--- /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 __REFORMAT_H
+#define __REFORMAT_H
+
+typedef struct
+ {
+ Alignment *A;
+ Weights *W;
+ Sequence *S;
+ int **M;
+ Structure *RNA_ST;
+ NT_node T;
+ Constraint_list *CL;
+ char format[100];
+ char file[100];
+ int rm_gap;
+
+}Sequence_data_struc;
+
+typedef struct
+ {
+ char **symbol_list;
+ int n_symbol;
+ char *coor_file;
+ int rm_gap;
+ int keep_case;
+ int keep_name;
+ int use_consensus;
+}Action_data_struc;
+
+/*Control of alignment sizes*/
+int set_landscape_msa (int len);
+int get_msa_line_length (int line, int aln_len);
+
+int seq_reformat (int argc, char **argv);
+
+Sequence_data_struc *read_data_structure ( char *in_format, char *in_file,Action_data_struc *RAD);
+Alignment * read_fasta_aln_noceck ( char *name, Alignment *A);
+Alignment * main_read_aln ( char *name, Alignment *A);
+Sequence * read_sequences ( char *name);
+Sequence * read_alifold ( char *name);
+Alignment *alifold2aln ( char *name);
+Sequence * main_read_seq ( char *mname);
+int output_format_aln ( char *format, Alignment *A, Alignment *EA,char *name);
+int main_output ( Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char *out_format, char *out_file);
+
+char * identify_seq_format ( char *file);
+char * name2type_name ( char *name);
+char identify_format (char **fname);
+char **identify_list_format ( char **list, int n);
+
+int type_is_exon_boundaries(char **seq, int n);
+
+int format_is_oligo ( char *file);
+int format_is_msf ( char *file);
+int format_is_fasta( char *file);
+// int format_is_fasta_aln( char *file);
+int format_is_fasta_aln ( char *file, int i_know_that_it_not_seq);
+int format_is_fasta_seq( char *file);
+int is_pir_name (char *name);
+int format_is_pir ( char *file);
+int format_is_pir_aln( char *file);
+int format_is_pir_seq( char *file);
+int pir_name (char *name);
+int format_is_conc_aln (char *file);
+int format_is_saga ( char *file);
+int format_is_swissprot (char *name);
+
+int is_seq ( char *name);
+int is_aln ( char *name);
+int has_pdb (char *name);
+int is_stockhom_aln ( char *name);
+int is_blast_file (char *name);
+int is_sap_file (char *name);
+int is_pdb_file ( char *name);
+int is_simple_pdb_file ( char *name);
+char *fix_pdb_file (char *name);
+
+int is_pdb_name ( char *name);
+char* get_pdb_id(char *name);
+char* get_pdb_struc(char *name, int start, int end);
+char* seq_is_pdb_struc ( Sequence *S, int i);
+char* is_pdb_struc ( char *name); /*Returns NULL if not a PDB structure Or a the name of a file containing a PDB structure*/
+int is_matrix (char *name);
+
+int is_lib (char *name);
+int is_lib_01 (char *name);
+int is_lib_02 (char *name);
+int is_lib_list ( char *name);
+int is_single_seq_weight_file (char *fname);
+int is_treelist(char *name);
+int is_newick (char *name);
+int is_nexus (char *file);
+
+int is_method ( char *file);
+
+char *format_name2aln_format_name (char *name);
+int is_in_format_list ( char *name);
+int is_out_format_list ( char *name);
+int is_struc_in_format_list ( char *name);
+int is_struc_out_format_list ( char *name);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT MISC */
+/* */
+/***************************************************************************************** */
+
+char *** read_rename_file ( char *fname, int mode);
+void get_barton_list_tc_seq ( char *in_file);
+int process_barton_entry (char *buf, char *name);
+
+Structure *read_rna_struc_number ( Alignment *A, char *fname);
+char ** read_lib_list (char *name, int *n);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT WEIGHTS */
+/* */
+/***************************************************************************************** */
+Weights* get_amps_sd_scores ( char *fname);
+Weights *read_seq_weight (char **name, int nseq, char* seq_weight);
+/*******************************************************************************************/
