1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
|
/* File: utilities.h
* Author: Gemma Barson, 2010-01-05
* 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: Utility functions for the SeqTools package.
*----------------------------------------------------------------------------
*/
#ifndef _utilities_h_included_
#define _utilities_h_included_
#include <gtk/gtk.h>
#define UNSET_INT -1 /* this value indicates an unset integer */
#define DEFAULT_LABEL_X_PAD 0 /* default x padding to use for header labels */
#define DEFAULT_PRINT_RESOLUTION 300 /* default resolution for printing in DPI */
#define TABLE_XPAD 12 /* default x padding around table elements */
#define TABLE_YPAD 2 /* default y padding around table elements */
#define MIN_FONT_SIZE 2
#define MAX_FONT_SIZE 20
#define MACHINE_RES 0.000000001
#define SEQTOOLS_GFF_VERSION 3 /* the default GFF version */
/* Really the buffers that use this should be dynamic but I'm not going to do that, this
* code is so poor that it doesn't warrant the effort.... */
#define NAMESIZE 12
#define MAXLINE 10000
/* Utility macro to check that our gtk version meets the given minimum version. Use this in
* an #if statement */
#define CHECK_GTK_VERSION(MAJOR, MINOR) GTK_MAJOR_VERSION > (MAJOR) || (GTK_MAJOR_VERSION == (MAJOR) && GTK_MINOR_VERSION >= (MINOR))
/* Debug logging macros. #define DEBUG to enable debug output. */
#ifdef DEBUG
#define DEBUG_OUT(format, args...) debugLogLevel(0); printf(format, ##args); fflush(stdout);
#else
#define DEBUG_OUT(format, args...)
#endif
#ifdef DEBUG
#define DEBUG_ENTER(format, args...) debugLogLevel(1); printf("-->"); printf(format, ##args); printf("\n"); fflush(stdout);
#else
#define DEBUG_ENTER(format, args...)
#endif
#ifdef DEBUG
#define DEBUG_EXIT(format, args...) debugLogLevel(-1); printf("<--"); printf(format, ##args); printf("\n"); fflush(stdout);
#else
#define DEBUG_EXIT(format, args...)
#endif
/* Generic SeqTools error domain */
#define SEQTOOLS_ERROR g_quark_from_string("SeqTools")
/* Error codes */
typedef enum
{
SEQTOOLS_ERROR_PARSING_COLOR, /* error parsing color string */
SEQTOOLS_ERROR_SEQ_SEGMENT, /* error getting the requested segment of a sequence */
SEQTOOLS_ERROR_NO_STYLE, /* style does not exist */
SEQTOOLS_ERROR_EXECUTING_CMD, /* error executing command */
SEQTOOLS_ERROR_SEQ_TYPE, /* error determining sequence type */
SEQTOOLS_ERROR_NO_EXE /* executable does not exist */
} SeqToolsError;
/* This enum defines the columns for a combo box with the common combination
* of two columns: an int relating to an enum, and a text description. */
typedef enum _BlxComboColumns
{
COMBO_ENUM_COL,
COMBO_TEXT_COL,
N_COMBO_COLUMNS
} BlxComboColumns;
/* Printing scale type - we can scale to fit the page width, or height, or both */
typedef enum
{
PRINT_FIT_WIDTH,
PRINT_FIT_HEIGHT,
PRINT_FIT_BOTH
} PrintScaleType;
#if defined(MACINTOSH)
#define SYSERR_FORMAT "system error %d"
#else
#define SYSERR_FORMAT "system error %d - %s"
#endif
/* Special characters for displaying in sequences */
#define SEQUENCE_CHAR_DELETION '.' /* represents a deletion */
#define SEQUENCE_CHAR_GAP '-' /* represents a gap. Note that gaps in the reference sequence will be highlighted as assembly gaps */
#define SEQUENCE_CHAR_PAD '-' /* used for padding when the sequence is unavailable */
#define SEQUENCE_CHAR_BLANK '-' /* used to display a blank when we're not interested in what the actual base is */
#define SEQUENCE_CHAR_INVALID ' ' /* used to replace non-utf8 characters (which GTK can't display) */
#define SEQUENCE_CHAR_STOP '*' /* STOP codon */
#define SEQUENCE_CHAR_MET 'M' /* MET codon */
/* Color strings that can be passed to create a GdkColor */
#define BLX_BLACK "#000000"
#define BLX_WHITE "#ffffff"
#define BLX_GREY "#bebebe"
#define BLX_LIGHT_GREY "#cacaca"
#define BLX_VERY_LIGHT_GREY "#eeeeee"
#define BLX_DARK_GREY "#929292"
#define BLX_VERY_DARK_GREY "#5f5f5f"
#define BLX_YELLOW "#ffff00"
