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/* File: blxcontext.hpp
* Author: Gemma Barson, 2016-04-06
* Copyright (c) 2016 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: A Blixem context class, containing all status information
* required for a blixem instance.
*----------------------------------------------------------------------------
*/
#ifndef DEF_BLXCONTEXT_H
#define DEF_BLXCONTEXT_H
#include <gtk/gtk.h>
#include <blixemApp/blixem_.hpp>
#include <set>
// We filter features based on different types; for now, just 'matches' and 'everything else'.
enum class GroupType {NONE, MATCH, OTHER};
class BlxContext
{
public:
// Constructors
BlxContext(CommandLineOptions *options,
const IntRange* const refSeqRange_in,
const IntRange* const fullDisplayRange_in,
const char *paddingSeq_in,
GArray* featureLists_in[],
GList *seqList_in,
GSList *supportedTypes_in,
GtkWidget *widget_in,
GtkWidget *statusBar_in,
const gboolean External_in,
GSList *styles_in);
~BlxContext();
// Access
double charWidth() const;
double charHeight() const;
BlxStrand activeStrand() const;
// Query
bool isSeqSelected(const BlxSequence *seq) const;
SequenceGroup *getFirstSequenceGroup(const BlxSequence *seqToFind) const;
std::list<const SequenceGroup*> getSequenceGroups(const BlxSequence *seqToFind) const;
GList *getSelectedSeqsByType(const BlxSequenceType type) const;
BlxSequence* getSelectedTranscript(int *num_transcripts) const;
std::set<GQuark> getSelectedSources() const;
GList* getFeaturesInSourceList(std::set<GQuark> sources) const;
void highlightBoxCalcBorders(GdkRectangle *drawingRect, GdkRectangle *highlightRect,
const IntRange *fullRange, const IntRange *highlightRange,
const int yPadding);
// Modify
void saveSettingsFlags(GKeyFile *key_file);
void killAllSpawned();
void calculateDepth(const int numUnalignedBases);
int calculateTotalDepth(const IntRange *range, const BlxStrand strand);
int getDepth(const int coord, const char *base_char = NULL, const BlxStrand strand = BLXSTRAND_NONE);
int getDepthForCounter(const int coord, const DepthCounter counter);
bool filterGroupType(const GroupType groupType) const;
bool isGroupVisible(const SequenceGroup *group, const BlxSequenceType feature_type = BLXSEQUENCE_UNSET) const;
bool isGroupVisible(std::list<const SequenceGroup*> groups, const BlxSequenceType featureType) const;
SequenceGroup* getQuickGroup(const bool isFilter);
void destroySequenceGroup(SequenceGroup **seqGroup);
void deleteAllSequenceGroups();
void disableAllGroups();
void disableAllQuickGroups();
GtkWidget *statusBar; /* The Blixem window's status bar */
char *refSeq; /* The reference sequence (always forward strand, always DNA sequence) */
const char *refSeqName; /* The name of the reference sequence */
IntRange refSeqRange; /* The range of the reference sequence */
IntRange fullDisplayRange; /* The range of the displayed sequence */
int refSeqOffset; /* how much the coordinate system has been offset from the input coords */
BlxBlastMode blastMode; /* The type of blast matching that was used */
BlxSeqType seqType; /* The type of the match sequences, e.g. DNA or peptide */
char **geneticCode; /* The genetic code used to translate DNA <-> peptide */
int numFrames; /* The number of reading frames */
GArray *bulkFetchDefault; /* The default method(s) of bulk fetching sequences (can be overridden by an MSPs data-type properties) */
GArray *userFetchDefault; /* The default method(s) for interactively fetching individual sequences */
GArray *optionalFetchDefault; /* The default method(s) for bulk fetching optional sequence data */
GHashTable *fetchMethods; /* List of fetch methods, keyed on name as a GQuark */
char* dataset; /* the name of a dataset, e.g. 'human' */
gboolean optionalColumns; /* load data for optional columns on startup to populate additional info like tissue-type */
gboolean saveTempFiles; /* whether to save temporary files created to store results of file conversions */
MSP *mspList; /* List of all MSPs. Obsolete - use featureLists array instead */
GArray* featureLists[BLXMSP_NUM_TYPES]; /* Array indexed by the BlxMspType enum. Each array entry contains a zero-terminated array of all the MSPs of that type. */
GList *matchSeqs; /* List of all match sequences (as BlxSequences). */
GSList *supportedTypes; /* List of supported GFF types */
const char *paddingSeq; /* A sequence of padding characters, used if the real sequence could not be found. All padded MSPs
* use this same padding sequence - it is constructed to be long enough for the longest required seq. */
gboolean displayRev; /* True if the display is reversed (i.e. coords decrease as you read from left to right, rather than increase). */
gboolean external; /* True if Blixem was run externally or false if it was run internally from another program */
GList *selectedSeqs; /* A list of sequences that are selected (as BlxSequences) */
GList *sequenceGroups; /* A list of SequenceGroups */
DotterRefType dotterRefType; /* Whether to dotter a ref seq range or a transcript */
DotterMatchType dotterMatchType; /* Saved type of match to call dotter on */
char *dotterAdhocSeq; /* Saves the sequence text the user pastes into the dotter dialog */
gboolean dotterHsps; /* Whether the dotter "HSPs only" option is on by default */
gboolean dotterSleep; /* Whether the sleep-dotter option is on by default */
int dotterStart; /* Start coord to call dotter on, or UNSET_INT to calculate automatically */
int dotterEnd; /* End coord to call dotter on, or UNSET_INT to calculate automatically */
int dotterZoom; /* Zoom param to call dotter with, if using manual params */
GArray *defaultColors; /* Default colors used by Blixem */
gboolean usePrintColors; /* Whether to use print colors (i.e. black and white) */
char *windowColor; /* If not null, background color for the window */
GList *columnList; /* A list of details about all the columns in the detail view (might have been better to use an array here but it's a short list so not important) */
GSList *styles;
gboolean flags[BLXFLAG_NUM_FLAGS]; /* Array of all the flags the user can toggle. Indexed by the BlxFlags enum. */
GtkWidget *dialogList[BLXDIALOG_NUM_DIALOGS]; /* Array of all the persistent dialogs in the application */
GSList *spawnedProcesses; /* List of processes spawned by Blixem */
BlxModelId modelId; /* which tree model to use (i.e. normal or squashed) */
/* This array holds the depth (num alignments) at each coord of the ref seq for
* different types of counter. For each counter there is an array the same lenth as the
* reference sequence. This could cause memory problems with a large region. Generally
* though the length of the reference sequence is not that great and we are more concerned with
* fast access as the user interacts with the display.*/
int *depthArray[DEPTHCOUNTER_NUM_ITEMS];
int minDepth; /* minimum value in the depthArray */
int maxDepth; /* maximum value in the depthArray */
long ipresolve; /* specify whether curl should use ipv4/ipv6 */
const char *cainfo; /* specify location of curl cainfo file */
bool fetch_debug; /* enable verbose debug output in fetch methods */
private:
void createColors(GtkWidget *widget);
void initialiseFlags(CommandLineOptions *options);
void loadSettings();
double m_charWidth;
double m_charHeight;
};
#endif /* DEF_BLXCONTEXT_H */
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