+/* */
+/* */
+/* INPUT SEQUENCES */
+/* */
+/***************************************************************************************** */
+char ***read_group ( char *file);
+Sequence* get_pdb_sequence ( char *fname);
+Sequence* get_struc_gor ( char *fname);
+Sequence* get_dialign_sequence ( char *fname);
+Sequence* get_pima_sequence ( char *fname);
+Sequence* get_sequence_dali ( char *fname);
+Sequence* get_pir_sequence ( char *fname, char *comment_name);
+Sequence* perl_reformat2fasta ( char *perl_script, char *file);
+
+Sequence* get_fasta_sequence ( char *fname, char *comment_name);
+Sequence* get_fasta_sequence_num ( char *fname, char *comment_name);
+Sequence* get_fasta_sequence_raw ( char *fname, char *comment_name);
+Sequence *get_file_list ( char *fname);
+Sequence *get_tree_file_list ( char *fname);
+
+Sequence* get_gor_sequence ( char *fname, char *comment_name);
+Sequence* get_swissprot_sequence ( char *fname, char *comment_name);
+int fscanf_seq_name ( FILE *fp, char *sname);
+
+void read_check ( Alignment *A, char *check_file);
+void read_stockholm_aln ( char *fname, Alignment *A);
+void read_aln ( char *fname, Alignment *A);
+void read_number_aln ( char *fname, Alignment *A);
+Alignment *read_blast_aln ( char *fname, Alignment *A);
+void read_msf_aln ( char *fname, Alignment *A);
+void read_amps_aln ( char *in_file, Alignment *A);
+int get_amps_seq_name ( char **name, char* fname);
+Alignment *read_gotoh_aln ( char *fname, Alignment *A);
+
+void undump_msa ( Alignment *A, char *tmp);
+void dump_msa ( char *file,Alignment *A, int nseq, int *lseq);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT MATRICES */
+/* */
+/***************************************************************************************** */
+int output_freq_mat ( char *outfile, Alignment *A);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT P-Values */
+/* */
+/***************************************************************************************** */
+float output_maln_pval ( char *outfile, Alignment *A);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT WEIGHTS */
+/* */
+/***************************************************************************************** */
+void output_similarities (char *file, Alignment *A, char *mode);
+void output_similarities_pw (char *file, Alignment *A, Alignment *B, char *mode);
+Alignment * similarities_file2aln ( char *file);
+int** input_similarities (char *file, Alignment *A, char *mode);
+
+void output_statistics (char *file, Alignment *A, char *mode);
+void output_pw_weights4saga ( Weights *W, float **w_list, char *wfile);
+int output_seq_weights ( Weights *W, char *wfile);
+FILE * display_weights (Weights *W, FILE *fp);
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT SEQ */
+/* */
+/***************************************************************************************** */
+char** clean_seq_names (char **names, int n, int mode);
+char *clean_seq_name (char *name, int mode);
+
+
+void output_pir_seq1 (char *fname, Alignment*A );
+void output_pir_seq (char *fname, Alignment*A );
+void output_gor_seq (char *fname, Alignment*A );
+void output_mult_fasta_seq (char *fname, Alignment*A, int n );
+
+void main_output_fasta_seq ( char *fname, Alignment *A, int header);
+void output_fasta_simple ( char *name, Sequence *S);
+void output_fasta_seqS (char *fname, Sequence *S );
+void output_fasta_seq1 (char *fname, Alignment*A );
+void output_fasta_seq2 (char *fname, Alignment*A );
+char *output_fasta_seqX (char *name, char *mode, Sequence *S, Alignment *A, int i);
+
+void output_pir_check (char *fname,int nseq, char **A );
+void output_fasta_seq (char *fname, Alignment*A );
+void output_gotoh_seq (char *fname, Alignment*A );
+void output_est_prf (char *fname, Alignment *A);
+void output_gor_seq (char *fname, Alignment*A );
+/*******************************************************************************************/