#define BLX_DARK_YELLOW "#d0d000"
#define BLX_PALE_YELLOW "#ffffcc"
#define BLX_BLUE "#0000ff"
#define BLX_DARK_BLUE "#000080"
#define BLX_ROYAL_BLUE "#4169e1"
#define BLX_SKY_BLUE "#87cefa"
#define BLX_PALE_BLUE "#c0d8f0"
#define BLX_CYAN "#15ced2"
#define BLX_LIGHT_CYAN "#6defe9"
#define BLX_VIOLET "#78b4f0"
#define BLX_DARK_VIOLET "#5c98d5"
#define BLX_MID_BLUE "#6495ED"
#define BLX_SLATE_BLUE "#7C7FFF"
#define BLX_RED "#ff0000"
#define BLX_LIGHT_RED "#ff7373"
#define BLX_SALMON_RED "#ffa07a"
#define BLX_DARK_RED "#800000"
#define BLX_VERY_DARK_RED "#400000"
#define BLX_ORANGE_RED "#ff4500"
#define BLX_ORANGE "#ffa500"
#define BLX_PALE_ORANGE "#ff9c00"
#define BLX_MAGENTA "#ff00ff"
#define BLX_PALE_MAGENTA "#ffccff"
#define BLX_PURPLE "#A020F0"
#define BLX_PALE_VIOLET "#EE82EE"
#define BLX_CERISE "#DE3163"
#define BLX_GREEN "#00ff00"
#define BLX_LIGHT_GREEN "#C1FFC1"
#define BLX_LAWN_GREEN "#7cfc00"
#define BLX_DARK_GREEN "#00bb00"
#define BLX_VERY_DARK_GREEN "#015800"
#define BLX_BROWN "#A52A2A"
typedef struct _BlxColor
{
char *name; /* meaningful name for the color e.g. "Match" */
char *desc; /* meaningful description for what the color is used for e.g. "background color for exact matches" */
gboolean transparent; /* If this is true, the colors are not specified and the
* background color should be used instead. */
/* If the overridden flags are true, transparency has been overridden and the
* colors ARE set but should only be used where transparency is
* not allowed. */
gboolean normal_overridden;
gboolean selected_overridden;
gboolean print_overridden;
gboolean printSelected_overridden;
GdkColor normal; /* the color in normal operation */
GdkColor selected; /* the color in a selected state */
GdkColor print; /* the color used for printing */
GdkColor printSelected; /* the selected-state color used for printing */
} BlxColor;
/* This handle holds a list of pointers to all memory allocated via this handle.
* Use handleDestroy to free the handle and all its allocated memory. */
typedef struct _BlxHandle
{
GSList *memoryList;
} BlxHandleStruct, *BlxHandle;
/* This struct is used to pass user data to the message handlers */
typedef struct _BlxMessageData
{
char *titlePrefix;
GtkWindow *parent;
GtkStatusbar *statusBar;
} BlxMessageData;
/* Define a drawing style for an MSP */
typedef struct _BlxStyle
{
char *styleName;
BlxColor fillColor;
BlxColor lineColor;
BlxColor fillColorUtr; /* used only for transcript features; fillColor and lineColor are for CDS portions and these are for UTR portions */
BlxColor lineColorUtr; /* used only for transcript features; fillColor and lineColor are for CDS portions and these are for UTR portions */
} BlxStyle;
/* Utility structs to hold a range of integers/doubles */
class IntRange
{
public:
// Constructors
IntRange() : m_min(0), m_max(0), m_min_is_set(false), m_max_is_set(false) {};
IntRange(const IntRange &range);
IntRange(const IntRange *range);
IntRange(const int val1, const int val2);
// Access functions
bool isSet() const;
int start(const bool rev = false, const bool negate = false) const;
int end(const bool rev = false, const bool negate = false) const;
int min(const bool inclusive = false, const bool rev = false) const;
int max(const bool inclusive = false, const bool rev = false) const;
int length() const;
int centre() const;
// Modify functions
void reset();
void set(const int val1, const int val2);
void set(const IntRange &range);
void set(const IntRange *range);
bool setMin(const int val);
bool setMax(const int val);
void sort(const bool forwards = false);
void boundsLimit(const IntRange* const limit, const gboolean maintainLen);
private:
int m_min;
int m_max;
bool m_min_is_set;
bool m_max_is_set;
};
typedef struct _DoubleRange
{
gdouble min;
gdouble max;
} DoubleRange ;
/* Fundamental strand direction. */
typedef enum
{
BLXSTRAND_NONE,
BLXSTRAND_FORWARD,
BLXSTRAND_REVERSE
} BlxStrand ;
/* Fundamental type of sequence (DNA really means nucleotide, because it could be RNA as well). */
typedef enum
{
BLXSEQ_NONE,
BLXSEQ_DNA,
BLXSEQ_PEPTIDE
} BlxSeqType ;
/* Fundamental blast mode used */
typedef enum
{
BLXMODE_UNSET,
BLXMODE_BLASTX,
BLXMODE_TBLASTX,
BLXMODE_BLASTN,
BLXMODE_TBLASTN,
BLXMODE_BLASTP
} BlxBlastMode ;
/* Function pointer for callback functions used by widgets on dialog boxes. */
typedef gboolean (*BlxResponseCallback)(GtkWidget *widget, const gint responseId, gpointer data);
/* This struct holds generic callback information. It can be stored as a widget
* property and called on the widget on request (e.g. by a dialog when it applies changes). */
typedef struct _CallbackData
{
BlxResponseCallback func; /* Callback function to be called */
gpointer data; /* User data to pass to the callback function */
} CallbackData;
/* Custom dialog response types, which can be used in addition
* to the default types specified by GtkResponseType */
typedef enum
{
BLX_RESPONSE_FORWARD,
BLX_RESPONSE_BACK,
BLX_RESPONSE_RESET,
BLX_RESPONSE_CLEAR
} BlxResponseType;
/* Class to hold a pair of coordinate ranges, one holding ref seq coords, the other match coords */
class CoordRange
{
public:
CoordRange() : qStart(0), qEnd(0), sStart(0), sEnd(0) {};
int qStart; /* start coord on the reference (Query) seq */
int qEnd; /* end coord on the reference (Query) seq */
int sStart; /* start coord on the match (Subject) seq */
int sEnd; /* end coord on the match (Subject) seq */
};
/* Used to specify the degree of colinearity between two alignment blocks. */
typedef enum
{
COLINEAR_INVALID,
COLINEAR_NOT, /* blocks not colinear. */
COLINEAR_IMPERFECT, /* blocks colinear but not contiguous. */
COLINEAR_PERFECT, /* blocks colinear and contiguous. */
COLINEARITY_N_TYPE
} ColinearityType ;
/* Supported drag-and-drop target types */
typedef enum {TARGET_STRING, TARGET_URL} DragDropTargetType;
GdkDrawable* widgetGetDrawable(GtkWidget *widget);
void widgetSetDrawable(GtkWidget *widget, GdkDrawable *drawable);
gboolean widgetGetHidden(GtkWidget *widget);
void widgetSetHidden(GtkWidget *widget, const gboolean hidden);
void hideUserHiddenWidget(GtkWidget *widget, gpointer data);
void widgetClearCachedDrawable(GtkWidget *widget, gpointer data);
void callFuncOnAllChildWidgets(GtkWidget *widget, gpointer data);
void blxSetWidgetColor(GtkWidget* widget, const char *colorName);
gboolean onExposePrintable(GtkWidget *widget, GdkEventExpose *event, gpointer data);
GtkWidget* createLabel(const char *text, const gdouble xalign, const gdouble yalign, const gboolean ellipsize, const gboolean enableCopyPaste, const gboolean showWhenPrinting);
GtkWidget* getLabelWidget(GtkWidget *widget);
void labelSetFont(GtkWidget *widget, PangoFontDescription *fontDesc);
GdkDrawable* createBlankPixmap(GtkWidget *widget);
GdkDrawable* createBlankSizedPixmap(GtkWidget *widget, GdkDrawable *window, const int width, const int height);
gboolean clickedInRect(GdkEventButton *event, GdkRectangle *rect, const int minWidth);
BlxSeqType determineSeqType(char *seq, GError **error);
void argvAdd(int *argc, char ***argv, const char *s);
char* getSystemErrorText();
gpointer handleAlloc(BlxHandle *handle, size_t numBytes);
BlxHandle handleCreate();
void handleDestroy(BlxHandle *handle);
BlxStyle* getBlxStyle(const char *styleName, GSList *styles, GError **error);
void sortValues(int *val1, int *val2, gboolean forwards);
int numDigitsInInt(int val);
gboolean getColorFromString(const char *colorStr, GdkColor *color, GError **error);
void getSelectionColor(const GdkColor* const origColor, GdkColor *result);
void getDropShadowColor(const GdkColor* const origColor, GdkColor *result);
void convertToGrayscale(const GdkColor* const origColor, GdkColor *result);
void adjustColorBrightness(const GdkColor* const origColor, const double factor, GdkColor *result);
void getCoordRangeExtents(CoordRange *range, int *qRangeMin, int *qRangeMax, int *sRangeMin, int *sRangeMax);
gboolean isDelimiter(const char c);
char* removeDelimiters(char *text);
GArray* keyFileGetCsv(GKeyFile *keyFile, const char *group, const char *key, GError **error);
void freeStringList(GList **stringList, const gboolean freeDataItems);
void centreRangeOnCoord(IntRange *range, const int coord, const int length);
gboolean valueWithinRange(const int value, const IntRange* const range);
gboolean rangesOverlap(const IntRange* const range1, const IntRange* const range2);
gboolean rangesAdjacent(const IntRange* const range1, const IntRange* const range2);
gboolean rangesEqual(const IntRange* const range1, const IntRange* const range2);
void boundsLimitValue(int *value, const IntRange* const range);
gboolean pointInRect(const int x, const int y, const GdkRectangle* const rect);
char convertBaseToCorrectCase(const char charToConvert, const BlxSeqType seqType);
void convertDisplayRangeToDnaRange(const IntRange* const displayRange,
const BlxSeqType displaySeqType,
const int numFrames,
const gboolean displayRev,
const IntRange* const refSeqRange,
IntRange *result);
int convertDisplayIdxToDnaIdx(const int inputIdx,
const BlxSeqType inputIdxType,
const int frame,
const int baseNum,
const int numFrames,
const gboolean displayRev,
const IntRange* const dnaIdxRange);
int convertDnaIdxToDisplayIdx(const int dnaIdx,
const BlxSeqType displaySeqType,
const int frame,
const int numFrames,
const gboolean displayRev,
const IntRange* const dnaIdxRange,
int *baseNum);
char getStrandAsChar(const BlxStrand strand);
int roundNearest(const double val);
int roundToValue(const int inputVal, const int roundTo);
int roundToValueFromList(const int inputVal, GSList *roundValues, int *roundedTo);
int roundUpToValueFromList(const int inputVal, GSList *roundValues, int *roundedTo);
char getSequenceIndex(char *seq,
const int qIdx,
const gboolean complement,
const IntRange* const seqRange,
const BlxSeqType seqType);
int getStartDnaCoord(const IntRange* const displayRange,
const int frame,
const BlxSeqType displaySeqType,
const gboolean displayRev,
const int numFrames,
const IntRange* const refSeqRange);
int getEndDnaCoord(const IntRange* const displayRange,
const int frame,
const BlxSeqType displaySeqType,
const gboolean displayRev,
const int numFrames,
const IntRange* const refSeqRange);
int wildcardSearch(const char *textToSearch, const char *searchStr);
char* convertIntToString(const int value);
char* convertDoubleToString(const gdouble value, const int numDp);
int convertStringToInt(const char *inputStr);
gboolean isWhitespaceChar(const char curChar);
gboolean isNewlineChar(const char curChar);
char* abbreviateText(const char *inputStr, const int maxLen);
gboolean stringsEqual(const char *str1, const char *str2, const gboolean caseSensitive);
gboolean isValidIupacChar(const char inputChar, const BlxSeqType seqType);
void stringProtect(GIOChannel *ioChannel, const char *string, GError **error);
char* stringUnprotect(char **textp, char *target);
int invertCoord(const int coord, const IntRange* const range, const gboolean invert);
void popupMessageHandler(const gchar *log_domain, GLogLevelFlags log_level, const gchar *message, gpointer data);
void defaultMessageHandler(const gchar *log_domain, GLogLevelFlags log_level, const gchar *message, gpointer data);
void g_message_info(const char *formatStr, ...);
GtkWidget* showMessageDialog(const char *title,
const char *messageText,
GtkWidget *parent,
const int initWidth,
const int maxHeight,
const gboolean wrapText,
const gboolean useMarkup,
PangoFontDescription *fontDesc,
GtkTextView **textView);
void destroyMessageList();
GtkWidget* createScrollableTextView(const char *messageText,
const gboolean wrapText,
PangoFontDescription *fontDesc,
const gboolean useMarkup,
int *width,
int *height,
GtkTextView **textViewOut);
void widgetSetCallbackData(GtkWidget *widget, BlxResponseCallback callbackFunc, gpointer callbackData);
