--- /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*******************************/
+
+/****************************************************************************/
+/* */
+/* */
+/* Alignment Methods */
+/* */
+/* */
+/****************************************************************************/
+Alignment * sorted_aln (Alignment *A, Constraint_list *CL);
+Alignment * sorted_aln_seq (int seq, Alignment *A, Constraint_list *CL);
+Alignment * full_sorted_aln (Alignment *A, Constraint_list *CL);
+
+/******************************************************************/
+/* MAIN DRIVER */
+/* */
+/* */
+/******************************************************************/
+int * set_profile_master (Alignment *A,int *ns, int **ls, Constraint_list *CL);
+int *unset_profile_master (Alignment *A,int *ns, int **ls, Constraint_list *CL);
+
+Constraint_list *profile2list ( Job_TC *job,int nprf);
+Constraint_list *seq2list (Job_TC *Job);
+Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL);
+int method_uses_structure(TC_method *M);
+int method_uses_profile(TC_method *M);
+
+/******************************************************************/
+/* MULTIPLE ALIGNMENTS */
+/* */
+/* */
+/******************************************************************/
+Alignment * compute_prrp_aln (Alignment *A, Constraint_list *CL);
+Alignment * compute_clustalw_aln (Alignment *A, Constraint_list *CL);
+Alignment * compute_tcoffee_aln_quick (Alignment *A, Constraint_list *CL);
+Alignment * seq2clustalw_aln (Sequence *S);
+Alignment * aln2clustalw_aln (Alignment *A, Constraint_list *CL);
+Alignment * realign_block ( Alignment *A, int col1, int col2, char *pg);
+/******************************************************************/
+/* DNA */
+/* */
+/* */
+/******************************************************************/
+Constraint_list * align_coding_nucleotides (char *seq, char *method, char *weight, char *mem_mode, Constraint_list *CL);
+/******************************************************************/
+/* STRUCTURES */
+/* */
+/* */
+/******************************************************************/
+Constraint_list * seq_msa (TC_method *M , char *in_seq, Constraint_list *CL);
+
+Constraint_list *align_pdb_pair (char *seq_in, char *dp_mode,char *evaluate_mode, char *file, Constraint_list *CL, Job_TC *job);
+Constraint_list * align_pdb_pair_2 (char *seq, Constraint_list *CL);
+
+Constraint_list * pdb_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * pdbid_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * profile_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * thread_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * thread_pair2 ( TC_method *M,int s1, int s2, Constraint_list *CL);
+Constraint_list * sap_pair (char *seq, char *weight, Constraint_list *CL);
+Constraint_list * lsqman_pair (char *seq, Constraint_list *CL);
+Constraint_list * rnapdb_pair (TC_method *M , char *in_seq, Constraint_list *CL);
+
+/******************************************************************/
+/* GENERIC PAIRWISE METHODS */
+/* */
+/* */
+/******************************************************************/
+Constraint_list *best_pair4prot (Job_TC *job);
+Constraint_list *best_pair4rna (Job_TC *job);
+Alignment * fast_pair (Job_TC *job);
+Constraint_list *hash_pair (TC_method *M , char *in_seq, Constraint_list *CL);
+
+void toggle_case_in_align_two_sequences(int value);
+Alignment * align_two_sequences ( char *seq1, char *seq2, char *matrix, int gop, int gep, char *align_mode);
+Alignment * align_two_aln ( Alignment *A1, Alignment *A2, char *in_matrix, int gop, int gep, char *in_align_mode);
+NT_node make_root_tree ( Alignment *A,Constraint_list *CL,int gop, int gep,Sequence *S, char *tree_file,int maximise);
+NT_node ** make_tree ( Alignment *A,Constraint_list *CL,int gop, int gep,Sequence *S, char *tree_file, int maximise);
+int ** get_pw_distances ( Alignment *A,Constraint_list *CL,int gop, int gep, char **out_seq, char **out_seq_name, int out_nseq, char *tree_file, char *tree_mode, int maximise);
+Alignment *stack_progressive_nol_aln_with_seq_coor(Constraint_list *CL,int gop, int gep,Sequence *S, int **seq_coor, int nseq);
+Alignment *stack_progressive_aln_with_seq_coor (Constraint_list*CL,int gop, int gep, Sequence *S, int **coor, int nseq);
+Alignment *stack_progressive_aln(Alignment *A, Constraint_list *CL, int gop, int gep);
+Alignment *est_progressive_aln(Alignment *A, Constraint_list *CL, int gop, int gep);
+void analyse_seq ( Alignment *A, int s);
+
+char ** list_file2dpa_list_file (char **list_file, int *len,int maxnseq, Sequence *S);
+Alignment * seq2aln_group (Alignment *A, int T, Constraint_list *CL);
+
+Alignment *profile_aln (Alignment *A, Constraint_list *CL);
+Alignment * iterative_tree_aln (Alignment *A,int n, Constraint_list *CL);
+Alignment * iterative_aln ( Alignment*A, int nseq, Constraint_list *CL);
+Alignment * seq_aln ( Alignment*A, int nseq, Constraint_list *CL);
+Alignment *tsp_aln (Alignment *A, Constraint_list *iCL, Sequence *S);
+Alignment *iterate_aln ( Alignment*A, int nit, Constraint_list *CL);
+Alignment *realign_aln ( Alignment*A, Constraint_list *CL);
+Alignment *very_fast_aln (Alignment*A, int nseq, Constraint_list *CL);
+Alignment *simple_progressive_aln (Sequence *S, NT_node **T, Constraint_list *CL, char *mat);
+Alignment *frame_aln (Alignment *A, int n,Constraint_list *CL);
+Alignment *dpa_aln (Alignment *A, Constraint_list *CL);
+Alignment *new_dpa_aln (Alignment *A, Constraint_list *CL);
+Alignment * make_delayed_tree_aln (Alignment *A,int n, Constraint_list *CL);
+
+NT_node* delayed_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+int node2seq_list (NT_node P, int *ns, int *ls);
+Alignment* delayed_tree_aln1 ( NT_node P,Alignment*A,Constraint_list *CL, int threshold);
+Alignment* delayed_tree_aln2 ( NT_node P,Alignment*A,Constraint_list *CL, int threshold);
+
+NT_node* tree2ao (NT_node LT, NT_node RT,Alignment *A, int nseq,Constraint_list *CL);//tree2align_order
+NT_node* tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+NT_node* local_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+NT_node* seqan_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+
+
+NT_node* tree_realn ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+
+int split_condition (int nseq, int score, Constraint_list *CL);
+
+int profile_pair_wise (Alignment *A, int n1, int *l1, int n2, int *l2, Constraint_list *CL);
+int pair_wise (Alignment *A, int*ns, int **l_s,Constraint_list *CL );
+int hh_pair_wise (Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int co_pair_wise (Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int empty_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL, int glocal);
+
+
+Pwfunc get_pair_wise_function (Pwfunc func, char *dp_mode, int *glocal);
+
+
+/*********************************************************************/
+char *build_consensus ( char *seq1, char *seq2, char *dp_mode);
+int fastal (int argv, char **arg);
+int tree_aln_N ( NT_node P, Sequence *S, int N, int argc, char **argv);
+
git://source.jalview.org / jabaws.git / blobdiff