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/* File: blxdotter.h
* Author: Gemma Barson, 2010-02-03
* Copyright (c) 2010 - 2012 Genome Research Ltd
* ---------------------------------------------------------------------------
* SeqTools 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 3
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
* ---------------------------------------------------------------------------
* This file is part of the SeqTools sequence analysis package,
* written by
* Gemma Barson (Sanger Institute, UK) <gb10@sanger.ac.uk>
*
* based on original code by
* Erik Sonnhammer (SBC, Sweden) <Erik.Sonnhammer@sbc.su.se>
*
* and utilizing code taken from the AceDB and ZMap packages, written by
* Richard Durbin (Sanger Institute, UK) <rd@sanger.ac.uk>
* Jean Thierry-Mieg (CRBM du CNRS, France) <mieg@kaa.crbm.cnrs-mop.fr>
* Ed Griffiths (Sanger Institute, UK) <edgrif@sanger.ac.uk>
* Roy Storey (Sanger Institute, UK) <rds@sanger.ac.uk>
* Malcolm Hinsley (Sanger Institute, UK) <mh17@sanger.ac.uk>
*
* Description: Provides functionality to call Dotter as an external
* application.
*
* Determines which sequences to call Dotter with based on the
* current selection in Blixem. Provides a dialog allowing the
* user to set certain parameters and optionally calculates a
* sensible coordinate range to call Dotter with.
*
* Generally Dotter will be called with one alignment sequence vs
* a relevant portion of the reference sequence. It can also be
* called on the reference sequence vs itself. This is useful if
* the reference sequence has been constructed from several
* sequences concatenated together and one wishes to identify
* alignments between those sequences.
*----------------------------------------------------------------------------
*/
#ifndef _blx_dotter_h_included_
#define _blx_dotter_h_included_
#include <gtk/gtk.h>
#include <blixemApp/blixem_.hpp>
void showDotterDialog(GtkWidget *blxWindow, const gboolean bringToFront);
gboolean callDotterOnSelectedSeqs(GtkWidget *blxWindow, const gboolean hspsOnly, const gboolean sleep, const DotterRefType refType, GError **error);
#endif /* _blx_dotter_h_included_ */
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