+/* */
+/* */
+/* OUTPUT ALN */
+/* */
+/***************************************************************************************** */
+void output_pir_aln ( char *fname,Alignment*A);
+void output_model_aln ( char *fname,Alignment*A );
+char * output_fasta_sub_aln (char *fname, Alignment*A, int ns, int *ls );
+char * output_fasta_sub_aln2 (char *fname, Alignment*A, int *ns, int **ls );
+
+void ouput_suchard_aln ( char *fname,Alignment*A);
+void output_fasta_aln ( char *fname, Alignment *A);
+void output_mfasta_aln ( char *fname, Alignment *A);
+
+void output_xmfa_aln ( char *fname, Alignment *A);
+void output_msf_aln ( char *fname,Alignment*B);
+FILE * output_generic_interleaved_aln (FILE *fp, Alignment *B, int line, char gap, char *mode);
+void output_stockholm_aln (char *file, Alignment *A, Alignment *ST);
+void output_clustal_aln( char *name, Alignment*B);
+void output_strict_clustal_aln( char *name, Alignment*B);
+void output_generic_clustal_aln( char *name, Alignment*B, char *format);
+void output_saga_aln ( char *name, Alignment*B);
+void output_rphylip_aln ( char *name, Alignment*B);
+void output_phylip_aln ( char *name, Alignment*B);
+void output_mocca_aln ( char *name, Alignment*B,Alignment*S);
+void output_rnalign (char *out_file, Alignment*A,Sequence *STRUC);
+void output_pw_lib_saga_aln (char *lib_name, Alignment *A );
+void output_lib (char *lib_name, Alignment *A );
+void output_compact_aln( char *name, Alignment *B);
+
+void print_sub_aln ( Alignment *B, int *ns, int **ls);
+void print_aln ( Alignment *B);
+FILE * output_aln( Alignment *B, FILE *fp);
+
+
+FILE * output_aln_score ( Alignment *B, FILE *fp);
+FILE * output_aln_with_res_number ( Alignment *B, FILE *fp);
+
+
+FILE* output_Alignment ( Alignment *B, FILE *fp);
+FILE* output_Alignment_without_header ( Alignment *B, FILE *fp);
+FILE * output_Alignment_score ( Alignment *B, FILE *fp);
+FILE * output_Alignment_with_res_number ( Alignment *B, FILE *fp);
+void output_constraints ( char *fname, char *mode, Alignment *A);
+
+Alignment *input_conc_aln ( char *name, Alignment *A);
+void output_conc_aln ( char *name, Alignment *B);
+void output_glalign ( char *name, Alignment *B, Alignment *S);
+void output_lalign_header( char *name, Alignment *B);
+void output_lalign ( char *name, Alignment *B);
+void output_lalign_aln ( char *name, Alignment *B);
+
+/**************************************************************************************************/
+/* */
+/* */
+/* INPUT/OUTPUT MATRICES */
+/* */
+/**************************************************************************************************/
+int is_blast_matrix (char *fname);
+int is_pavie_matrix (char *fname);
+int is_clustalw_matrix (char *fname);
+
+int is_distance_matrix_file (char *name);
+int is_similarity_matrix_file (char *name);
+
+void aln2proba_mat (Sequence *S);
+void aln2mat (Sequence *S);
+void aln2mat_diaa (Sequence *S);
+int **seq2latmat ( Sequence *S, char *fname);
+int output_mat (int **mat, char *fname, char *alp, int offset);
+int ** read_blast_matrix ( char *mat_name);
+int output_blast_mat (int **mat, char *fname);
+double* mat2cmp (int **mat1, int **mat2);
+
+void output_pavie_mat (int **mat, char *fname, double gep, char *alp);
+int ** read_pavie_matrix ( char *mat_name);
+
+/****************************************************************************************************/
+/*************************** *************************************/
+/*************************** PROCESSING *************************************/
+/*************************** *************************************/
+/*******************************************************************************************/
+/* */
+/* */
+/* THREADING */
+/***************************************************************************************** */
+
+
+
+
