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|
/* File: blixem_.h
* Author: Ed Griffiths, 2001-11-29
* Copyright (c) 2009 - 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: Internal header for Blixem package-wide code
*----------------------------------------------------------------------------
*/
#ifndef DEF_BLIXEM_P_H
#define DEF_BLIXEM_P_H
#include <gtk/gtk.h>
#include <config.h>
#include <seqtoolsUtils/utilities.hpp>
#include <seqtoolsUtils/blxmsp.hpp>
#include <seqtoolsUtils/version.hpp>
#include <seqtoolsUtils/seqtoolsFetch.hpp>
#include <gbtools/gbtools.hpp>
class BlxContext;
/* blixem program version and information. */
#define BLIXEM_TITLE "Blixem"
#define BLIXEM_PREFIX BLIXEM_TITLE" - " /* The prefix to use for window titles etc. */
#define BLIXEM_PREFIX_ABBREV "B: " /* An abbreviated version of the prefix to save space e.g. good for displaying in the taskbar */
#define BLIXEM_DESC "Multiple alignment visualisation tool."
/* The Seqtools package version should be specified in src/version.m4. autoconf will then set PACKAGE_VERSION in config.h */
#define BLIXEM_VERSION_STRING SEQTOOLS_VERSION
#define BLIXEM_PACKAGE_VERSION UT_MAKE_VERSION_INFO_STRING(PACKAGE_NAME, SEQTOOLS_VERSION)
#define BLIXEM_TITLE_STRING UT_MAKE_TITLE_STRING(BLIXEM_TITLE, BLIXEM_VERSION_STRING)
#define BLIXEM_VERSION_COMPILE BLIXEM_VERSION_STRING " " UT_MAKE_COMPILE_DATE()
#define BLIXEM_COPYRIGHT_STRING UT_MAKE_COPYRIGHT_STRING("2009-2015")
#define BLIXEM_WEBSITE_STRING "http://www.sanger.ac.uk/resources/software/seqtools/"
#define BLIXEM_LICENSE_STRING UT_MAKE_LICENCE_STRING(BLIXEM_TITLE)
#define COLUMN_WIDTHS_GROUP "column-widths" /* group name in the config file */
#define COLUMN_SUMMARY_GROUP "summary-columns" /* group name in the config file for
columns to include in the summary info */
/* Define the columns' default widths and titles. */
#define BLXCOL_DEFAULT_WIDTH 50 /* default width for generic columns */
#define BLXCOL_SEQNAME_WIDTH 120 /* default width for the name column */
#define BLXCOL_SCORE_WIDTH 40 /* default width for the score column */
#define BLXCOL_ID_WIDTH 45 /* default width for the ID column */
#define BLXCOL_SOURCE_WIDTH 85 /* default width for source column */
#define BLXCOL_GROUP_WIDTH 58 /* default width for group column */
#define BLXCOL_START_WIDTH 50 /* default width for the start coord column */
#define BLXCOL_END_WIDTH 80 /* default width for end coord column (bigger because it also spans the scrollbar) */
#define BLXCOL_SEQUENCE_WIDTH 40 /* default width for sequence column */
#define BLXCOL_ORGANISM_WIDTH 40 /* default width for organism column */
#define BLXCOL_GENE_NAME_WIDTH 58 /* default width for gene-name column */
#define BLXCOL_STRAIN_WIDTH 85 /* default width for strain column */
#define BLXCOL_TISSUE_TYPE_WIDTH 100 /* default width for tissue-type column */
/*
* config file groups/keywords, these should not be changed willy nilly as they
* are used external programs and users when constructing config files.
* If you change things or add additional groups or values, then you should
* update the getConfig function.
