if (mode==SOFT_COPY)
- {
- NCL->seq_for_quadruplet=CL->seq_for_quadruplet;
- }
- NCL->o2a_byte=CL->o2a_byte;
-
- /*struc List*/
- NCL->STRUC_LIST=(mode==HARD_COPY)?duplicate_sequence (CL->STRUC_LIST):CL->STRUC_LIST;
- sprintf ( NCL->align_pdb_param_file, "%s", CL->align_pdb_param_file);
- sprintf ( NCL->align_pdb_hasch_mode, "%s", CL->align_pdb_hasch_mode);
-
-
- NCL->W=(mode==HARD_COPY)?duplicate_weights (CL->W):CL->W;
- NCL->DM=(mode==HARD_COPY)?duplicate_distance_matrix (CL->DM):CL->DM;
- NCL->ktupDM=(mode==HARD_COPY)?duplicate_distance_matrix (CL->ktupDM):CL->ktupDM;
- NCL->RunName=CL->RunName;
-
- if ( mode==HARD_COPY && CL->translation){NCL->translation=vcalloc ((CL->S)->nseq, sizeof (int)); for ( a=0; a< (CL->S)->nseq; a++)NCL->translation[a]=CL->translation[a];}
- else{NCL->translation=CL->translation;}
-
- NCL->out_aln_format=(mode==HARD_COPY)?duplicate_char (CL->out_aln_format, -1, -1):CL->out_aln_format;
- NCL->n_out_aln_format=CL->n_out_aln_format;
-
- /*Packing Sequence: To use with domain analysis*/
- NCL->packed_seq_lu=(mode==HARD_COPY)?duplicate_int (CL->packed_seq_lu, -1, -1):CL->packed_seq_lu;
- /*DATA*/
- if (CL->fp)(mode==HARD_COPY)?NCL->fp=vtmpfile():CL->fp;
-
- if ( mode==HARD_COPY)
- {
- NCL->residue_index=duplicate_residue_index (NCL->residue_index);
- }
- else NCL->residue_index=CL->residue_index;
-
-
- if ( mode==HARD_COPY)
- {
- NCL->M=copy_int ( CL->M,NCL->M,-1, -1);
- }
- else
- NCL->M=CL->M;
-
-
- /*List Information*/
- NCL->ne=CL->ne;
- sprintf ( NCL->list_name, "%s", CL->list_name);
- NCL->entry_len=CL->entry_len;
- NCL->el_size=CL->el_size;
-
- /*Normalisation information*/
- NCL->filter_lib=CL->filter_lib;
- NCL->normalise=CL->normalise;
- NCL->overweight=CL->overweight;
- NCL->max_ext_value=CL->max_ext_value;
- NCL->max_value=CL->max_value;
-
- /*Pair wise alignment method*/
- NCL->pw_parameters_set=CL->pw_parameters_set;
- NCL->gop=CL->gop;
- NCL->f_gop=CL->f_gop;
- NCL->gep=CL->gep;
- NCL->f_gep=CL->f_gep;
-
- NCL->nomatch=CL->nomatch;
-
- NCL->TG_MODE=CL->TG_MODE;
- NCL->F_TG_MODE=CL->F_TG_MODE;
-
- sprintf ( NCL->dp_mode, "%s", CL->dp_mode);
- NCL->maximise=CL->maximise;
- sprintf ( NCL->matrix_for_aa_group, "%s", CL->matrix_for_aa_group);
- sprintf ( NCL->method_matrix, "%s", CL->method_matrix);
-
- NCL->diagonal_threshold=CL->diagonal_threshold;
- NCL->ktup=CL->ktup;
-
- NCL->use_fragments=CL->use_fragments;
- NCL->fasta_step=CL->fasta_step;
- NCL->lalign_n_top=CL->lalign_n_top;
- NCL->sw_min_dist=CL->sw_min_dist;
- NCL->matrices_list=(mode==HARD_COPY)?duplicate_char (CL->matrices_list, -1, -1):CL->matrices_list;
- NCL->n_matrices=CL->n_matrices;
-
- sprintf (NCL->distance_matrix_mode, "%s", CL->distance_matrix_mode);
- sprintf (NCL->distance_matrix_sim_mode, "%s", CL->distance_matrix_sim_mode);
-
- sprintf (NCL->tree_mode, "%s", CL->tree_mode);
- NCL->tree_aln=(mode==HARD_COPY)?copy_aln (CL->tree_aln, NULL):CL->tree_aln;
- /*Functions used for dynamic programming and Evaluation*/
- NCL->no_overaln=CL->no_overaln;
- NCL->profile_mode=CL->profile_mode;
- sprintf ( NCL->profile_comparison, "%s",CL->profile_comparison);
- NCL->get_dp_cost=CL->get_dp_cost;
- NCL->evaluate_residue_pair=CL->evaluate_residue_pair;
- NCL->pair_wise=CL->pair_wise;
-
- NCL->weight_field=CL->weight_field;
- NCL->max_n_pair=CL->max_n_pair;
-
- /*threading parameters*/
- NCL->Prot_Blast=(mode==HARD_COPY)?duplicate_blast_param ( CL->Prot_Blast):CL->Prot_Blast;
- NCL->DNA_Blast =(mode==HARD_COPY)?duplicate_blast_param ( CL->DNA_Blast):CL->DNA_Blast;
- NCL->Pdb_Blast =(mode==HARD_COPY)?duplicate_blast_param ( CL->Pdb_Blast):CL->Pdb_Blast;
- NCL->TC =(mode==HARD_COPY)?duplicate_TC_param ( CL->TC):CL->TC;
-
- /*Split parameters*/
- NCL->split=CL->split;
- NCL->split_nseq_thres= CL->split_nseq_thres;
- NCL->split_score_thres= CL->split_score_thres;
- /*Structural status*/
- NCL->check_pdb_status=CL->check_pdb_status;
- /*log*/
- sprintf ( NCL->method_log, "%s",CL->method_log);
- sprintf ( NCL->evaluate_mode, "%s",CL->evaluate_mode);
- /* Gene Prediction*/
- sprintf ( NCL->genepred_score, "%s",CL->genepred_score);
-
- /*Parameters for domain extraction*/
- NCL->moca=(mode==HARD_COPY)?duplicate_moca ( CL->moca):CL->moca;
-
-
-
- /*Functions for hiding forbiden pairs of residues*/
- /* Copy only for soft_copy*/
- if (mode==SOFT_COPY)
- {
- NCL->forbiden_pair_list=CL->forbiden_pair_list;
- }
- /*extention properties:*/
- NCL->nseq_for_quadruplet=CL->nseq_for_quadruplet;
- if (mode==HARD_COPY && CL->seq_for_quadruplet)
- {NCL->seq_for_quadruplet=vcalloc ( S->nseq, sizeof(int));
- for ( a=0; a< S->nseq; a++)
- NCL->seq_for_quadruplet[a]=CL->seq_for_quadruplet[a];
- }
- else if (mode==SOFT_COPY)
- {
- NCL->seq_for_quadruplet=CL->seq_for_quadruplet;
- }
-
- /*extention properties: Do only a soft copy*/
- /* Not To be copied yet */
- if ( mode==SOFT_COPY)
- {
- NCL->extend_jit=CL->extend_jit;
- NCL->extend_threshold=CL->extend_threshold;
- sprintf ( NCL->extend_clean_mode, "%s", CL->extend_clean_mode);
- sprintf ( NCL->extend_compact_mode, "%s", CL->extend_compact_mode);
- }
-
- /*Lookup table parameteres*/
- NCL->chunk= CL->chunk;
- /* Do NOT copy NCL->seq_indexed, NCL->start_index, NCL->max_L_len, NCL->chunk*/
- /*
- if ( mode==SOFT_COPY)
- {
- NCL->seq_indexed=CL->seq_indexed;
- NCL->start_index=CL->start_index;
- NCL->end_index=CL->start_index;
- NCL->max_L_len=CL->max_L_len;
- }
- */
- /*PDB STRUCTURE ALIGNMENTS*/
- /* Do only a soft copy */
- if ( mode==SOFT_COPY)
- {
- NCL->T=CL->T;
- }
- /*MISC*/
- NCL->cpu=CL->cpu;
- NCL->local_stderr=CL->local_stderr;
- sprintf (NCL->multi_thread, "%s", CL->multi_thread);
-
- return NCL;
- }
-Constraint_list *free_constraint_list_full (Constraint_list *CL)
-{
- free_sequence (free_constraint_list (CL), -1);
- return NULL;
-}
-Sequence *free_constraint_list (Constraint_list *CL)
- {
- Sequence *S;
- int a, b;
- Constraint_list *pCL;
-
-
- /*Prepare the selective freeing of the CL data structure:
- If the CL has been obtained from copy, every pointer that is identical to the parent CL (CL->pCL)
- will not be saved.
