--- /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_DP_GOTOH_NW_H
+#define __UTIL_DP_GOTOH_NW_H
+/*pair wise aln implementations*/
+
+int idscore_pairseq (char *s1, char *s2, int gop, int gep, int **m, char *mode);
+int idscore_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int glocal_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int gotoh_pair_wise_lgp ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int test_pair_wise (Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+
+int glocal2_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+int linked_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int linked_pair_wise_collapse ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int cl2pair_list_ecl_ext_pc ( Alignment *A, int *ns, int **ls, Constraint_list *CL, int ***list_in, int *n_in);
+int procoffee_pair_wise ( Alignment *A, int *nsi, int **lsi, Constraint_list *CL);
+
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/////////////// ///////////////
+/////////////// ///////////////
+/////////////// Profile_PW ///////////////
+/////////////// ///////////////
+/////////////// ///////////////
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+int **aln2prf (Alignment *A, char *matrix);
+char *add_sequence2prf (char *seq, char *al,int **prf, int lj, int gop, int gep);
+
+#endif
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