*/
/* For overall blixem settings. */
#define BLIXEM_OLD_BULK_FETCH "default-fetch-mode" /* for compatibility with old config files (new config files use SEQTOOLS_BULK_FETCH) */
/* Fetch settings */
#define FETCH_MODE_KEY "fetch-mode" /* any group with this key is a fetch method, and this specifies what type of fetch to do */
/* Required keys for http-and pipe-fetch groups */
#ifdef PFETCH_HTML
#define HTTP_FETCH_LOCATION "url"
#define HTTP_FETCH_PORT "port"
#define HTTP_FETCH_ARGS "request"
#define HTTP_FETCH_COOKIE_JAR "cookie-jar"
#define HTTP_FETCH_PROXY "proxy"
#define HTTP_FETCH_IPRESOLVE "ipresolve"
#define HTTP_FETCH_CAINFO "cainfo"
#define PIPE_FETCH_LOCATION "command"
#define PIPE_FETCH_ARGS "args"
#endif
/* Required keys for socket-fetch groups */
#define SOCKET_FETCH_LOCATION "command"
#define SOCKET_FETCH_NODE "node"
#define SOCKET_FETCH_PORT "port"
#define SOCKET_FETCH_ARGS "args"
/* Required keys for www-fetch groups */
#define WWW_FETCH_LOCATION "url"
#define WWW_FETCH_ARGS "request"
/* Required keys for db-fetch groups */
#define DB_FETCH_LOCATION "location"
#define DB_FETCH_QUERY "query"
#define DB_FETCH_COLUMNS "columns"
/* Required keys for command-fetch groups */
#define COMMAND_FETCH_SCRIPT "command"
#define COMMAND_FETCH_ARGS "args"
/* Generic fetch keys (applicable to more than one method) */
#define FETCH_OUTPUT "output" /* output format */
#define FETCH_SEPARATOR "separator" /* separator, when combining multiple sequences */
#define FETCH_ERRORS "errors" /* list of messages that indicate errors */
#define FETCH_DEBUG "curl-debug" /* enable verbose debug output */
/* For settings */
#define BLIXEM_SETTINGS_FILE ".blixemrc" /* default file name for saving blixem settings to */
#define SETTINGS_GROUP "user-settings"
#define STYLES_FILE_KEY "stylesfile" /* styles-file key in the [blixem] group */
#define SETTING_NAME_INVERT_SORT "invert-sort"
#define SETTING_NAME_HIGHLIGHT_DIFFS "highlight-diffs"
#define SETTING_NAME_HIGHLIGHT_VARIATIONS "highlight-variations"
#define SETTING_NAME_SHOW_VARIATION_TRACK "show-variations-track"
#define SETTING_NAME_SHOW_UNALIGNED "show-unaligned"
#define SETTING_NAME_SHOW_UNALIGNED_SELECTED "show-unaligned-selected-seq"
#define SETTING_NAME_LIMIT_UNALIGNED_BASES "limit-unaligned"
#define SETTING_NAME_SHOW_POLYA_SITE "show-polya-site"
#define SETTING_NAME_SHOW_POLYA_SITE_SELECTED "show-poly-site-selected-seq"
#define SETTING_NAME_SHOW_POLYA_SIG "show-poly-sig"
#define SETTING_NAME_SHOW_POLYA_SIG_SELECTED "show-polya-sig-selected-seq"
#define SETTING_NAME_SHOW_SPLICE_SITES "show-splice-sites"
#define SETTING_NAME_SHOW_MAYBE_CANONICAL "show-maybe-canonical"
#define SETTING_NAME_SQUASH_MATCHES "squash-matches"
#define SETTING_NAME_SHOW_COLINEARITY "show-colinearity"
#define SETTING_NAME_SHOW_COLINEARITY_SELECTED "show-colinearity-selected"
/* would be good to get rid of this.... */
#define FULLNAMESIZE 255
#define MKSTEMP_CONST_CHARS_GFF "BLIXEM_gff" /* the prefix to use when creating a temp file name */
#define MKSTEMP_REPLACEMENT_CHARS "XXXXXX" /* the required string that will be replaced by unique chars when creating a temp file name */
#define HIGHLIGHT_BOX_Y_PAD 2 /* this provides space between highlight box and the top/bottom of the grid */
#define HIGHLIGHT_BOX_MIN_WIDTH 5 /* minimum width of the highlight box */
/* Blixem config/fetch error domain */
#define BLX_CONFIG_ERROR g_quark_from_string("Blixem config")
#define BLX_FETCH_ERROR g_quark_from_string("Blixem config")
/* Error codes */
typedef enum
{
BLX_CONFIG_ERROR_NO_GROUPS, /* no groups in config file */
BLX_CONFIG_ERROR_INVALID_KEY_TYPE, /* invalid key type given in config file */
BLX_CONFIG_ERROR_MISSING_KEY, /* a required key is missing */
BLX_CONFIG_ERROR_INVALID_FETCH_MODE, /* invalid fetch mode specified */
BLX_CONFIG_ERROR_INVALID_OUTPUT_FORMAT, /* invalid output format specified for fetch mode */
BLX_CONFIG_ERROR_WARNINGS, /* warnings found while reading config file */
BLX_CONFIG_ERROR_SUBSTITUTION, /* error with substitution string */
BLX_CONFIG_ERROR_INVALID_FETCH_METHOD, /* null fetch method */
BLX_CONFIG_ERROR_NO_EXE, /* fetch method executable does not exist */
BLX_CONFIG_ERROR_NULL_FETCH, /* fetch method is null */
BLX_CONFIG_ERROR_NO_ARGS, /* mandatory args weren't specified */
BLX_CONFIG_ERROR_INVALID_IPRESOLVE /* invalid value given for ipresolve config */
} BlxConfigError;
/* Error codes */
typedef enum
{
BLX_FETCH_ERROR_SOCKET, /* error creating socket */
BLX_FETCH_ERROR_HOST, /* unknown host */
BLX_FETCH_ERROR_CONNECT, /* error connecting to host */
BLX_FETCH_ERROR_SEND, /* error sending to socket */
BLX_FETCH_ERROR_PATH /* executable not found in path */
} BlxFetchError;
/* Function pointer to a function that performs a fetch of a particular sequence */
typedef void(*FetchFunc)(const char *seqName, gpointer fetchMethod, const gboolean bulk, GtkWidget *blxWindow);
/* The following are used to define default colors for certain types of features in Blixem.