- */
-
-
- if ( !CL)return NULL;
- else S=CL->S;
-
- if ( CL->copy_mode==SOFT_COPY && !CL->pCL)
- {vfree(CL); return S;}
- else if ( CL->copy_mode==SOFT_COPY)
- {
-
- pCL=CL->pCL;
- CL->residue_index=NULL;
-
- if ( CL->M ==pCL->M )CL->M=NULL;
-
- if (CL->start_index ==pCL->start_index )CL->start_index=NULL;
- if (CL->end_index ==pCL->end_index )CL->end_index=NULL;
-
- if ( CL->fp ==pCL->fp )CL->fp=NULL;
- if ( CL->matrices_list ==pCL->matrices_list )CL->matrices_list=NULL;
-
-
- if ( CL->STRUC_LIST ==pCL->STRUC_LIST )CL->STRUC_LIST=NULL;
- if ( CL->W ==pCL->W )CL->W=NULL;
- if ( CL->DM ==pCL->DM )CL->DM=NULL;
- if ( CL->ktupDM ==pCL->ktupDM )CL->ktupDM=NULL;
-
-
- if ( CL->translation ==pCL->translation )CL->translation=NULL;
- if ( CL->moca ==pCL->moca )CL->moca=NULL;
- if ( CL->Prot_Blast ==pCL->Prot_Blast )CL->Prot_Blast=NULL;
- if ( CL->DNA_Blast ==pCL->DNA_Blast )CL->DNA_Blast=NULL;
- if ( CL->Pdb_Blast ==pCL->Pdb_Blast )CL->Pdb_Blast=NULL;
- if ( CL->seq_for_quadruplet ==pCL->seq_for_quadruplet )CL->seq_for_quadruplet=NULL;
- if ( CL->TC ==pCL->TC )CL->TC=NULL;
-
- }
-
-
- /*End of selective freeing of the CL data structure*/
-
-
-
- if ( CL->residue_index)free_arrayN(CL->residue_index, 3);
-
- if ( CL->M)free_int (CL->M, -1);
- if ( CL->fp)vfclose (CL->fp);
- if ( CL->matrices_list)free_char(CL->matrices_list,-1);
-
-
- if ( CL->start_index)free_int ( CL->start_index,-1);
- if ( CL->end_index)free_int ( CL->end_index,-1);
-
-
-
-
- if ( CL->STRUC_LIST)free_sequence ( CL->STRUC_LIST, (CL->STRUC_LIST)->nseq);
- if ( CL->W)free_weights (CL->W);
-
- CL->DM=free_distance_matrix (CL->DM);
- CL->ktupDM=free_distance_matrix (CL->ktupDM);
-
- if ( CL->translation)vfree(CL->translation);
- if ( CL->moca)free_moca (CL->moca);
- if ( CL->Prot_Blast)free_blast_param ( CL->Prot_Blast);
- if ( CL->DNA_Blast) free_blast_param ( CL->DNA_Blast);
- if ( CL->Pdb_Blast) free_blast_param ( CL->Pdb_Blast);
- if ( CL->TC) free_TC_param ( CL->TC);
-
- if (CL->seq_for_quadruplet)vfree (CL->seq_for_quadruplet);
-
- vfree(CL);
- return S;
- }
-
-Distance_matrix * free_distance_matrix ( Distance_matrix *DM)
-{
- if (!DM)return NULL;
- free_int ( DM->similarity_matrix,-1);
- free_int ( DM->distance_matrix,-1);
- free_int ( DM->score_similarity_matrix,-1);
- vfree (DM);
- return NULL;
-}
-Distance_matrix * duplicate_distance_matrix ( Distance_matrix *DMin)
-{
- Distance_matrix *DM;
- if (!DMin) return NULL;
-
- DM=vcalloc ( 1, sizeof (Distance_matrix));
- DM->similarity_matrix=duplicate_int ( DMin->similarity_matrix, -1, -1);
- DM->distance_matrix=duplicate_int ( DMin->distance_matrix, -1, -1);
- DM->score_similarity_matrix=duplicate_int ( DMin->score_similarity_matrix, -1, -1);
- return DM;
-}
-
-/************************************************************************/
-/* */
-/* MOCA Functions */
-/* */
-/* */
-/************************************************************************/
-Moca * duplicate_moca ( Moca *m)
- {
- Moca *nm;
-
- if ( m==NULL)return m;
-
- nm=vcalloc ( 1, sizeof (Moca));
-
- nm->moca_scale=m->moca_scale;
- nm->evaluate_domain=m->evaluate_domain;
- nm->moca_threshold=m->moca_threshold;
- nm->cache_cl_with_domain=m->cache_cl_with_domain;
- if ( m->forbiden_residues)nm->forbiden_residues=copy_int (m->forbiden_residues,nm->forbiden_residues, -1, -1);
- nm->make_nol_aln=m->make_nol_aln;
-
-
- return nm;
- }
-Moca * free_moca ( Moca *m)
- {
- if ( m->forbiden_residues)free_int ( m->forbiden_residues, -1);
- vfree ( m);
- return NULL;
- }
-/************************************************************************/
-/* */
-/* TC_param Functions */
-/* */
-/* */
-/************************************************************************/
-TC_param * duplicate_TC_param ( TC_param*B)
-{
- TC_param *N;
- N=vcalloc (1, sizeof ( TC_param));
- memcpy(B, N, sizeof(TC_param));
- return N;
- }
-TC_param * free_TC_param ( TC_param*B)
-{
- vfree (B);
- return NULL;
-}
-/************************************************************************/
-/* */
-/* Blast_param Functions */
-/* */
-/* */
-/************************************************************************/
-Blast_param * duplicate_blast_param ( Blast_param*B)
-{
- Blast_param *N;
- N=vcalloc (1, sizeof ( Blast_param));
- sprintf ( N->blast_server, "%s", B->blast_server);
- sprintf ( N->db, "%s", B->db);
- N->min_id=B->min_id;
- N->max_id=B->min_id;
- N->min_cov=B->min_cov;
- return N;
-}
-Blast_param * free_blast_param ( Blast_param*B)
-{
- vfree (B);
- return NULL;
-}
-
-/************************************************************************/
-/* */
-/* PDB Functions */
-/* */
-/* */
-/************************************************************************/
-Structure* declare_structure ( int n, char **array)
- {
- Structure *S;
- int a;
-
- S=vcalloc (1, sizeof (Structure));
- S->n_fields=1;
- S->nseq=n;
-
- S->struc=vcalloc ( n, sizeof (int**));
- S->len=vcalloc ( n, sizeof (int));
- for ( a=0; a< n; a++)
- {
