--- /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*******************************/
+
+struct orp
+{
+ char name[100];
+ char mode[100];
+ int ncomp;
+ int nseq;
+ int len;
+
+ Alignment *A;
+ Alignment *P;
+ Alignment *S;
+
+ int *pos;
+ char ***motif;
+ float sp;
+ float sn;
+ float sen2;
+ float best;
+ int tp;
+ int tn;
+ int fp;
+ int fn;
+
+ int offset;
+ float evalue;
+ struct orp *PR;
+};
+
+typedef struct orp ORP;
+
+typedef Alignment * (*filter_func) (Alignment *, Alignment*, int,int, char *);
+/************************************************************************************/
+/* ALIGNMENT ANALYZE : SAR */
+/************************************************************************************/
+int display_simple_sar_analyze_pair_col (Alignment *A, Alignment *SAR, char *mode);
+int **simple_sar_analyze_pair_col ( Alignment *inA, Alignment *SAR, char *mode);
+int ***simple_sar_predict ( Alignment *inA, Alignment *SAR, char *mode);
+int display_simple_sar_analyze_col ( Alignment *inA, Alignment *SAR, char *mode);
+Alignment *sar_analyze4 (Alignment *A, Alignment *SAR, char *name);/*28/08/06*/
+Alignment *sar_analyze3 (Alignment *A, Alignment *SAR, char *name);
+Alignment *sar_analyze2 (Alignment *A, Alignment *SAR, char *name);
+Alignment *sar_analyze (Alignment *A, Alignment *SAR, char *name);
+int aln2sar_column_list ( Alignment *A, char *filter);
+float get_sar_sim (char *seq1, char *seq2);
+float get_sar_sim2 (char *seq1, char *seq2);
+Alignment *aln2weighted_sar_score ( Alignment *A,Alignment *B, char *weight_file, char *compound);
+float seq2weighted_sar_score ( char *seq, int **weight);
+
+int sarset2subsarset ( Alignment *A, Alignment *S, Alignment **subA, Alignment **subS, Alignment *SUB);
+int sar2subsar (Alignment *A, Alignment *S, Alignment **subA, Alignment **subS, char **slist, int nl);
+int sar2subsar_file ( Alignment *A, Alignment *S, char *aln, char *sar);
+
+Alignment *weight2sar (Alignment *A, Alignment *SAR, char *weight_file, int limit);
+Alignment * sar2simpred (Alignment *A, Alignment *SAR, char *pos, char *compound, int L,int U );
+Alignment * sar2simpred2 (Alignment *A, Alignment *SAR, char *seqlist, char *posfile, char *compound, int L1 );
+
+Alignment *display_sar ( Alignment *A, Alignment *SAR, char *compound);
+NT_node sar2tree (Alignment *A, char *mode);
+/************************************************************************************/
+/* ALIGNMENT ANALYZE : SAR FOR OR */
+/************************************************************************************/
+
+Alignment * or_scan (Alignment *A, Alignment *B, char *param);
+Alignment * or_sar (Alignment *A, Alignment *B, char *param, int print);
+ORP * or_loo ( Alignment *inA, Alignment *inS, char *mode, int *pos,int print);
+
+
+ORP * combine_n_predictions (ORP **R,Alignment *A, Alignment *B);
+ORP* combine_2_predictions ( ORP *IN, ORP *TO,Alignment *A, Alignment *B);
+ORP * display_or_summary (ORP *CP, char *mode, FILE *fp, int print);
+
+Alignment * or_comp_loo ( Alignment *inA, Alignment *inS, char *mode, int *pos,int print);
+int * or_comp_pos ( Alignment *inA, Alignment *inS, char *mode,int print);
+float or_id_evaluate ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+char* or_id_evaluate2 ( Alignment *A, Alignment *S, char *mode, int *pos, int print, float *score);
+float or_loo_evaluate ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+float or_loo_evaluate2 ( Alignment *A, Alignment *S, char *mode, int *pos, int print);
+
+Alignment * or_test ( Alignment *inA, Alignment *inS, char *mode);
+Alignment * or_jack(Alignment *A, Alignment *S, char *param);
+Alignment * or_predict(Alignment *A, Alignment *S, char *mode);
+Alignment * or_aln2pos_aln (Alignment *A, Alignment *S, char *mode);
+ORP* or_self_predict(Alignment *inA, Alignment *inS, char *mode, int *pos, int print);
+Alignment * or_sim(Alignment *A, Alignment *S, char *mode);
+
+Alignment *display_pos (Alignment *A, Alignment *B, int *pos, char *mode);
+
+float evaluate_prediction (Alignment *R, Alignment *P, char *mode, int print);
+ORP* new_evaluate_prediction (ORP *P, char *mode, int print);
+
+Alignment * aln2prediction (Alignment *A,char ***motif, int *pos);
+int * aln2predictive_positions (Alignment *A, Alignment *B, char *mode, int print);
+int * aln2predictive_positions_mat (Alignment *A, Alignment *B, char *mode, int print);
+int * aln2predictive_positions_scan (Alignment *A, Alignment *B, char *mode, int print);
+char *** compounds2motifs (Alignment *A, Alignment *B, int *pos, int depth, char *mode, int print);
+char ** compound2motif (Alignment *A, Alignment *B, int *pos, int depth, int c, char *mode, int print);
+double pos2sim (Alignment *A, Alignment *B, int *pos);
+double sar_aln2r (Alignment *A, Alignment *B, int *pos, int print);
+double sar_aln2delta (Alignment *A, Alignment *B, int *pos, int print);
+Alignment * jack_sar(Alignment *A, Alignment *S, char *param);
+Alignment *set_sar (Alignment *A, Alignment *S, char *param);
+char * get_compound_name (int c, char *mode);
+Alignment *get_prediction_target (Alignment *A, Alignment *S, char *param);
+int * file2pos_list (Alignment *A, char *posfile);
+ORP * declare_or_prediction ( int ncomp, int nseq, int len);
+void free_orp_list ( ORP**P);
+void free_orp ( ORP*P);
+double evaluate_sar_score1 ( int len, int n11, int n1a, int n1b);
+double evaluate_sar_score2 ( int len, int n11, int n1a, int n1b);
+
+Sequence * compare_sar_sequence( Sequence *S1, Sequence *S2, int depth);
git://source.jalview.org / jabaws.git / blobdiff