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/* File: dotter.h
* Author: Erik Sonnhammer, 1999-08-26
* 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:
* Exported functions:
* Only 3 parameters are mandatory, the rest can be set to NULL.
* A minimal call would look like:
*
* dotter(type, 0, 0, qseq, 0, 0, sseq, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
*
* NOTE: qseq and sseq must be g_malloc'ed in the calling routine.
* They are g_free'd by Dotter.
*----------------------------------------------------------------------------
*/
#ifndef DEF_DOTTER_H
#define DEF_DOTTER_H
#include <seqtoolsUtils/blxmsp.hpp>
/* Possible graphical formats the plot can be exported as */
typedef enum _DotterExportFormat
{
DOTTER_EXPORT_NONE, /* Don't export the plot to a graphical format */
DOTTER_EXPORT_PDF, /* PDF */
DOTTER_EXPORT_PS, /* Postscript */
DOTTER_EXPORT_SVG /* Scalable vector graphics */
} DotterExportFormat;
/* Options specifying the initial state for dotter */
typedef struct _DotterOptions
{
int qoffset; /* qoffset + 1 gives the value of the first coord on the ref seq */
int soffset; /* soffset + 1 gives the value of the first coord on the match seq */
gboolean selfcall; /* whether called internally, i.e. so that features/sequences will be piped into dotter rather than read from files */
int qlen; /* length of the ref seq */
int slen; /* length of the match seq */
int dotterZoom; /* initial zoom level */
int install : 1; /* whether to add -install to the dotter args (for private colormaps) */
int pixelFacset;
int seqInSFS; /* whether the sequences are in the features file, i.e. there are no separate sequence files */
float memoryLimit;
char *savefile; /* file to save the dot-plot to (batch mode; saves the dot-matrix so it can be loaded later and interacted with) */
char *exportfile; /* file to export the dot-plot to (batch mode; exports to a graphical format, e.g. pdf or ps. Default is pdf unless file extension indicates otherwise) */
char *loadfile; /* file to load a dot-plot from */
char *FSfilename; /* file containing features i.e. MSPs */
char *mtxfile; /* caller-supplied matrix file */
char *winsize; /* caller-supplied sliding-window size */
char *qname; /* reference (horizontal) sequence name */
char *qseq; /* reference (horizontal) sequence data */
char *sname; /* match (vertical) sequence name */
char *sseq; /* match (vertical) sequence data */
gboolean mirrorImage; /* display mirror image in self comparisons (i.e. so we only have to calculate half of the dot-plot) */
gboolean watsonOnly; /* only show the watson (forward) strand of the ref seq */
gboolean crickOnly; /* only show the crick (reverse) strand of the ref seq */
gboolean hspsOnly; /* only draw HSPs (i.e. don't calculate the dot-plot, just draw lines where we know HSPs should be) */
gboolean swapGreyramp; /* swap the default black/white points on the greyramp tool (inverts the colors) */
gboolean breaklinesOn; /* whether to enable breaklines between sequences */
gboolean hozScaleRev; /* revese the horizontal scale */
gboolean vertScaleRev; /* revese the vertical scale */
gboolean negateCoords; /* negate the displayed coords when the scale is reversed, i.e. so they still appear to increase from left-to-right */
gboolean abbrevTitle; /* abbrev window title prefix to save space */
BlxMessageData msgData; /* data to be passed to the message handlers */
char *windowColor; /* if not null, background color for the window */
} DotterOptions;
void dotter(
const BlxBlastMode blastMode, /* Mandatory, one of { BLASTP, BLASTN, BLASTX }
P -> Protein-Protein
N -> DNA-DNA
X -> DNA-Protein */
DotterOptions *options, /* Optional, may be NULL
Various options for display features */
const BlxStrand refSeqStrand, /* which strand of the reference sequence was passed */
const BlxStrand matchSeqStrand, /* which strand of the match sequence was passed */
int qcenter, /* Optional, may be NULL
Coordinate to centre horisontal sequence on */
int scenter, /* Optional, may be NULL
Coordinate to centre horisontal sequence on */
MSP *MSPs, /* Optional, may be NULL
List of MSPs containing genes and blast matches */
GList *seqList, /* Optional, may be NULL
List of all match sequences, as BlxSequences */
int MSPoff /* Optional, may be NULL
Coordinate offset of MSPs */
);
#endif /* !defined DEF_DOTTER_H */
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