- S->len[a]=strlen(array[a]);
- S->struc[a]=declare_int ( strlen ( array[a])+2, 1);
- }
- return S;
- }
-
-Structure *extend_structure ( Structure *S)
- {
- int a, b;
-
-
- for ( a=0; a< S->nseq; a++)
- {
- for ( b=0; b< S->len[a]; b++)
- S->struc[a][b]=vrealloc ( S->struc[a][b],( S->n_fields+1)*sizeof (int));
- }
- S->n_fields++;
- return S;
- }
-Sequence * reset_sequence_len (Sequence *S)
-{
- int min,max,a,l;
-
- if ( !S || !S->nseq)return 0;
- max=min=strlen (S->seq[0]);
- for (a=0; a<S->nseq; a++)
- {
- l=strlen (S->seq[a]);
- min=MIN(l,min);
- max=MAX(l,max);
- S->len[a]=l;
- }
- S->max_len=max;
- S->min_len=min;
- return S;
-}
-Sequence * declare_sequence ( int min, int max, int nseq)
- {
- Sequence *LS;
-
-
-
- LS=vcalloc (1, sizeof ( Sequence));
-
- LS->seq_comment=declare_char ( nseq,COMMENT_SIZE);
- LS->aln_comment=declare_char ( nseq,COMMENT_SIZE);
-
- LS->file=declare_char( nseq,STRING+1);
- LS->seq=declare_char ( nseq, max+1);
- LS->name=declare_char( nseq,MAXNAMES+1);
-
- LS->len=vcalloc ( nseq, sizeof (int));
- LS->max_len=max;
- LS->min_len=min;
- LS->nseq=nseq;
- LS->max_nseq=nseq;
- LS->type=vcalloc(30, sizeof (char));
- LS->T=declare_arrayN(2, sizeof (Template), nseq, 1);
-
-
- LS->dc=declare_int (nseq, 2);
- return LS;
- }
-Sequence * realloc_sequence (Sequence *OUT, int new_nseq, int max_len)
- {
-
-
- if ( new_nseq<OUT->max_nseq)return OUT;
-
- OUT->min_len =MIN(OUT->min_len,max_len);
- OUT->max_len =MAX(OUT->max_len,max_len);
- OUT->seq_comment =new_realloc_char ( OUT->seq_comment, new_nseq,COMMENT_SIZE);
- OUT->aln_comment =new_realloc_char ( OUT->aln_comment, new_nseq,COMMENT_SIZE);
-
- OUT->seq =new_realloc_char ( OUT->seq, new_nseq,OUT->max_len+1);
- OUT->name =new_realloc_char ( OUT->name, new_nseq,MAXNAMES+1);
-
-
- OUT->file =new_realloc_char ( OUT->file, new_nseq,STRING+1);
- OUT->len =vrealloc ( OUT->len, (new_nseq+1)*sizeof (int));
-
- OUT->T=(Template**)realloc_arrayN (2, (void **)OUT->T,sizeof (Template), new_nseq, 1);
- OUT->dc=(int **)realloc_arrayN (2, (void **)OUT->dc,sizeof (int), new_nseq, 2);
-
- OUT->max_nseq=new_nseq;
- return OUT;
- }
-
-Sequence * duplicate_sequence (Sequence *S )
- {
- Sequence *LS;
- int a, b;
-
-
- if (S==NULL)return S;
- LS=declare_sequence (S->min_len, S->max_len, S->nseq);
- for (b=0, a=0; a<S->nseq; a++)
- {
- if (S->seq && S->seq[a])
- {
-
- sprintf ( LS->file[b], "%s", S->file[a]);
- if ( S->seq_comment && S->seq_comment[a])sprintf ( LS->seq_comment[b], "%s", S->seq_comment[a]);
- if ( S->aln_comment && S->aln_comment[a])sprintf ( LS->aln_comment[b], "%s", S->aln_comment[a]);
- if ( S->seq && S->seq[a])sprintf ( LS->seq[b], "%s", S->seq[a]);
- if ( S->name&& S->name[a])sprintf ( LS->name[b], "%s", S->name[a]);
- LS->dc[b][0]=S->dc[a][0];
- LS->dc[b][1]=S->dc[a][1];
- LS->len[b]=S->len[a];
- LS->T[b][0]=S->T[a][0];
-
- b++;
-
- }
- }
-
- LS->max_len=S->max_len;
- LS->min_len=S->min_len;
- LS->nseq=b;
-
- if (S->W)LS->W=duplicate_weights (S->W);
- sprintf ( LS->type, "%s", S->type);
- sprintf ( LS->template_file, "%s", S->template_file);
- LS->max_nseq=S->nseq;
-
- return LS;
- }
-
-void free_sequence ( Sequence *LS, int nseq)
- {
-
-
- if ( !LS) return;
-
-
- free_char ( LS->file, -1);
- free_char ( LS->seq_comment, -1);
- free_char ( LS->aln_comment, -1);
- free_char ( LS->seq, -1);
- free_char ( LS->name,-1);
- free_int (LS->dc, -1);
- free_arrayN((void*)LS->T, 2);
- vfree (LS->type);
- vfree (LS->len);
- free_weights (LS->W);
-
- vfree (LS);
-
- }
-/************************************************************************/
-/* */
-/* Weights Functions */
-/* */
-/* */
-/************************************************************************/
-Weights* declare_weights ( int nseq)
- {
- Weights *W;
-
- W=vcalloc ( 1, sizeof ( Weights));
- W->comments=vcalloc ( 1000, sizeof (char));
- W->nseq=nseq;
- W->mode=vcalloc (FILENAMELEN, sizeof (char));
- W->seq_name= declare_char ( W->nseq*2, 200);
- W->PW_SD=declare_float ( W->nseq, W->nseq);
- W->PW_ID=declare_float ( W->nseq, W->nseq);
- W->SEQ_W=vcalloc ( W->nseq, sizeof ( float));
- return W;
- }
-Weights* duplicate_weights (Weights *W)
- {
- Weights *NW;
- int a, b, c;
-
- NW=declare_weights (W->nseq);
- sprintf ( NW->comments, "%s", W->comments);
- sprintf ( NW->mode, "%s", W->mode);
- for (a=0, c=0; a< W->nseq; a++)
- {
- if ( W->seq_name[a])
- {
- sprintf ( NW->seq_name[c], "%s", W->seq_name[a]);
- NW->SEQ_W[c]=W->SEQ_W[a];
- for(b=0; b< W->nseq; b++)
- {
- NW->PW_SD[c][b]=W->PW_SD[a][b];
- NW->PW_ID[c][b]=W->PW_ID[a][b];
- }
- c++;
- }
- }
- return NW;
- }
-Weights* free_weights ( Weights* W)
- {
-
- if ( !W)return NULL;
-
- vfree(W->comments);
-
-
- vfree(W->mode);
-
- free_char(W->seq_name, -1);
- free_float(W->PW_SD,-1);
- free_float(W->PW_ID, -1);
- vfree(W->SEQ_W);
- vfree(W);
- return NULL;
- }
-
-
-Alignment* copy_aln ( Alignment *A, Alignment *B)
- {
- int a, b;
- int nnseq;
- int nlen;
- /* c[100]=10;*/
-
-
-
- if ( A==NULL){free_aln(B); return NULL;}
