--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*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*******************************/
+#ifndef __UTIL_DECLARE_H
+#define __UTIL_DECLARE_H
+
+
+typedef struct Tmpname Tmpname;
+struct Memcontrol
+ {
+ size_t size;
+ size_t size_element;
+ char check[3];
+ struct Memcontrol *p;
+ struct Memcontrol *n;
+ };
+typedef struct Memcontrol Memcontrol;
+void free_pair_wise();//Frees static memory in the pair_wise functions
+/************************************************************************/
+/* */
+/* CONSTRAINT_LIST */
+/* */
+/* */
+/************************************************************************/
+int *** duplicate_residue_index (int ***r);
+int *** declare_residue_index (Sequence *S);
+
+Constraint_list *free_constraint_list4lib_computation (Constraint_list *CL);
+Constraint_list *duplicate_constraint_list4lib_computation (Constraint_list *CL);
+Constraint_list * declare_constraint_list_simple ( Sequence *S);
+Constraint_list * declare_constraint_list ( Sequence *S, char *name, int *L, int ne,FILE *fp, int **M);
+Constraint_list *cache_dp_value4constraint_list ( char mode[],Constraint_list *CL);
+Constraint_list *duplicate_constraint_list_soft (Constraint_list *CL);
+Constraint_list *duplicate_constraint_list (Constraint_list *CL);
+Constraint_list *copy_constraint_list (Constraint_list *CL, int mode);
+Sequence * free_constraint_list (Constraint_list *CL);
+Constraint_list * free_constraint_list_full (Constraint_list *CL);
+Distance_matrix * free_distance_matrix ( Distance_matrix *DM);
+Distance_matrix * duplicate_distance_matrix ( Distance_matrix *DMin);
+/************************************************************************/
+/* */
+/* Blast_param Functions */
+/* */
+/* */
+/************************************************************************/
+Blast_param * duplicate_blast_param ( Blast_param*B);
+Blast_param * free_blast_param ( Blast_param*B);
+/************************************************************************/
+/* */
+/* TC_param Functions */
+/* */
+/* */
+/************************************************************************/
+TC_param * duplicate_TC_param ( TC_param*B);
+TC_param * free_TC_param ( TC_param*B);
+/************************************************************************/
+/* */
+/* MOCA Functions */
+/* */
+/* */
+/************************************************************************/
+Moca * duplicate_moca ( Moca *m);
+Moca * free_moca ( Moca *m);
+/************************************************************************/
+/* */
+/* PDB Functions */
+/* */
+/* */
+/************************************************************************/
+Structure * declare_structure ( int n, char **array);
+Structure * extend_structure ( Structure *S);
+/************************************************************************/
+/* */
+/* Weights Functions */
+/* */
+/* */
+/************************************************************************/
+Weights* declare_weights ( int nseq);
+Weights* duplicate_weights (Weights *W);
+Weights* free_weights ( Weights* W);
+
+FILE* print_mem_usage (FILE *fp, char *comment);
+void set_max_mem (int m);
+int verify_memory (int s);
+int my_assert ( void *p, int index);
+
+void * vmalloc ( size_t size);
+void * vcalloc ( size_t nobj, size_t size);
+void * vcalloc_nomemset ( size_t nobj, size_t size);
+void * sub_vcalloc ( size_t nobj, size_t size, int MODE);
+
+void * vrealloc ( void *p, size_t size);
+void vfree2 ( void **p);
+void vfree ( void *p);
+void * free_arrayN (void *p, int ndim);
+void vfree_all (void *p);
+/*********************************************************************/
+/* */
+/* SIZES */
+/* */
+/* */
+/*********************************************************************/
+void write_size_short (int x, short *array, int offset);
+void write_size_char (int x, char *array, int offset);
+void write_size_int (int x, int *array, int offset);
+void write_size_float (int x, float *array, int offset);
+void write_size_double(int x, double *array, int offset);
+
+int read_size_short ( void *array, size_t size );
+int read_size_char ( void *array, size_t size );
+int read_size_int ( void *array, size_t size );
+int read_size_float ( void *array, size_t size );