* One of several different actual colors from the BlxColor struct may be used depending
* on state, e.g. we use a different color if "print colors" (i.e. black and
* white mode) is on. */
typedef enum
{
BLXCOLOR_MIN, /* dummy value so that we don't get a zero ID */
BLXCOLOR_BACKGROUND, /* background color of the widgets */
BLXCOLOR_REF_SEQ, /* default background color for the reference sequence */
BLXCOLOR_MATCH, /* background color for an exact match */
BLXCOLOR_CONS, /* background color for a conserved match */
BLXCOLOR_MISMATCH, /* background color for a mismatch */
BLXCOLOR_INSERTION, /* color for an insertion marker */
BLXCOLOR_EXON_START, /* color for the start boundary line of an exon */
BLXCOLOR_EXON_END, /* color for the end boundary line of an exon */
BLXCOLOR_CODON, /* color in which to highlight the nucleotides for the currently-selected codon */
BLXCOLOR_MET, /* background color for MET codons in the three frame translation */
BLXCOLOR_STOP, /* background color for STOP codons in the three frame translation */
BLXCOLOR_GRID_LINE, /* color of the gridlines in the big picture grids */
BLXCOLOR_GRID_TEXT, /* color of the text in the big picture grids */
BLXCOLOR_HIGHLIGHT_BOX, /* color of the highlight box in the big picture */
BLXCOLOR_PREVIEW_BOX, /* color of the preview box in the big picture */
BLXCOLOR_MSP_LINE, /* color of the MSP lines in the big picture */
BLXCOLOR_SNP, /* background color for SNPs */
BLXCOLOR_GROUP, /* default highlight color for generic groups */
BLXCOLOR_MATCH_SET, /* default highlight color for the special match-set group */
BLXCOLOR_EXON_FILL, /* fill color for an exon in the big picture */
BLXCOLOR_EXON_LINE, /* line color for an exon in the big picture */
BLXCOLOR_CDS_FILL, /* fill color for a CDS in the big picture (coding region) */
BLXCOLOR_CDS_LINE, /* line color for a CDS in the big picture (coding region) */
BLXCOLOR_UTR_FILL, /* fill color for an UTR in the big picture (non-coding/untranslated region) */
BLXCOLOR_UTR_LINE, /* line color for an UTR in the big picture (non-coding/untranslated region) */
BLXCOLOR_UNALIGNED_SEQ, /* color in which to show additional sequence in the match that is not part of the alignment */
BLXCOLOR_CANONICAL, /* background highlight color for canonical intron bases */
BLXCOLOR_NON_CANONICAL, /* background highlight color for non-canonical intron bases */
BLXCOLOR_MAYBE_CANONICAL,/* background highlight color for splice sites that are "maybe"
* canonical, that is, that would be canonical if on the other
* strand (helps to identify problems in data; common with BAM) */
BLXCOLOR_POLYA_TAIL, /* background color for polyA tails in the detail view */
BLXCOLOR_POLYA_SIGNAL, /* background color for non-annotated polyA signals in the detail view */
BLXCOLOR_POLYA_SIGNAL_ANN,/* background color for annotated polyA signals in the detail view */
BLXCOLOR_POLYA_SITE_ANN,/* background color for annotated polyA sites in the detail view */
BLXCOLOR_TREE_GRID_LINES,/* color of the tree grid lines (i.e. column separator lines) */
BLXCOLOR_CLIP_MARKER, /* color of the marker line used to indicate a match has been clipped */
BLXCOLOR_COVERAGE_PLOT, /* color of the coverage plot */
BLXCOLOR_ASSEMBLY_GAP, /* highlight color for assembly gaps */
BLXCOLOR_SELECTION, /* highlight color for selections */
BLXCOLOR_PARTIAL_EXON_CROSSHATCH, /* color of cross-hatch lines for partial exons */
BLXCOLOR_COLINEAR_PERFECT, /* color of lines joining alignment blocks that are perfectly colinear */
BLXCOLOR_COLINEAR_IMPERFECT, /* color of lines joining alignment blocks that are imperfectly colinear */
BLXCOLOR_COLINEAR_NOT, /* color of lines joining alignment blocks that are not colinear */
BLXCOL_NUM_COLORS
} BlxColorId;
/* Utility struct to pass around a set of colors from a styles file */
typedef struct _BlxStyleColors
{
char *fillColor;
char *lineColor;
char *fillColorSelected;
char *lineColorSelected;
char *fillColorCds;
char *lineColorCds;
char *fillColorCdsSelected;
char *lineColorCdsSelected;
gboolean normalFound;
gboolean cdsFound;
} BlxStyleColors;
/* This enum contains a list of all the boolean options that the user can toggle on/off */
typedef enum
{
BLXFLAG_MIN, /* Start index for looping through flags */
BLXFLAG_INVERT_SORT, /* Inverts the default sort order */
BLXFLAG_HIGHLIGHT_DIFFS, /* Hides matching bases and highlights mis-matching ones */
BLXFLAG_HIGHLIGHT_VARIATIONS, /* Whether to highlight bases that have variations in the reference sequence */
BLXFLAG_SHOW_VARIATION_TRACK, /* Shows the Variations track */
BLXFLAG_SHOW_UNALIGNED, /* Shows additional bits of the match sequence that are not part of the aligned section */
BLXFLAG_SHOW_UNALIGNED_SELECTED,/* Only show unaligned bits of sequence for the currently-selected sequence(s) */
BLXFLAG_LIMIT_UNALIGNED_BASES, /* If the show-unaligned-sequence option is on, limits how many bases from the unaligned sequence are shown */
BLXFLAG_SHOW_POLYA_SITE, /* Show polyA tails */
BLXFLAG_SHOW_POLYA_SITE_SELECTED,/* Only show polyA tails for the currently-selected sequence(s) */
BLXFLAG_SHOW_POLYA_SIG, /* Show polyA signals in the reference sequence */
BLXFLAG_SHOW_POLYA_SIG_SELECTED,/* Only show polyA signals for the currently-selected sequence(s) */
BLXFLAG_SHOW_SPLICE_SITES, /* Highlights splice sites in the reference sequence for the currently-selected MSPs */
BLXFLAG_SHOW_MAYBE_CANONICAL, /* Highlights "maybe canonical" splice sites */
BLXFLAG_OPTIONAL_COLUMNS, /* Gets set to true if the optional columns have been loaded */
BLXFLAG_SHOW_CDS, /* True if CDS/UTR regions should be shown; false if plain exons should be shown */
BLXFLAG_NEGATE_COORDS, /* True if coords should be negated when display is reversed (so coords appear to increase left-to-right when really they decrease) */
BLXFLAG_SAVE_TEMP_FILES, /* save any temporary files that blixem creates, e.g. the GFF file created by the region-fetch fetch mode */
BLXFLAG_ABBREV_TITLE, /* whether to abbreviate the window titles to save space */
BLXFLAG_LINK_FEATURES, /* whether features with the same name should be linked */
BLXFLAG_SHOW_COLINEARITY, /* whether to show colinearity lines between alignment blocks */
BLXFLAG_SHOW_COLINEARITY_SELECTED, /* whether to show colinearity lines for selected sequence only */
BLXFLAG_NUM_FLAGS /* Total number of flags e.g. for creating arrays and loops etc */
} BlxFlag;
/* Structure representing a group of sequences. This groups several BlxSequences together and
* sets various flags so that we can hide/highlight/etc all of the sequences in a group. */
typedef struct _SequenceGroup
{
char *groupName; /* user-friendly name for the group (should be unique to save confusion) */
int groupId; /* unique ID number for the group */
int order; /* field for sorting - lower numbers will be listed first */
GList *seqList; /* list of BlxSequences */
gboolean ownsSeqNames; /* If true, the group will free the sequence names when it is destroyed */
gboolean hidden; /* true if the group should be hidden from the detail view */
gboolean isFilter; /* true if this is a filter (i.e. hide everything not in a
* filter) */
gboolean isQuickGroup; /* true if the group was created by a quick-group or
* quick-filter option */
gboolean highlighted; /* true if the group should be highlighted */
GdkColor highlightColor; /* the color to highlight the group's sequences in (in both the big picture and the detail view) */
} SequenceGroup;
/* This enum gives a more meaningful way of indexing the "opts" string */
typedef enum
{
BLXOPT_MODE = 0, /* Blast mode: L = tblastx, N = blastn, P = blastp, T = tblastn, X = blastx */
BLXOPT_START_NEXT_MATCH = 1, /* 'M' means start at next match. Blank to ignore. */
BLXOPT_SHOW_BIG_PICT = 2, /* 'B' to show big picture, 'b' to hide it */
BLXOPT_REV_BIG_PICT = 3, /* 'R' to show the reverse strand in the big picture; 'r' just show the forward strand (blxparser.c) */
BLXOPT_FULL_EMBL_INFO = 4, /* 'F' to parse full embl info on startup; blank to just parse the sequence data (quicker) */
BLXOPT_FULL_ZOOM = 5, /* 'Z' to use full zoom by default; blank otherwise (blxparser.c) */
BLXOPT_INVERT_SORT = 6, /* 'I' to invert the default sort order; blank otherwise */
BLXOPT_HSP_GAPS = 7, /* 'G' for HSP gaps mode; blank otherwise (blxparser.c) */
BLXOPT_SORT_MODE = 8, /* Initial sort mode: i=ID, n=name, p=position, s=score, t=tissue type, m=strain, g=gene name, o=organism;
* OR: set to 'd' to automatically dotter the first sequence; blank otherwise (blxselect.c) */
BLXOPT_NUM_OPTS /* Total number of options (must always be last in list) */
} BlxOptsIdx ;
/* This enum contains IDs for all the persistent dialogs in the application, and should be used
* to access a stored dialog in the dialogList array in the BlxContext. Note that the dialogList
* array will contain null entries until the dialogs are created for the first time */
typedef enum
{
BLXDIALOG_NOT_PERSISTENT = 0, /* Reserved for dialogs that do not have an entry in the array */
BLXDIALOG_HELP, /* The Help dialog */
BLXDIALOG_SETTINGS, /* The Settings dialog */
BLXDIALOG_SORT, /* The Sort dialog */
BLXDIALOG_FIND, /* The Find dialog */
BLXDIALOG_GROUPS, /* The Groups dialog */
BLXDIALOG_VIEW, /* The View dialog */
BLXDIALOG_DOTTER, /* The Dotter dialog */
BLXDIALOG_NUM_DIALOGS /* The number of dialogs. Must always be the last entry in this enum */
} BlxDialogId;
/* This enum determines the how to find the match to call dotter on */
typedef enum
{
BLXDOTTER_MATCH_SELECTED, /* call dotter on the currently-selected match sequence */
BLXDOTTER_MATCH_ADHOC, /* call dotter on a manually-pasted sequence */
BLXDOTTER_MATCH_SELF /* call dotter on the reference sequence vs itself */
} DotterMatchType ;
/* This enum determines how to find the reference sequence range to call dotter on */
typedef enum
{
BLXDOTTER_REF_AUTO, /* call dotter on an automatically-calculated ref seq range */
BLXDOTTER_REF_MANUAL, /* call dotter on a manually entered ref seq range */
BLXDOTTER_REF_TRANSCRIPT /* call dotter on a transcript range */
} DotterRefType;
/* This enum gives access into the depthArray for the specific counter (i.e. per-base or all) */
typedef enum
{
DEPTHCOUNTER_NONE,
DEPTHCOUNTER_ALL_F, // all reads at this coord on + strand
DEPTHCOUNTER_GAP_F, // all reads at this coord on + strand
DEPTHCOUNTER_A_F, // all reads with 'a' at this coord on forward strand
DEPTHCOUNTER_C_F, // all reads with 'c' at this coord on forward strand
DEPTHCOUNTER_G_F, // all reads with 'g' at this coord on forward strand
DEPTHCOUNTER_T_F, // all reads with 't' or 'u' at this coord on forward strand
DEPTHCOUNTER_N_F, // all reads with 'n' at this coord on forward strand
DEPTHCOUNTER_ALL_R, // all reads at this coord on - strand
DEPTHCOUNTER_GAP_R, // all reads at this coord on - strand
DEPTHCOUNTER_A_R, // all reads with 'a' at this coord on reverse strand
DEPTHCOUNTER_C_R, // all reads with 'c' at this coord on reverse strand
DEPTHCOUNTER_G_R, // all reads with 'g' at this coord on reverse strand
DEPTHCOUNTER_T_R, // all reads with 't' or 'u' at this coord on reverse strand
DEPTHCOUNTER_N_R, // all reads with 'n' at this coord on reverse strand
DEPTHCOUNTER_NUM_ITEMS /*must be last*/
} DepthCounter;
/* Struct to hold all the settings that come from the command line options */
class CommandLineOptions
{
public:
char *refSeq; /* the section of reference sequence we're viewing */
char *refSeqName; /* the name of the reference sequence */
IntRange refSeqRange; /* the range of the reference sequence (before any offset is applied) */
int refSeqOffset; /* if non-zero, all parsed coords will be offset by this amount */
int startCoord; /* which coord to start the initial display range at */
gboolean startCoordSet; /* true if the start coord has been specified on the command line */
MSP *mspList; /* the list of alignments */
GList *columnList; /* the list of display columns */
char **geneticCode; /* the genetic code */
BlxStrand activeStrand; /* which strand will initially be the active one */
gboolean negateCoords; /* if this option is true, the display will show coords as negative when the reverse strand is active */
gboolean zoomWhole; /* whether to zoom out to view the entire big picture range on startup */
int bigPictZoom; /* initial zoom level for the big picture (as a multiple of the initial detail view range) */
IntRange bigPictRange; /* initial range for the big picture (will override bigPictZoom if both are set) */
gboolean bigPictON; /* whether to show the big picture by default */
gboolean hideInactive; /* whether to show the inactive strand in the big picture/detail view */
BlxColumnId initSortColumn; /* initial column to sort by */
gboolean sortInverted; /* whether initial sort order should be inverted */
gboolean highlightDiffs; /* whether the initial display should highlight mismatches rather than matches */
gboolean dotterFirst; /* open dotter when blixem starts */
gboolean startNextMatch; /* start at the coord of the next match from the default start coord */
gboolean squashMatches; /* start with the 'squash matches' option on */
gboolean optionalColumns; /* load data for optional columns on startup to populate additional info like tissue-type and strain */
gboolean saveTempFiles; /* save any temporary files that blixem creates */
gboolean coverageOn; /* show the coverage view on start-up */
gboolean abbrevTitle; /* if true, use a abbreviated window titles to save space */
gboolean mspFlagDefaults[MSPFLAG_NUM_FLAGS]; /* default values for MSP flags */
BlxBlastMode blastMode; /* the blast match mode */
BlxSeqType seqType; /* whether the display shows sequences as peptides or nucleotides */
int numFrames; /* the number of reading frames */
GHashTable *fetchMethods; /* table of fetch methods (keyed on name as a GQuark) */
GArray *bulkFetchDefault; /* the default method(s) for bulk fetching sequences (can be overridden by an MSPs data-type properties) */
GArray *userFetchDefault; /* the default method(s) for fetching individual sequences interactively */
GArray *optionalFetchDefault; /* the default method(s) for bulk fetching optional sequence data */
char *dataset; /* the name of a dataset, e.g. 'human' */
BlxMessageData msgData; /* data to be passed to the message handlers */
gboolean mapCoords; /* whether the map-coords command-line argument was specified */
int mapCoordsFrom; /* the coord to map from */
int mapCoordsTo; /* the coord to map to */
char *windowColor; /* if not null, set the main window background color to this */
bool fetch_debug; /* whether to include verbose debug output for fetch */
long ipresolve; /* whether to make curl use ipv4 or ipv6 */
const char *cainfo; /* location of curl cainfo file */
};
/* blixem can use either efetch (default) or a pfetch server to get
* sequences, to use pfetch node/port information must be specified. */
typedef struct
{
char *net_id ;
int port ;
} PfetchParams ;
/* Used to pass around info about a match sequence when getting fetch command arguments */
typedef struct
{
const char *match_name;
const char *ref_name;
int match_start;
int match_end;
const char *dataset;
const char *source;
const char *filename;
} MatchSequenceData ;
/* Class to perform a user-fetch operation */
class UserFetch
{
public:
UserFetch();
UserFetch(const BlxSequence *blxSeq,
const gboolean displayResults,
GtkWidget *blxWindow,
GtkWidget *dialog,
#ifdef PFETCH_HTML
long ipresolve,
const char *cainfo,
#endif
bool debug);
void performFetch();
GtkTextBuffer *getTextBuffer();
void setTextBuffer(GtkTextBuffer *text_buffer);
#ifdef PFETCH_HTML
bool httpFetchSequence(const BlxFetchMethod *fetchMethod);
#endif
void socketFetchSequence(const BlxFetchMethod *fetchMethod);
void commandFetchSequence(const BlxFetchMethod *fetchMethod);
void internalFetchSequence(const BlxFetchMethod *fetchMethod);
void wwwFetchSequence(const BlxFetchMethod *fetchMethod);
void sqliteFetchSequence(const BlxFetchMethod *fetchMethod);
private:
const BlxSequence *blxSeq;
gboolean displayResults;
int attempt;
GtkWidget *blxWindow;
GtkWidget *dialog;