-
- nnseq=MAX(A->nseq, A->max_n_seq);
- nlen=A->len_aln+1;
- if (B)
- B=realloc_alignment2 (B, nnseq, nlen);
- else
- B=declare_aln2 (nnseq, nlen);
- B->S=A->S;
-
-
- /*SIZES*/
- B->max_len=A->max_len;
- B->min_len=A->min_len;
- B->declared_len=nlen;
- B->max_n_seq=nnseq;
-
- B->nseq=A->nseq;
- B->len_aln=A->len_aln;
-
-
-/*sequence Information*/
- if ( A->generic_comment)
- {
- vfree(B->generic_comment);
- B->generic_comment=vcalloc (strlen(A->generic_comment)+1, sizeof (char));
- sprintf ( B->generic_comment, "%s", A->generic_comment);
- }
- if ( (A->S)==NULL){vfree (B->len); B->len=vcalloc ( A->max_n_seq, sizeof (int));}
- ga_memcpy_int ( A->len, B->len, B->nseq);
-
- B->seq_comment=copy_char ( A->seq_comment, B->seq_comment, -1,-1);
- B->aln_comment=copy_char ( A->aln_comment, B->aln_comment, -1,-1);
-
- B->name=copy_char ( A->name, B->name, -1,-1);
-
- B->file=copy_char ( A->file, B->file, -1,-1);
- B->tree_order=copy_char ( A->tree_order, B->tree_order, -1,-1);
- B->expanded_order=A->expanded_order;
- free_char ( B->seq_al, -1);
- B->seq_al=declare_char(B->max_n_seq, B->declared_len);
- // HERE ("A: MAX_NSEQ=%d %d %d %d",B->nseq, B->max_n_seq, B->declared_len, B->len_aln);
- // HERE ("B: MAX_NSEQ=%d %d %d %d",A->nseq, A->max_n_seq, A->declared_len, A->len_aln);
- for ( a=0; a< nnseq; a++)
- {
- if (A->seq_al[a])
- {
- for ( b=0; b< A->len_aln; b++)
- B->seq_al[a][b]=A->seq_al[a][b];
- }
- }
-
-
-
- B->order=copy_int ( A->order, B->order, -1, -1);
- B->S=A->S;
- if (A->seq_cache)
- {
- B->seq_cache=copy_int ( A->seq_cache, B->seq_cache,-1,-1);
- }
-
- if (A->cdna_cache)
- {
- B->cdna_cache=copy_int ( A->cdna_cache, B->cdna_cache,-1,-1);
- }
-
- B->P=copy_profile (A->P);
-
- B->Dp_result=A->Dp_result;
-
-/*Score*/
-
- if ( (A->S)==NULL){vfree (B->score_seq); B->score_seq=vcalloc ( A->max_n_seq, sizeof (int));}
- ga_memcpy_int( A->score_seq,B->score_seq,B->nseq);
- B->score_res=A->score_res;
-
- B->score_aln=A->score_aln;
- B->score=A->score;
- B->ibit=A->ibit;
- B->cpu=A->cpu;
- B->finished=A->finished;
-
-/*Output Options*/
- B->output_res_num=A->output_res_num;
- B->residue_case=A->residue_case;
- B->expand=A->expand;
-
- B->CL=A->CL;
- B->random_tag=A->random_tag;
-
-/*Make the function Recursive */
- if ( A->A)
- {
- B->A=copy_aln (A->A, NULL);
- }
- else B->A=NULL;
-
- return B;
- }
-
-Alignment* shrink_aln ( Alignment *A, int nseq, int *list)
- {
- Alignment *B=NULL;
- int a,seq;
-
- B=copy_aln (A, B);
- for ( a=0; a< nseq; a++)
- {
- seq=list[a];
- sprintf ( A->seq_comment[a], "%s",B->seq_comment[seq]);
- sprintf ( A->aln_comment[a], "%s",B->aln_comment[seq]);
-
- sprintf ( A->seq_al [a], "%s",B->seq_al [seq]);
- A->order[a][0]=B->order[seq][0];
- A->order[a][1]=B->order[seq][1];
- A->order[a][2]=B->order[seq][2];
- A->order[a][3]=B->order[seq][3];
- A->order[a][4]=B->order[seq][4];
-
- A->score_seq[a]=B->score_seq[seq];
- A->len[a]=B->len[seq];
- }
- A->nseq=nseq;
- A->len_aln=strlen (A->seq_al[0]);
- free_aln (B);
- return A;
- }
-Alignment* extract_sub_aln2 ( Alignment *B, int ns, char **ls)
- {
- int *list;
- Alignment *A;
-
- list=name_array2index_array(ls, ns, B->name, B->nseq);
- A=extract_sub_aln ( B,ns, list);
- vfree (list);
- return A;
- }
-Alignment* extract_sub_aln ( Alignment *B, int nseq, int *list)
- {
- Alignment *A=NULL;
- int a,b,n,seq;
-
- A=declare_aln2(nseq, B->len_aln+1);
- for ( n=0,a=0; a< nseq; a++)
- {
- seq=list[a];
- if ( seq==-1)continue;
- else n++;
- sprintf ( A->seq_comment[a], "%s",B->seq_comment[seq]);
- sprintf ( A->aln_comment[a], "%s",B->aln_comment[seq]);
- sprintf ( A->name[a], "%s",B->name[seq]);
-
-
- for (b=0; b<=B->len_aln; b++)A->seq_al [a][b]=B->seq_al [seq][b];
- A->order[a][0]=B->order[seq][0];
- A->order[a][1]=B->order[seq][1];
- A->order[a][2]=B->order[seq][2];
- A->order[a][3]=B->order[seq][3];
- A->order[a][4]=B->order[seq][4];
-
- A->score_seq[a]=B->score_seq[seq];
- A->len[a]=B->len[seq];
- }
- A->nseq=n;
- A->len_aln=B->len_aln;
- return A;
- }
-
-Alignment *declare_aln2 ( int nseq, int len)
- {
- Sequence *S;
- Alignment *A;
-
- S=vcalloc ( 1, sizeof ( Sequence));
- S->nseq=nseq;
- S->max_len=len;
-
- A=declare_aln (S);
- A->S=NULL;
- vfree(S);
- return A;
- }
-
-
-
-Alignment *declare_aln ( Sequence *S){return declare_Alignment(S);}
-
-Alignment *declare_Alignment ( Sequence *S)
- {
- Alignment *LA;
- int a;
-
- /*ordre:
- [x][0]= which is the xth seq of aln
- [x][1]= how many deleted residues before the first one
- */
-
-
- LA=vcalloc (1, sizeof ( Alignment));
- aln_stack (LA, DECLARE_ALN);
- if ( S==NULL)
- {
- LA->declared_len=MAX_LEN_ALN;
- LA->max_n_seq=MAX_N_SEQ;
- }
- else
- {
- LA->declared_len=2*S->max_len+1;
- LA->max_n_seq=S->nseq+1;
- }
- LA->S=S;
-
-
- LA->seq_comment=declare_char (LA->max_n_seq, COMMENT_SIZE);
- LA->aln_comment=declare_char (LA->max_n_seq, COMMENT_SIZE);
-
-
- LA->seq_al=declare_char ( LA->max_n_seq,LA->declared_len );
- LA->name=declare_char (LA->max_n_seq, MAXNAMES+1);
-
-
- LA->file=declare_char (LA->max_n_seq, STRING);
- LA->tree_order=declare_char (LA->max_n_seq, STRING);
- LA->order= declare_int (LA->max_n_seq , 5);
- //order[a][0]: sequence index in S
- //order[a][1]: offset of the sequence
- //order[a][2]: used by sw_gotoh_pair_wise
- //order[a][3]: used by sw_gotoh_pair_wise
- //order[a][4]: weight, -1
- LA->score_seq= vcalloc (LA->max_n_seq, sizeof (int));
-
- for ( a=0; a< LA->max_n_seq; a++)LA->order[a][0]=a;
-
- LA->len_aln=0;
- LA->score_aln=0;
- LA->len=vcalloc (LA->max_n_seq, sizeof (int));
-
- if (S && S->name)for ( a=0; a<S->nseq; a++)
- {
- sprintf ( LA->name[a], "%s", S->name[a]);
-
- }
-
- return LA;
-
- }
-Alignment * realloc_aln ( Alignment *A, int new_len){return realloc_alignment(A, new_len);}
-Alignment * realloc_alignment ( Alignment *A, int new_len)
- {
- if (A==NULL)A=declare_Alignment (NULL);
-
- return realloc_alignment2( A, A->max_n_seq,new_len);
- }
-
-Alignment * realloc_aln2 ( Alignment *A, int n_nseq, int n_len){return realloc_alignment2(A, n_nseq, n_len);}
-
-
-
-Alignment * realloc_alignment2 ( Alignment *A, int n_nseq, int n_len)
- {
- int a;
- int len, nseq;
- int delta_len, delta_nseq;
-
- if ( A==NULL) A=declare_Alignment(NULL);
-
- n_len++;
- n_nseq++;
-
- len=A->declared_len;
- nseq=A->max_n_seq;
-
- n_len=MAX(len, n_len);
- n_nseq=MAX(nseq,n_nseq);
- delta_nseq=MAX(0,n_nseq-nseq);
- delta_len =MAX(0,n_len-len);
-
- if ( delta_nseq<=0 && delta_len<=0)return A;
-
-
- else
- {
- A->len =vrealloc( A->len , sizeof (int)*n_nseq);
- for (a=nseq; a< n_nseq; a++)A->len[a]=0;
-
- A->declared_len =n_len;
- A->max_n_seq =n_nseq;
-
-
- A->seq_comment=new_realloc_char ( A->seq_comment, n_nseq, -1);
- A->aln_comment=new_realloc_char ( A->aln_comment, n_nseq, -1);
-
- A->name =new_realloc_char ( A->name, n_nseq, -1);
-
-
- A->file =new_realloc_char ( A->file, n_nseq, -1);
-
- A->tree_order =new_realloc_char ( A->tree_order, n_nseq, -1);
- A->seq_al =new_realloc_char ( A->seq_al, n_nseq, n_len);
- A->order =new_realloc_int ( A->order, n_nseq, -1);
-
- if ( A->seq_cache) A->seq_cache=new_realloc_int ( A->seq_cache, n_nseq,n_len);
- if ( A->cdna_cache)A->cdna_cache=new_realloc_int ( A->cdna_cache, n_nseq,n_len);
-
-
- A->score_seq =vrealloc( A->score_seq, sizeof (int)*(n_nseq));
- for ( a=nseq; a< n_nseq; a++)A->score_seq[a]=0;
-
-
-
- }
- return A;
- }
-
-
-long aln_stack (Alignment *A, int mode)
-{
- static long *list;
- static int size;
- static int max_size;
-
-
- if (A==NULL) return 0;
- else if ( mode==DECLARE_ALN)
- {
- if ( size==max_size)
- {
- max_size+=1000;
- list=vrealloc (list, max_size*sizeof (long));
- }
- list[size++]=(long)A;
- return 0;
- }
- else if (mode==FREE_ALN)
- {
- int a, b;
- for (a=0; a<size; a++)
- {
- if (list[a]==(long)A)
- {
- for (b=a+1; b<size;b++)
- {
- list[b-1]=list[b];
- }
- list[b-1]=0;
- size--;
- return 1;
- }
- }
- return 0;
- }
- else if ( mode==EXTRACT_ALN)
- {
- return list[size--];
- }
- else
- {
- printf_exit (EXIT_FAILURE, stderr, "ERROR: Unknown mode for aln_stack");
- return 0;
- }
-}
-
-Sequence* free_aln ( Alignment *LA){ return free_Alignment(LA);}
-Alignment *free_data_in_aln (Alignment *A)
-{
- //Frees only the sequence data (keeps profile information)
- A->seq_al=free_char (A->seq_al, -1);
- A->seq_comment=free_char (A->seq_comment, -1);
- A->aln_comment=free_char (A->aln_comment, -1);
- A->name=free_char (A->name, -1);
- A->expanded_order=free_char (A->expanded_order, -1);
-
- A->order=free_int (A->order, -1);
- A->seq_cache=free_int (A->seq_cache, -1);
- A->cdna_cache=free_int (A->cdna_cache, -1);
- A->score_res=free_int (A->score_res, -1);
- free_sequence (A->S, -1);
- A->S=NULL;
- return A;
-
-}
-Sequence* free_Alignment ( Alignment *LA)
- {
- /* Does not free the A->S field (sequences of A)*/
-
- Sequence *S;
- //aln_stack checks the alignment has not already been freed
- if ( LA==NULL || !aln_stack(LA,FREE_ALN)){return NULL;}
-
- S=LA->S;
- free_char ( LA->file, -1);
- free_char ( LA->seq_al, -1);
- free_int ( LA->seq_cache, -1);
- free_int ( LA->cdna_cache, -1);
- free_char ( LA->name,-1);
-
- free_char ( LA->tree_order,-1);
- vfree ( LA->generic_comment);
- free_char ( LA->seq_comment, -1);
- free_char ( LA->aln_comment, -1);
-
- free_int ( LA->order, -1);
-
- vfree ( LA->score_seq);
- vfree ( LA->len);
-
- free_profile (LA->P);
- if ( LA->A){free_Alignment (LA->A);LA->A=NULL;}
-
-
- vfree ( LA);
- return S;
- }
-
-Alignment * update_aln_random_tag ( Alignment *A)
-{
- static int tag;
- if ( !A) return A;
-
- A->random_tag=++tag;
- return A;
-}
-
-Profile *copy_profile (Profile *P1)
-{
-
- Profile *P;
-
- if ( !P1) return NULL;
- P=declare_profile ( P1->alphabet, P1->max_len);
- P->count=copy_int (P1->count, P->count, -1, -1);
- P->count2=copy_int (P1->count2, P->count2, -1, -1);
- P->count3=copy_int (P1->count3, P->count3, -1, -1);
-
- return P;
-
-}
-
-
-Profile *declare_profile(char *alphabet, int len)
-{
- Profile *P;
- P=vcalloc ( 1, sizeof ( Profile));
- P->alp_size=strlen(alphabet);
- P->max_len=len;
- P->alphabet=vcalloc ( strlen (alphabet)+2, sizeof (char));
- sprintf ( P->alphabet, "%s", alphabet);
-
- P->count=declare_int( P->alp_size+2, len);
- P->count2=declare_int(100, len);
- P->count3=declare_int(100, len);
-
- return P;
-}
-Profile * free_profile ( Profile *P)
-{
- if (!P) return NULL;
- else
- {
- vfree (P->alphabet);
- free_int ( P->count, -1);
- free_int ( P->count2, -1);
- vfree (P);
- }
- return NULL;
-}
-
-
-/************************************************************************/
-/* */
-/* ALLOCATION */
-/* */
-/* */
-/************************************************************************/
-
-
-double alloc_mem;
-double max_mem;
-double tot_mem;
-Memcontrol *memlast;
-
-FILE* print_mem_usage (FILE *fp, char *comment)
-{
- fprintf ( fp, "# %s Memory Usage: Current= %.3f Mb, Max= %.3f Mb\n", comment,(float)((float)alloc_mem/(1024*1024)),(float)((float)tot_mem/(1024*1024)) );
- return fp;
-}
-void set_max_mem (int m)
-{
- max_mem=m*1024*1024;
-}
-
-int verify_memory (int s)
-{
- alloc_mem+=s;
-
- tot_mem=(alloc_mem>tot_mem)?alloc_mem:tot_mem;
-
- if (max_mem && alloc_mem>max_mem)
- {
- fprintf (stderr, "\n%s Requires Too Much Memory: %d Megabytes [FATAL:%s]\n", PROGRAM,(int)(alloc_mem/1024*1024),PROGRAM);
- fprintf (stderr, "Tip: Rerun your Job with a smaller dataset\n");
-
- myexit (EXIT_FAILURE);
- }
- else
- return 1;
- return 0;
-
-}
-
-int my_assert ( void *p, int index)
-{
- static int warning;
-
- if (!warning)
- {
- fprintf ( stderr, "\n****************************************************************\n");
- fprintf ( stderr, "\n DEBUG MODE [Rebuild For Better Performances] \n");
- fprintf ( stderr, "\n*****************************************************************\n");
- warning=1;
- }
-
- if ( !is_dynamic_memory(p)) return 1;
- else if ( read_array_size_new (p)<=index)
- {
- fprintf ( stderr, "\nFaulty Allocation: Size=%d Access=%d\n", read_array_size (p,0),index);
- return 0;
- }
- else
- {
- return 1;
- }
-}
-
-
-
-void * vmalloc ( size_t size)
- {
- void * x;
- Memcontrol *M;
-
- verify_memory (size+2*sizeof (Memcontrol));
-
- if ( size==0)
- return NULL; /*crash ("\n0 bytes in vmalloc\n");*/
- else
- {
-
- x= malloc (size + 2*sizeof (Memcontrol));
- //x=dlmalloc (size + 2*sizeof (Memcontrol));
- if ( x==NULL)
- {
- printf_exit (EXIT_FAILURE,stderr, "\nFAILED TO ALLOCATE REQUIRED MEMORY (vmalloc)\n");
-
- }
- else
- {
- M=x;
- M[0].size=size;
- M[0].size_element=0;
- sprintf ( M[0].check, "dy");
- M+=2;
- x=M;
- return x;
- }
- }
- return NULL;}
-
-
-
-void *vcalloc (size_t nobj, size_t size)
-{
- return sub_vcalloc (nobj,size, MEMSET0);
-}
-void *vcalloc_nomemset ( size_t nobj, size_t size)
-{
- return sub_vcalloc (nobj, size, NO_MEMSET0);
-}
-void *sub_vcalloc ( size_t nobj, size_t size, int MODE)
- {
- void *x;
- Memcontrol *M;
-
- if ( nobj<=0 || size<=0)return NULL;/*crash ("\n0 bytes in vmalloc\n");*/
- else x=vmalloc (nobj*size);
-
-
- M=x;M-=2;M[0].size_element=size;M+=2;x=M;
-
- if ( x==NULL)
- {
- crash ( "\nFAILED TO ALLOCATE REQUIRED MEMORY (vcalloc)\n");
- return NULL;
- }
- else
- {
- if ( MODE==MEMSET0)
- {
- x=memset (x,0, nobj*size);
- }
- else
- {
- if (nobj)x=memset (x, 0, size);
- }
- return x;
- }
- }
-
-void *vrealloc ( void *p, size_t size)
- {
- void *x;
- Memcontrol *M;
- size_t i_size;
- int a;
-
-
- if ( p==NULL)
- {
- x=vmalloc (size);
- memset (x, 0, size);
-
- return x;
- }
- else
- {
- M=p;
- M-=2;
- i_size=M[0].size;
- p=M;
-
-
- if ( size<=0){return NULL;vfree (p);return NULL;}
- else
- {
- verify_memory (size - i_size);
- x=realloc ( p, size+2*sizeof(Memcontrol));
-
- if ( x==NULL){crash ( "\nFAILED TO ALLOCATE REQUIRED MEMORY (realloc)\n");return NULL;}
- M=x;
- M[0].size=size;
- M+=2;
- x=M;
- for ( a=i_size; a< size; a++)((char*)x)[a]=0;
- return x;
- }
- }
- return NULL;
- }
-void vfree ( void *p)
- {
- Memcontrol *M;
- size_t size;
-
- if ( !p)return;
- else
- {
- M=p;
- M-=2;
- size=M[0].size;
-
- p=M;
- free(p);
-
- verify_memory (-(size+2*sizeof(Memcontrol)));
- }
- }
-void vfree_all (void *p)
-{
- Memcontrol *n;
- while (memlast)
- {
- n=memlast->p;
- vfree (memlast+2);
- memlast=n;
- }
-}
-/*********************************************************************/
-/* */
-/* SIZES */
-/* */
-/* */
-/*********************************************************************/
-#define WRITE_SIZE(type,function)\
-void function ( int x, type *array, int os)\
- {\
- fprintf(stderr, "\nwrite_size is a deprecated function [Warning:%s]\n", PROGRAM);return;\
- }
-WRITE_SIZE(short,write_size_short)
-WRITE_SIZE(char,write_size_char)
-WRITE_SIZE(int,write_size_int)
-WRITE_SIZE(float,write_size_float)
-WRITE_SIZE(double,write_size_double)
-
-#define READ_ARRAY_SIZE(type, function)\
-int function (void *array, size_t size)\
- {\
- return read_array_size (array, size);\
- }
-READ_ARRAY_SIZE(short,read_size_short)
-READ_ARRAY_SIZE(char,read_size_char)