gboolean widgetCallAllCallbacks(GtkWidget *widget, gpointer data);
void onResponseDialog(GtkDialog *dialog, gint responseId, gpointer data);
void onCloseDialog(GtkDialog *dialog, gpointer data);
void dialogClearContentArea(GtkDialog *dialog);
GtkWidget* getPersistentDialog(GtkWidget* dialogList[], const int dialogId);
void addPersistentDialog(GtkWidget* dialogList[], const int dialogId, GtkWidget *widget);
void setPrimaryClipboardText(const char *text);
void setDefaultClipboardText(const char *text);
void requestPrimaryClipboardText(GtkClipboardTextReceivedFunc callback, gpointer data);
void requestDefaultClipboardText(GtkClipboardTextReceivedFunc callback, gpointer data);
int parseMatchLine(const char *inputText,
char **matchNameOut,
int *matchStartOut,
int *matchEndOut,
int *matchLenOut);
GList* parseMatchList(const char *inputText);
GtkWidget* getNamedChildWidget(GtkWidget *widget, const gchar *searchName);
gint runConfirmationBox(GtkWidget *blxWindow, const char *title, const char *messageText);
void prefixError(GError *error, const char *prefixStr, ...);
void postfixError(GError *error, const char *formatStr, ...);
void reportAndClearIfError(GError **error, GLogLevelFlags log_level);
#ifdef DEBUG
void debugLogLevel(const int increaseAmt);
#endif
void drawRect(GdkDrawable *drawable, GdkColor *color, const int x, const int y, const int width, const int height, const double alpha, cairo_operator_t op);
void drawHighlightBox(GdkDrawable *drawable, const GdkRectangle* const rect, const gint minWidth, GdkColor *color);
void blxPrintWidget(GtkWidget *widget, GdkDrawable *drawable, GtkWindow *window, GtkPrintSettings **printSettings, GtkPageSetup **pageSetup, const char *filename, const gboolean printCachedOnly, const PrintScaleType scaleType);
void setStatusBarShadowStyle(GtkWidget *statusBar, const char *shadowStyle);
BlxColor* getBlxColor(GArray *defaultColors, const int colorId);
GdkColor* getGdkColor(int colorId, GArray *defaultColors, const gboolean selected, const gboolean usePrintColors);
GdkColor* blxColorGetColor(BlxColor *blxColor, const gboolean selected, const gboolean usePrintColors);
const GdkColor* blxColorGetColor(const BlxColor *blxColor, const gboolean selected, const gboolean usePrintColors);
gboolean blxColorOverridden(const BlxColor *blxColor, const gboolean selected, const gboolean usePrintColors);
gboolean blxColorOverrideTransparency(BlxColor *dest, const BlxColor *source, const gboolean lighten, const gboolean selected, const gboolean usePrintColors);
char* convertColorToString(GdkColor *color);
void destroyBlxColor(BlxColor *blxColor);
gboolean colorsEqual(GdkColor *color1, GdkColor *color2);
void createBlxColor(GArray *defaultColors,
int colorId,
const char *name,
const char *desc,
const char *normalCol,
const char *printCol,
const char *normalColSelected,
const char *printColSelected);
gdouble pixelsPerBase(const gint displayWidth,
const IntRange* const displayRange);
gdouble convertBaseIdxToRectPos(const gint dnaIdx,
const GdkRectangle* const rect,
const IntRange* const dnaDispRange,
const gboolean horizontal,
const gboolean displayRev,
const gboolean clip);
gchar* getSequenceSegment(const char* const dnaSequence,
IntRange *qRange,
const BlxStrand strand,
const BlxSeqType srcSeqType,
const BlxSeqType destSeqType,
const int frame,
const int numFrames,
const IntRange* const refSeqRange,
const BlxBlastMode blastMode,
char **geneticCode,
const gboolean displayRev,
const gboolean reverseResult,
const gboolean allowComplement,
GError **error);
const char* findFixedWidthFont(GtkWidget *widget);
const char* findFixedWidthFontFamily(GtkWidget *widget, GList *pref_families);
void getFontCharSize(GtkWidget *widget, PangoFontDescription *fontDesc, gdouble *width, gdouble *height, const gboolean fixedWidthFont = FALSE);
GtkWidget* createToolbarHandle();