+Structure * declare_rna_structure_num (Sequence *SA);
+
+char *thread_aa_seq_on_dna_seq( char *s);
+void thread_seq_struc2aln ( Alignment *A, Sequence *ST);
+Alignment *thread_dnaseq_on_prot_aln (Sequence *S, Alignment *A);
+void cache_id ( Alignment *A);
+
+
+
+int process_est_sequence ( Sequence *S, int *cluster_list);
+char * invert_seq ( char *seq);
+int get_best_match ( char *seq1, char *seq2);
+int** extract_m_diag_streches ( int ** m, int l1, int l2,char *seq1, char *seq2, int *n_mdiag);
+int is_strech ( char *AA, char *seq1, char *seq2, int len, int x, int y);
+
+int search_for_cluster ( int seq, int cluster_number, int *cluster_list, int T, int nseq, int **S);
+int * SHC ( int nseq, int **NST, int **ST);
+int mutate_sol (int *sol, int nseq);
+int evaluate_sol ( int*sol, int nseq, int **ST, int **NST);
+
+
+
+char **make_symbols ( char *name, int *n);
+Alignment *code_dna_aln (Alignment *A);
+char* back_translate_dna_codon ( char aa, int deterministic);
+int translate_dna_codon ( char *seq, char stop);
+char* mutate_amino_acid ( char aa, char *mode);
+Alignment * mutate_aln ( Alignment *A, char *r);
+
+int extend_seqaln (Sequence *S, Alignment *A);
+int unextend_seqaln (Sequence *S, Alignment *A);
+char *extend_seq (char *seq);
+char *unextend_seq (char *seq);
+
+Sequence * transform_sequence ( Sequence *S, char *mode);
+Alignment *translate_splice_dna_aln (Alignment *A,Alignment *ST );
+Alignment * mutate_cdna_aln ( Alignment *A);
+
+char *test_dna2gene (char *dna, int *w);
+Sequence *dnaseq2geneseq (Sequence *S, int **w);
+
+int ** shift_res_weights ( Sequence *R, int **w, int shift);
+int res_weights2min(Sequence *R, int **w);
+int res_weights2max(Sequence *R, int **w);
+int res_weights2avg(Sequence *R, int **w);
+int output_wexons (char *name, Alignment *A);
+int scan_res_weights4ac (Sequence *R, int **w, int start, int end, int step);
+float *res_weights2accuracy_counts ( Sequence *R, int **w,int T, float *result);
+float* genepred_seq2accuracy_counts (Sequence *R, Sequence *T,float *result);
+void genepred_seq2accuracy_counts4all (Sequence *R, Sequence *Ts); //JM
+float* genepred2accuracy_counts (char *ref, char *target , float *result);
+
+char *dna2gene (char *dna, int *w);
+char * translate_dna_seq_on3frame ( char *dna_seq, char stop, char *prot);
+
+char * translate_dna_seq ( char *dna_seq, int frame, char stop, char *prot);
+int is_stop (char r1, char r2, char r3);
+int seq2tblastx_db (char *file,Sequence *S, int strand);
+int seq2blastdb (char *out, Sequence *S);
+char * back_translate_dna_seq ( char *in_seq,char *out_seq, int mode);
+Alignment *back_translate_dna_aln (Alignment *A);
+Sequence *translate_dna_seqS (Sequence *S, int frame, int stop);
+Alignment *translate_dna_aln (Alignment *A, int frame);
+char *dna_seq2pep_seq (char *seq, int frame);
+
+Alignment *clean_gdna_aln (Alignment *A);
+Alignment *clean_cdna_aln (Alignment *A);
+Alignment *clean_est (Alignment *A);
+/**************************************************************************************************/
+/******************************** ********************************************/
+/******************************** PROCESSING ********************************************/
+/*************** **************** ********************************************/
+void modify_data (Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char **action_list,int n_actions, Action_data_struc *RAD);
+
+//
+// Name MAnipulation
+//
+
+Alignment *clean_aln (Alignment *A);
+Sequence *clean_sequence ( Sequence *S);
+char ** translate_names (int n, char **name);
+char * translate_name ( char *name);
+char *decode_name (char *name, int mode);
+FILE * display_sequences_names (Sequence *S, FILE *fp, int check_pdb_status, int print_templates);
+Sequence *add_file2file_list (char *name, Sequence *S);
+
+#endif
git://source.jalview.org / jabaws.git / blobdiff