-READ_ARRAY_SIZE(int,read_size_int)
-READ_ARRAY_SIZE(float,read_size_float)
-READ_ARRAY_SIZE(double,read_size_double)
-
-
-int read_array_size_new (void *array)
-{
- return read_array_size ( array, 0);
-}
-int read_array_size (void *array, size_t size)
- {
- Memcontrol *p;
- if (array==NULL)return 0;
- p=(Memcontrol *)array;
- p-=2;
- if ( p[0].size_element ==0 && size==0)
- {
- fprintf ( stderr, "\nERROR in read_array_size: trying to read the size of a malloced block");
- }
- else if ( size ==0) return (int)p[0].size/p[0].size_element;
-
- return (int)p[0].size/size;
-
- }
-int is_dynamic_memory ( void *array)
-{
- Memcontrol *p;
- if (array==NULL)return 0;
- p=(Memcontrol *)array;
- p-=2;
- if ( strm (p[0].check, "dy"))return 1;
- return 0;
-}
-
-/************************************************************************/
-/* */
-/* DECLARE 2d ARRAYS */
-/* */
-/* */
-/************************************************************************/
-
-void * free_arrayN(void *p, int n)
-{
- int a, s;
- void **i;
-
-
- if ( p==NULL) return NULL;
- else if ( n==1)vfree ((void *)p);
- else
- {
- i=(void**)p;
- s=read_array_size ( (void *)p, sizeof ( void *));
- for ( a=0; a< s; a++)free_arrayN ((void *)i[a], n-1);
- vfree (p);
- }
- return NULL;
-}
-
-void * declare_arrayNnomemset (int ndim, size_t size, ...)
-{
- va_list ap;
- int *array;
- void **p;
- int a;
-
- va_start (ap, size);
-
- array=vcalloc (ndim, sizeof (int));
- for ( a=0; a< ndim; a++)
- {
- array[a]=va_arg (ap,int);
- if ( array[a]<0){va_end(ap);return NULL;}
-
- }
- va_end (ap);
-
- if ( ndim==2)
- {
-
- p=vcalloc_nomemset (array[0], sizeof ( void*));
- for (a=0; a< array[0]; a++)
- {
- p[a]=vcalloc_nomemset (array[1], size);
- }
- }
- else
- {
- p=declare_arrayN2nomemset (ndim, array, size);
- }
- vfree (array);
- return p;
-}
-
-void *declare_arrayN2nomemset ( int ndim, int *A, size_t size)
-{
- int a;
- void **p;
-
- if ( ndim>1)
- {
- p=vcalloc_nomemset (A[0], sizeof (void*));
- for ( a=0; a<A[0]; a++)
- p[a]=declare_arrayN2(ndim-1, A+1, size);
- }
- else
- {
- p=vcalloc_nomemset (A[0], size);
- }
- return p;
-}
-
-void * declare_arrayN (int ndim, size_t size, ...)
-{
- va_list ap;
- int *array;
- void **p;
- int a;
-
-
- va_start (ap, size);
-
- array=vcalloc (ndim, sizeof (int));
- for ( a=0; a< ndim; a++)
- {
- array[a]=va_arg (ap,int);
- if ( array[a]<0){va_end(ap);return NULL;}
-
- }
- va_end (ap);
-
- if ( ndim==2)
- {
-
- p=vcalloc_nomemset (array[0], sizeof ( void*));
- for (a=0; a< array[0]; a++)
- p[a]=vcalloc (array[1], size);
- }
- else
- {
- p=declare_arrayN2 (ndim, array, size);
- }
- vfree (array);
- return p;
-}
-
-void *declare_arrayN2 ( int ndim, int *A, size_t size)
-{
- int a;
- void **p;
-
- if ( ndim>1)
- {
- p=vcalloc_nomemset (A[0], sizeof (void*));
- for ( a=0; a<A[0]; a++)
- p[a]=declare_arrayN2(ndim-1, A+1, size);
- }
- else
- {
- p=vcalloc (A[0], size);
- }
- return p;
-}
-
-void **declare_array (int first, int second, size_t size)
-{
- return (void **)declare_arrayN (2,size,first, second);
-}
-
-
-#define DECLARE_ARRAY(type,wf,rf,function)\
-type** function (int first, int second)\
- {\
- return (type **)declare_arrayN (2,sizeof(type), first, second);\
- }
-
-int **declare_int2 (int f, int *s, int d)
-{
- int **r;
- int a;
- r=vcalloc ( f, sizeof (int*));
- for (a=0; a<f; a++)
- r[a]=vcalloc (s[a]+d, sizeof (int));
- return r;
-}
-
-
-
-
-
-DECLARE_ARRAY(short,write_size_short,read_size_short,declare_short)
-DECLARE_ARRAY(char,write_size_char,read_size_char,declare_char)
-DECLARE_ARRAY(int,write_size_int,read_size_int,declare_int)
-DECLARE_ARRAY(float,write_size_float,read_size_float,declare_float)
-DECLARE_ARRAY(double,write_size_double,read_size_double,declare_double)
-
-void **declare_array_nomemset (int first, int second, size_t size)
-{
- return (void **)declare_arrayNnomemset (2,size,first, second);
-}
-#define DECLARE_ARRAY_NMS(type,wf,rf,function)\
-type** function (int first, int second)\
- {\
- return (type **)declare_arrayNnomemset (2,sizeof(type), first, second);\
- }
-DECLARE_ARRAY_NMS(short,write_size_short,read_size_short,declare_short_nomemset)
-DECLARE_ARRAY_NMS(char,write_size_char,read_size_char,declare_char_nomemset)
-DECLARE_ARRAY_NMS(int,write_size_int,read_size_int,declare_int_nomemset)
-DECLARE_ARRAY_NMS(float,write_size_float,read_size_float,declare_float_nomemset)
-DECLARE_ARRAY_NMS(double,write_size_double,read_size_double,declare_double_nomemset)
-
-
-Alignment ** declare_aln_array ( int first)
- {
- Alignment ** array;
- int a;
-
-
- array=vcalloc (first, sizeof (Alignment*));
- for ( a=0; a< first; a++)
- array[a]=declare_Alignment (NULL);
- return array;
- }
-
-
-
-
-/************************************************************************/
-/* */
-/* Realloc 2d ARRAYS */
-/* */
-/* */
-/************************************************************************/
-void ** realloc_arrayN(int ndim,void **main_array,size_t size, ...)
