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/* File: belvuAlignment.h
* Author: Gemma Barson, 2011-04-12
* Copyright (c) 2011 - 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: Draws the alignment section in the main Belvu window
*----------------------------------------------------------------------------
*/
#ifndef _belvualignment_h_included_
#define _belvualignment_h_included_
#include <belvuApp/belvu_.hpp>
#include <gtk/gtk.h>
GtkWidget* createBelvuAlignment(BelvuContext *bc, const char *title, const int wrapWidth);
void belvuAlignmentRedrawAll(GtkWidget *belvuAlignment);
void belvuAlignmentRefreshAll(GtkWidget *belvuAlignment);
void updateOnAlignmentLenChanged(GtkWidget *belvuAlignment);
void onBelvuAlignmentFontSizeChanged(GtkWidget *belvuAlignment);
void updateOnVScrollSizeChaged(GtkWidget *belvuAlignment);
void centerHighlighted(BelvuContext *bc, GtkWidget *belvuAlignment);
void removeSelectedSequence(BelvuContext *bc, GtkWidget *belvuAlignment);
void removeGappySeqs(BelvuContext *bc, GtkWidget *belvuAlignment, const double cutoff);
void removePartialSeqs(BelvuContext *bc, GtkWidget *belvuAlignment);
void removeRedundantSeqs(BelvuContext *bc, GtkWidget *belvuAlignment, const double cutoff);
void removeOutliers(BelvuContext *bc, GtkWidget *belvuAlignment, const double cutoff);
void removeByScore(BelvuContext *bc, GtkWidget *belvuAlignment, const double cutoff);
void vScrollStartEnd(GtkWidget *belvuAlignment, const gboolean start);
void hScrollStartEnd(GtkWidget *belvuAlignment, const gboolean start);
void vScrollPageUpDown(GtkWidget *belvuAlignment, const gboolean up);
void hScrollPageLeftRight(GtkWidget *belvuAlignment, const gboolean left);
void vScrollUpDown(GtkWidget *belvuAlignment, const gboolean up, const int numRows);
void hScrollLeftRight(GtkWidget *belvuAlignment, const gboolean left, const int numChars);
int belvuAlignmentGetWidth(GtkWidget *belvuAlignment);
void calculateDrawingSizes(GtkWidget *belvuAlignment);
void updateHeaderColumnsSize(GtkWidget *belvuAlignment);
#endif /* _belvualignment_h_included_ */
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