GtkToolItem* addToolbarWidget(GtkToolbar *toolbar, GtkWidget *widget, const int position);
void onBeginPrint(GtkPrintOperation *print, GtkPrintContext *context, gpointer data);
void collatePixmaps(GtkWidget *widget, gpointer data);
void onDrawPage(GtkPrintOperation *print, GtkPrintContext *context, gint pageNum, gpointer data);
void setWidgetBackgroundColor(GtkWidget *widget, gpointer data);
void propagateEventButton(GtkWidget *srcWidget, GtkWidget *destWidget, GdkEventButton *event);
void propagateEventMotion(GtkWidget *srcWidget, GtkWidget *destWidget, GdkEventMotion *event);
void forceResize(GtkWidget *widget);
gboolean onComboChanged(GtkWidget *combo, const gint responseId, gpointer data);
GtkComboBox* createComboBox();
void addComboItem(GtkComboBox *combo, GtkTreeIter *parent, const int val, const char *text, const int initVal);
const char* getSaveFileName(GtkWidget *widget, const char *currentName, const char *defaultPath, const char *defaultExtension, const char *title);
char* getLoadFileName(GtkWidget *widget, const char *defaultPath, const char *title);
void enableMenuAction(GtkActionGroup *action_group, const char *actionName, const gboolean enable);
void setToggleMenuStatus(GtkActionGroup *action_group, const char *actionName, const gboolean active);
gboolean getToggleMenuStatus(GtkActionGroup *action_group, const char *actionName);
void setRadioMenuStatus(GtkActionGroup *action_group, const char *actionName, const gint value);
GtkWidget* externalCommand(const char *command, const char *progName, GtkWidget *widget, GError **error);
GString* getExternalCommandOutput(const char *command, GError **error);
GtkWidget* displayFetchResults(const char *title, const char *displayText, GtkWidget *widget, GtkWidget *dialog, GtkTextBuffer **textBuffer);
int scrollBarWidth();
void getTextSize(GtkWidget *widget, const char *text, int *width, int *height);
int getTextWidth(GtkWidget *widget, const char *text);
int getTextHeight(GtkWidget *widget, const char *text);
GtkWidget* createTextEntryFromInt(GtkWidget *widget,
GtkTable *table,
const int row,
const int col,
const int xpad,
const int ypad,
const char *mnemonic,
const int value,
BlxResponseCallback callback);
GtkWidget* createTextEntryFromDouble(GtkWidget *widget,
GtkTable *table,
const int row,
const int col,
const int xpad,
const int ypad,
const char *mnemonic,
const double value,
BlxResponseCallback callback);
void drawHScale(GtkWidget *widget,
GdkDrawable *drawable,
const IntRange* const range,
const GdkRectangle* const rect,
const int widthPerVal,
const int majorTickInterval,
const int labelInterval,
const int minorTickHeight,
const int majorTickHeight);
const char* getStringFromTextEntry(GtkEntry *entry);
void widgetSetFontSize(GtkWidget *widget, gpointer data);
void widgetSetFontSizeAndCheck(GtkWidget *belvuAlignment, const int newSize);
GtkRadioButton* createRadioButton(GtkTable *table,
const int col,
const int row,
GtkRadioButton *existingButton,
const char *mnemonic,
const gboolean isActive,
const gboolean createTextEntry,
const gboolean multiline,
BlxResponseCallback callbackFunc,
GtkWidget *blxWindow,
GSList **entryList);
const char* getSystemTempDir();
void errorHandler(const int sig);
/* seqtoolsWebBrowser.c */
gboolean seqtoolsLaunchWebBrowser(const char *link, GError **error);
/* translate.c */
char* blxTranslate(const char *seq, char **code);
void blxComplement(char *seq) ;
char* revComplement(char *comp, char *seq) ;
char complementChar(const char inputChar, GError **error);
void gtk_text_buffer_insert_markup (GtkTextBuffer *buffer,
GtkTextIter *iter,
const gchar *markup);
void gtk_text_buffer_insert_markup_with_tag (GtkTextBuffer *buffer,
GtkTextIter *iter,
const gchar *markup,
GtkTextTag *tag);
void gtk_text_buffer_set_markup_with_tag (GtkTextBuffer *buffer,
const gchar *markup,
GtkTextTag *tag);
void gtk_text_buffer_set_markup (GtkTextBuffer *buffer,
const gchar *markup);
#endif /* _utilities_h_included_ */
|