GtkTextBuffer *text_buffer;
bool debug;
#ifdef PFETCH_HTML
long ipresolve;
const char *cainfo;
#endif
};
/* Class to perform a bulk-fetch operation */
class BulkFetch
{
public:
BulkFetch(gboolean External,
gboolean saveTempFiles,
BlxSeqType seqType,
GList **seqList,
GList *columnList,
GArray *defaultFetchMethods,
GHashTable *fetchMethods,
MSP **mspList,
BlxBlastMode *blastMode,
GArray* featureLists[],
GSList *supportedTypes,
GSList *styles,
int refSeqOffset,
IntRange* const refSeqRange,
char *dataset,
gboolean optionalColumns,
GHashTable *lookupTable,
#ifdef PFETCH_HTML
long ipresolve,
const char *cainfo,
#endif
bool debug);
gboolean performFetch();
gboolean fetchList(GList *seqsToFetch, const BlxFetchMethod* const fetchMethod, GError **error);
gboolean httpFetchList(GList *seqsToFetch, const BlxFetchMethod* const fetchMethod, GError **error);
gboolean socketFetchList(GList *seqsToFetch, const BlxFetchMethod* const fetchMethod, GError **error);
void regionFetchList(GList *regionsToFetch, const BlxFetchMethod* const fetchMethod, GError **error);
void commandFetchList(GList *regionsToFetch, const BlxFetchMethod* const fetchMethod, GError **error);
private:
void regionFetchFeature(const MSP* const msp,
const BlxFetchMethod* const fetchMethod,
const char *script,
const char *dataset,
const char *tmpDir,
GError **error);
int attempt;
gboolean External;
gboolean saveTempFiles;
BlxSeqType seqType;
GList **seqList; /* list of BlxSequence structs for all required sequences */
GList *columnList;
GArray *defaultFetchMethods;
GHashTable *fetchMethods;
MSP **mspList;
BlxBlastMode *blastMode;
GArray** featureLists;
GSList *supportedTypes;
GSList *styles;
int refSeqOffset;
IntRange* refSeqRange;
char *dataset;
gboolean optionalColumns;
GHashTable *lookupTable;
bool debug;
#ifdef PFETCH_HTML
long ipresolve;
const char *cainfo;
#endif
};
/* blxview.c */
/* Function to show blixem window, can be called from any application. */
gboolean blxview(CommandLineOptions *options,
GArray* featureLists[],
GList *seqList,
GSList *supportedTypes,
PfetchParams *pfetch,
char *align_types,
gboolean External,
GSList *styles,
GHashTable *lookupTable) ;
BlxColumnInfo* getColumnInfo(const GList *columnList, const BlxColumnId columnId);
int getColumnWidth(const GList *columnList, const BlxColumnId columnId);
const char* getColumnTitle(const GList *columnList, const BlxColumnId columnId);
void getColumnXCoords(const GList *columnList, const BlxColumnId columnId, IntRange *xRange);
void saveColumnWidths(GList *columnList, GKeyFile *key_file);
void saveSummaryColumns(GList *columnList, GKeyFile *key_file);
gboolean showColumn(BlxColumnInfo *columnInfo);
void resetColumnWidths(GList *columnList);
void blviewRedraw(void);
GtkWidget* getBlixemWindow(void);
const IntRange* mspGetFullSRange(const MSP* const msp, const gboolean seqSelected, const BlxContext* const bc);
const IntRange* mspGetDisplayRange(const MSP* const msp);
const IntRange* mspGetFullDisplayRange(const MSP* const msp, const gboolean seqSelected, const BlxContext* const bc);
void mspCalculateFullExtents(MSP *msp, const BlxContext* const bc, const int numUnalignedBases);
void cacheMspDisplayRanges(const BlxContext* const bc, const int numUnalignedBases);
gboolean mspGetMatchCoord(const MSP *msp,
const int qIdx,
const gboolean seqSelected,
const int numUnalignedBases,
BlxContext *bc,
int *result_out);
void drawAssemblyGaps(GtkWidget *widget,
GdkDrawable *drawable,
GdkColor *color,
const gboolean displayRev,
GdkRectangle *rect,
const IntRange* const dnaRange,
const GArray *mspArray);
GList* blxCreateColumns(const gboolean optionalColumns, const gboolean customSeqHeader);
GSList* blxReadStylesFile(const char *keyFileName_in, GError **error);
const char* blxGetAppName();
const char* blxGetTitlePrefix(const BlxContext* const bc);
const char* blxGetCopyrightString();
const char* blxGetWebSiteString();
char* blxGetCommentsString();
const char* blxGetLicenseString();
const char* blxGetVersionString();
/* dotter.c */
//void selectFeatures(void);
/* blxparser.c */
gboolean mspHasFs(const MSP *msp);
char* readFastaSeq(FILE *seqfile, char *qname, int *startCoord, int *endCoord, const BlxSeqType seqType);
/* blxFetch.c */
BlxFetchMethod* getFetchMethodDetails(GQuark fetchMethodQuark, GHashTable *fetchMethods);
GString* getFetchCommand(const BlxFetchMethod* const fetchMethod, const BlxSequence *blxSeq, const MSP* const msp, const char *refSeqName, const int refSeqOffset, const IntRange* const refSeqRange, const char *dataset, GError **error);
GString* doGetFetchCommand(const BlxFetchMethod* const fetchMethod,MatchSequenceData *match_data, GError **error);
GString* getFetchArgs(const BlxFetchMethod* const fetchMethod, const BlxSequence *blxSeq,const MSP* const msp,const char *refSeqName,const int refSeqOffset,const IntRange* const refSeqRange,const char *dataset,GError **error);
GString* getFetchArgsMultiple(const BlxFetchMethod* const fetchMethod, GList *seqsToFetch, GError **error);
void finaliseFetch(GList *seqList, GList *columnList);
void sendFetchOutputToFile(GString *command, GKeyFile *keyFile, BlxBlastMode *blastMode,GArray* featureLists[],GSList *supportedTypes, GSList *styles, GList **seqList, MSP **mspListIn,const char *fetchName, const gboolean saveTempFiles, MSP **newMsps, GList **newSeqs, GList *columnList, GHashTable *lookupTable, const int refSeqOffset, const IntRange* const refSeqRange, GError **error);
const char* outputTypeStr(const BlxFetchOutputType outputType);
void fetchSeqsIndividually(GList *seqsToFetch, GtkWidget *blxWindow);
gboolean populateSequenceDataHtml(GList *seqsToFetch, const BlxSeqType seqType, const BlxFetchMethod* const fetchMethod) ;
gboolean populateFastaDataPfetch(GList *seqsToFetch, BlxFetchMethod *fetchMethod, gboolean External, const BlxSeqType seqType, GError **error) ;
gboolean populateFullDataPfetch(GList *seqsToFetch, BlxFetchMethod *fetchMethod, gboolean External, const BlxSeqType seqType, GError **error);
void blxInitConfig(const char *config_file, CommandLineOptions *options, GError **error) ;
GKeyFile* blxGetConfig(void) ;
void loadNativeFile(const char *filename, const char *buffer, GKeyFile *keyFile, BlxBlastMode *blastMode, GArray* featureLists[], GSList *supportedTypes, GSList *styles, MSP **newMsps, GList **newSeqs, GList *columnList, GHashTable *lookupTable, const int refSeqOffset, const IntRange* const refSeqRange, GError **error);
void blxMergeFeatures(MSP *newMsps, GList *newSeqs, MSP **mspList, GList **seqList);
/* Create/destroy sequences and MSPs */
void blviewResetGlobals();
BlxStyle* createBlxStyle(const char *styleName, const char *fillColor, const char *fillColorSelected, const char *lineColor, const char *lineColorSelected, const char *fillColorUtr, const char *fillColorUtrSelected, const char *lineColorUtr, const char *lineColorUtrSelected, GError **error);
void destroyBlxStyle(BlxStyle *style);
void createPfetchDropDownBox(GtkBox *box, GtkWidget *blxWindow);
/* Dotter/Blixem Package-wide variables...........MORE GLOBALS...... */
extern char *stdcode1[]; /* 1-letter amino acid translation code */
extern int aa_atob[];
extern int PAM120[23][23];
extern int dotterGraph;
extern float fsPlotHeight;
extern GtkWidget *blixemWindow;
/* blxFetchDb.c */
/* Function pointer for sqlite callback functions */
typedef int (*SqliteFunc)(void*,int,char**,char**);
void sqliteFetchSequences(GList *seqsToFetch, const BlxFetchMethod* const fetchMethod, GList *columnList, GError **error);
void sqliteFetchSequence(const BlxSequence* const blxSeq, const BlxFetchMethod* const fetchMethod,const gboolean displayResults, const int attempt,GtkWidget *blxWindow);
void sqliteValidateFetchMethod(const BlxFetchMethod* const fetchMethod, GError **error);
int sqliteDisplayResultsCB(void *data, int argc, char **argv, char **azColName);
void sqliteRequest(const char *database, const char *query, SqliteFunc callbackFunc, void *callbackData, GError **error);
#endif /* !defined DEF_BLIXEM_P_H */
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