-{
- va_list ap;
- int *array;
- void **p;
- int a;
-
- /*dim size==-1: keep current size*/
- /*Dim sizes are the absolute size (not the extension*/
- /*If array getting shorter, memory is Not Claimed back*/
-
- array=vcalloc (ndim, sizeof (int));
- va_start (ap, size);
- for ( a=0; a< ndim; a++)
- {
- array[a]=va_arg (ap,int);
- if ( array[a]<-1){va_end(ap);return NULL;}
- }
- va_end (ap);
-
- p=realloc_arrayN2 (ndim, main_array, array,size);
- vfree (array);
- return p;
-}
-
-void **realloc_arrayN2 ( int ndim, void ** p, int *A, size_t size)
-{
- int a;
- int o, n;
-
-
- if (ndim==0)return NULL;
-
- if ( ndim>1)
- {
- o=read_array_size (p,sizeof (void*));
- if (A[0]>o)p=vrealloc (p, sizeof (void*)*A[0]);
- n=(A[0]==-1)?o:A[0];
- for ( a=0; a<n; a++)
- p[a]=realloc_arrayN2(ndim-1,p[a], A+1, size);
- }
- else
- {
- o=read_array_size (p, size);
- if (A[0]>o)p=vrealloc (p, size*A[0]);
- }
- return p;
-}
-
-
-
-void ** realloc_array (void **array,size_t size, int first, int second, int ext1, int ext2)
-{
- int a;
- int d1, d2;
- if ( array==NULL)return declare_array (((first==-1)?0:first)+ext1, ((second==-1)?0:second)+ext2, size);
- else if ( first==-1)
- {
- first=read_array_size (array, sizeof (void *));
- }
- if (second==-1)second=read_array_size(array[0], size);
-
- d1=first+ext1;
- d2=second+ext2;
-
- for ( a=d1; a<first; a++)vfree (array[a]);
- array=vrealloc (array, sizeof (void*)*d1);
-
- if ( d2!=second)
- {
- for (a=0; a<d1 && a<first; a++)
- array[a]=vrealloc ( array[a], size*d2);
- }
- for ( a=first; a< d1; a++)
- array[a]=vrealloc ( array[a], size*d2);
- return array;
-}
-
-
-
-
-
-#define REALLOC_ARRAY(type,wf,rf,function1,function2,function3)\
-type ** function1 ( type **array, int first, int second, int ext1, int ext2)\
- {\
-return (type **)realloc_array ((void **)array, sizeof (type),first, second, ext1, ext2);\
-\
- }
-REALLOC_ARRAY(short,write_size_short,read_size_short,realloc_short,declare_short,free_short)
-REALLOC_ARRAY(char,write_size_char,read_size_char,realloc_char,declare_char,free_char)
-REALLOC_ARRAY(int,write_size_int,read_size_int,realloc_int,declare_int,free_int)
-REALLOC_ARRAY(float,write_size_float,read_size_float,realloc_float,declare_float,free_float)
-REALLOC_ARRAY(double,write_size_double,read_size_double,realloc_double,declare_double,free_double)
-
-
-
-#define NEW_REALLOC_ARRAY(type,wf,rf,function1,function2,function3)\
-type ** function1 ( type **array, int ext1, int ext2)\
- {int a, b;\
- int first, l1;\
- int second, l2;\
- type **new_array;\
-\
- first=rf(array,sizeof (type*));\
- second=rf(array[0],sizeof (type));\
- \
- if ( ext1==-1)ext1=first;\
- if ( ext2==-1)ext2=second;\
- l1=MIN(ext1, first);\
- l2=MIN(ext2, second);\
- new_array=declare_arrayN(2,sizeof(type),ext1, ext2);\
- for ( a=0; a<l1; a++)\
- for ( b=0; b<l2; b++)new_array[a][b]=array[a][b];\
- function3(array, -1);\
- return new_array;\
- }
-
-NEW_REALLOC_ARRAY(short,write_size_short,read_size_short,new_realloc_short,declare_short,free_short)
-NEW_REALLOC_ARRAY(char,write_size_char,read_size_char,new_realloc_char,declare_char,free_char)
-NEW_REALLOC_ARRAY(int,write_size_int,read_size_int,new_realloc_int,declare_int,free_int)
-NEW_REALLOC_ARRAY(float,write_size_float,read_size_float,new_realloc_float,declare_float,free_float)
-NEW_REALLOC_ARRAY(double,write_size_double,read_size_double,new_realloc_double,declare_double,free_double)
-Alignment ** realloc_aln_array ( Alignment **array, int ext1)
- {
- int a;
- int first;
-
-
- if ( array==NULL)
- {
- array=declare_aln_array(ext1);
- return array;
- }
- first=read_array_size ( array, sizeof ( Alignment *));
- if ( ext1>0)
- {
- array=vrealloc ( array, (sizeof (Alignment*))*(first+ext1));
- for ( a=first; a<first+ext1; a++)array[a]=declare_Alignment (NULL);
- }
- else if ( ext1==0);
- else if ( ext1<0)
- {
- for ( a=first-1; a>=(first+ext1);a--)free_Alignment (array[a]);
- array=vrealloc ( array, (sizeof (Alignment*))*(first+ext1));
- }
- return array;
- }
-
-/************************************************************************/
-/* */
-/* free 2d ARRAYS */
-/* */
-/* */
-/************************************************************************/
-#define FREE_ARRAY(type,wf,rf,function) \
-type ** function (type **array, int first)\
- {\
- return free_arrayN((void*)array, 2);\
- }
-FREE_ARRAY(short,write_size_short,read_size_short,free_short)
-FREE_ARRAY(char,write_size_char,read_size_char,free_char)
-FREE_ARRAY(int,write_size_int,read_size_int,free_int)
-FREE_ARRAY(float,write_size_float,read_size_float,free_float)
-FREE_ARRAY(double,write_size_double,read_size_double,free_double)
-
-
-
-Alignment ** free_aln_array (Alignment **array)
- {
- int a;
- int len;
-
-
- if ( array==NULL)return NULL;
- len=read_array_size ( array, sizeof (Alignment *));
- for ( a=1; a< len; a++)free_Alignment(array[a]);
- vfree ( array);
- return NULL;
- }
-
-Fname *declare_fname (int size)
- {
- Fname *F;
-
- size+=strlen (get_home_4_tcoffee())+FILENAMELEN+1;
-
- F=vcalloc ( 1, sizeof (Fname));
- F->name =vcalloc ( size, sizeof (char));
- F->path =vcalloc ( size, sizeof (char));
- F->suffix=vcalloc ( size, sizeof (char));
- F->full=vcalloc ( size, sizeof (char));
- return F;
- }
-
-Fname *free_fname ( Fname *F)
- {
- vfree (F->name);
- vfree (F->path);
- vfree (F->suffix);
- return NULL;
- }
-/******************************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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