+int read_size_double( void *array, size_t size );
+int read_array_size_new ( void *array);
+int read_array_size ( void *array, size_t size );
+int read_array_new ( void *array);
+int is_dynamic_memory ( void *array);
+
+/*********************************************************************/
+/* */
+/* REALLOCATION */
+/* */
+/* */
+/*********************************************************************/
+void **realloc_arrayN(int ndim,void **main_array,size_t size, ...);
+void **realloc_arrayN2 ( int ndim, void ** p, int *A, size_t size);
+
+
+void ** realloc_array (void **array,size_t size, int first, int second, int ext1, int ext2);
+short ** realloc_short ( short **array, int first, int second, int ext1, int ext2);
+char ** realloc_char ( char **array, int first, int second, int ext1, int ext2);
+int ** realloc_int ( int **array, int first, int second, int ext1, int ext2);
+float ** realloc_float ( float **array, int first, int second, int ext1, int ext2);
+double ** realloc_double ( double **array, int first, int second, int ext1, int ext2);
+Alignment ** realloc_aln_array ( Alignment **array, int ext1);
+/*The new realloc is recommended*/
+short ** new_realloc_short ( short **array, int ext1, int ext2);
+char ** new_realloc_char ( char **array, int ext1, int ext2);
+int ** new_realloc_int ( int **array, int ext1, int ext2);
+float ** new_realloc_float ( float **array, int ext1, int ext2);
+double ** new_realloc_double ( double **array, int ext1, int ext2);
+
+
+void * declare_arrayNnomemset (int ndim, size_t size, ...);
+void *declare_arrayN2nomemset ( int ndim, int *A, size_t size);
+
+void * declare_arrayN (int ndim, size_t size, ...);
+void *declare_arrayN2 ( int ndim, int *A, size_t size);
+
+char * resize_string (char *buf);
+void ** declare_array (int first, int second, size_t size);
+short ** declare_short ( int first, int second);
+char ** declare_char ( int first, int second);
+int ** declare_int ( int first, int second);
+int ** declare_int2 ( int first, int *second, int delta);
+
+float ** declare_float ( int first, int second);
+double ** declare_double ( int first, int second);
+
+void ** declare_array_nomemset (int first, int second, size_t size);
+short ** declare_short_nomemset ( int first, int second);
+char ** declare_char_nomemset ( int first, int second);
+int ** declare_int_nomemset ( int first, int second);
+float ** declare_float_nomemset ( int first, int second);
+double ** declare_double_nomemset ( int first, int second);
+
+
+Alignment ** declare_aln_array ( int first);
+
+short ** free_short ( short **array, int first);
+int ** free_int ( int **array, int first);
+char ** free_char ( char **array, int first);
+double ** free_double ( double **array, int first);
+float ** free_float ( float **array, int first);
+Alignment ** free_aln_array ( Alignment **array);
+Alignment *free_data_in_aln (Alignment *A);
+
+long aln_stack (Alignment *A, int mode);
+
+Sequence *free_Alignment ( Alignment *A);
+Sequence *free_aln ( Alignment *A);
+Alignment *declare_Alignment ( Sequence *S);
+Alignment *realloc_alignment ( Alignment *A, int new_len);
+Alignment *realloc_alignment2 ( Alignment *A, int new_nseq, int new_len);
+
+Alignment *declare_aln ( Sequence *S);
+Alignment *declare_aln2 (int nseq, int len);
+Alignment *realloc_aln ( Alignment *A, int new_len);
+Alignment *realloc_aln2 ( Alignment *A, int new_nseq, int new_len);
+Alignment *update_aln_random_tag (Alignment *A);
+
+Alignment *copy_aln ( Alignment *A, Alignment *B);
+Alignment* extract_sub_aln2 ( Alignment *A, int nseq, char **list);
+Alignment* extract_sub_aln ( Alignment *A, int nseq, int *list);
+Alignment* shrink_aln ( Alignment *A, int nseq, int *list);
+
+Profile *copy_profile (Profile *P1);
+Profile *declare_profile(char *alphabet, int len);
+Profile * free_profile ( Profile *P);
+
+Sequence * reset_sequence_len (Sequence *S);
+Sequence * declare_sequence ( int min, int max, int nseq);
+Sequence * realloc_sequence (Sequence *OUT, int new_nseq, int max_len);
+Sequence * duplicate_sequence (Sequence *S );
+Sequence * add_sequence ( Sequence *IN, Sequence *OUT, int i);
+void free_sequence ( Sequence *LS, int nseq);
+
+
+
+Fname *declare_fname ( int );
+Fname *free_fname ( Fname *F);
+
+#endif
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff