int gt_graphics_cairo_save_to_file(const GtGraphics *gg, const char *filename,
GtError *err)
{
const GtGraphicsCairo *g = (const GtGraphicsCairo*) gg;
cairo_surface_t *bgsurf = NULL;
cairo_t *bgc = NULL;
cairo_status_t rval;
GtFile *outfile;
gt_error_check(err);
gt_assert(g && filename);
/* do nothing if no surface was created */
if (g->from_context)
return 0;
switch (g->type)
{
case GT_GRAPHICS_PNG:
/* blend rendered image with background color */
bgsurf = cairo_image_surface_create(CAIRO_FORMAT_ARGB32, g->width,
g->height);
bgc = cairo_create(bgsurf);
cairo_set_source_rgba(bgc, g->bg_color.red, g->bg_color.green,
g->bg_color.blue, g->bg_color.alpha);
cairo_paint(bgc);
cairo_set_source_surface(bgc, g->surf, 0, 0);
cairo_paint(bgc);
rval = cairo_surface_write_to_png(bgsurf, filename);
gt_assert(rval == CAIRO_STATUS_SUCCESS ||
rval == CAIRO_STATUS_WRITE_ERROR);
if (rval == CAIRO_STATUS_WRITE_ERROR)
{
cairo_destroy(bgc);
cairo_surface_destroy(bgsurf);
gt_error_set(err, "an I/O error occurred while attempting "
"to write image file \"%s\"", filename);
return -1;
}
cairo_destroy(bgc);
cairo_surface_destroy(bgsurf);
break;
default:
cairo_show_page(g->cr);
cairo_surface_flush(g->surf);
cairo_surface_finish(g->surf);
outfile = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, filename, "w+", err);
if (outfile)
{
gt_file_xwrite(outfile, gt_str_get_mem(g->outbuf),
gt_str_length(g->outbuf));
gt_file_delete(outfile);
} else return -1;
break;
}
return 0;
}
static int run_orffinder(GtRegionMapping *rmap,
GtFeatureNode *gf,
unsigned long start,
GT_UNUSED unsigned long end,
unsigned int min,
unsigned int max,
bool all,
GtError *err)
{
int had_err = 0, i;
unsigned long sum;
GtCodonIterator* ci = NULL;
GtTranslator* translator = NULL;
GtORFIterator* orfi = NULL;
GtORFIteratorStatus state;
GtRange orf_rng, tmp_orf_rng[3];
GtStr *seq;
unsigned int orf_frame;
/* forward strand */
seq = gt_str_new();
had_err = gt_extract_feature_sequence(seq,
(GtGenomeNode*) gf,
gt_feature_node_get_type(gf),
false, NULL, NULL, rmap, err);
ci = gt_codon_iterator_simple_new(gt_str_get(seq), gt_str_length(seq), err);
gt_assert(ci);
translator = gt_translator_new(ci);
gt_assert(translator);
orfi = gt_orf_iterator_new(ci, translator);
gt_assert(orfi);
for (i = 0; i < 3; i++) {
tmp_orf_rng[i].start = GT_UNDEF_ULONG;
tmp_orf_rng[i].end = GT_UNDEF_ULONG;
}
while ((state = gt_orf_iterator_next(orfi, &orf_rng, &orf_frame,
err)) == GT_ORF_ITERATOR_OK) {
if (all) {
process_orf(orf_rng, orf_frame, GT_STRAND_FORWARD, gf,
start, min, max, err);
} else {
if (gt_range_length(&orf_rng) >
gt_range_length(&tmp_orf_rng[orf_frame])) {
tmp_orf_rng[orf_frame].start = orf_rng.start;
tmp_orf_rng[orf_frame].end = orf_rng.end;
}
}
}
if (state == GT_ORF_ITERATOR_ERROR)
had_err = -1;
if (!had_err) {
if (!all) {
for (i = 0; i < 3; i++) {
if (tmp_orf_rng[i].start != GT_UNDEF_ULONG) {
process_orf(tmp_orf_rng[i], (unsigned int) i, GT_STRAND_FORWARD, gf,
start, min, max, err);
}
}
}
gt_codon_iterator_delete(ci);
gt_translator_delete(translator);
gt_orf_iterator_delete(orfi);
orfi = NULL;
ci = NULL;
translator = NULL;
for (i = 0; i < 3; i++) {
tmp_orf_rng[i].start = GT_UNDEF_ULONG;
tmp_orf_rng[i].end = GT_UNDEF_ULONG;
}
/* reverse strand */
if (!had_err) {
GT_UNUSED int rval = 0;
unsigned long length = gt_str_length(seq);
char *strp = (char*) gt_str_get_mem(seq);
rval = gt_reverse_complement(strp, gt_str_length(seq), err);
gt_assert(!rval); /* XXX */
ci = gt_codon_iterator_simple_new(gt_str_get(seq), gt_str_length(seq),
err);
gt_assert(ci);
translator = gt_translator_new(ci);
gt_assert(translator);
orfi = gt_orf_iterator_new(ci, translator);
gt_assert(orfi);
sum = start + length - 1;
while ((state = gt_orf_iterator_next(orfi, &orf_rng, &orf_frame,
err)) == GT_ORF_ITERATOR_OK) {
if (all) {
process_orf(orf_rng, orf_frame, GT_STRAND_REVERSE, gf,
sum, min, max, err);
} else {
if (gt_range_length(&orf_rng) >
gt_range_length(&tmp_orf_rng[orf_frame])) {
tmp_orf_rng[orf_frame].start = orf_rng.start;
tmp_orf_rng[orf_frame].end = orf_rng.end;
}
}
}
if (state == GT_ORF_ITERATOR_ERROR)
had_err = -1;
if (!had_err) {
if (!all) {
for (i = 0; i < 3; i++) {
if (tmp_orf_rng[i].start != GT_UNDEF_ULONG) {
process_orf(tmp_orf_rng[i], (unsigned int) i, GT_STRAND_REVERSE,
gf, sum, min, max, err);
}
}
}
}
}
gt_str_delete(seq);
gt_codon_iterator_delete(ci);
gt_translator_delete(translator);
gt_orf_iterator_delete(orfi);
}
return had_err;
}
static int gt_sketch_runner(int argc, const char **argv, int parsed_args,
void *tool_arguments, GT_UNUSED GtError *err)
{
GtSketchArguments *arguments = tool_arguments;
GtNodeStream *in_stream = NULL,
*add_introns_stream = NULL,
*gff3_out_stream = NULL,
*feature_stream = NULL,
*sort_stream = NULL,
*last_stream;
GtFeatureIndex *features = NULL;
const char *file;
char *seqid = NULL;
GtRange qry_range, sequence_region_range;
GtArray *results = NULL;
GtStyle *sty = NULL;
GtStr *prog, *defaultstylefile = NULL;
GtDiagram *d = NULL;
GtLayout *l = NULL;
GtImageInfo* ii = NULL;
GtCanvas *canvas = NULL;
GtUword height;
bool has_seqid;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments);
prog = gt_str_new();
gt_str_append_cstr_nt(prog, argv[0],
gt_cstr_length_up_to_char(argv[0], ' '));
defaultstylefile = gt_get_gtdata_path(gt_str_get(prog), err);
gt_str_delete(prog);
if (!defaultstylefile)
had_err = -1;
if (!had_err) {
gt_str_append_cstr(defaultstylefile, "/sketch/default.style");
}
file = argv[parsed_args];
if (!had_err) {
/* create feature index */
features = gt_feature_index_memory_new();
parsed_args++;
/* create an input stream */
if (strcmp(gt_str_get(arguments->input), "gff") == 0)
{
in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
if (arguments->verbose)
gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) in_stream);
} else if (strcmp(gt_str_get(arguments->input), "bed") == 0)
{
if (argc - parsed_args == 0)
in_stream = gt_bed_in_stream_new(NULL);
else
in_stream = gt_bed_in_stream_new(argv[parsed_args]);
} else if (strcmp(gt_str_get(arguments->input), "gtf") == 0)
{
if (argc - parsed_args == 0)
in_stream = gt_gtf_in_stream_new(NULL);
else
in_stream = gt_gtf_in_stream_new(argv[parsed_args]);
}
last_stream = in_stream;
/* create add introns stream if -addintrons was used */
if (arguments->addintrons) {
sort_stream = gt_sort_stream_new(last_stream);
add_introns_stream = gt_add_introns_stream_new(sort_stream);
last_stream = add_introns_stream;
}
/* create gff3 output stream if -pipe was used */
if (arguments->pipe) {
gff3_out_stream = gt_gff3_out_stream_new(last_stream, NULL);
last_stream = gff3_out_stream;
}
/* create feature stream */
feature_stream = gt_feature_stream_new(last_stream, features);
/* pull the features through the stream and free them afterwards */
had_err = gt_node_stream_pull(feature_stream, err);
gt_node_stream_delete(feature_stream);
gt_node_stream_delete(gff3_out_stream);
gt_node_stream_delete(sort_stream);
gt_node_stream_delete(add_introns_stream);
gt_node_stream_delete(in_stream);
}
if (!had_err) {
had_err = gt_feature_index_has_seqid(features,
&has_seqid,
gt_str_get(arguments->seqid),
err);
}
/* if seqid is empty, take first one added to index */
if (!had_err && strcmp(gt_str_get(arguments->seqid),"") == 0) {
seqid = gt_feature_index_get_first_seqid(features, err);
if (seqid == NULL) {
gt_error_set(err, "GFF input file must contain a sequence region!");
had_err = -1;
}
}
else if (!had_err && !has_seqid) {
gt_error_set(err, "sequence region '%s' does not exist in GFF input file",
gt_str_get(arguments->seqid));
had_err = -1;
}
else if (!had_err)
seqid = gt_str_get(arguments->seqid);
results = gt_array_new(sizeof (GtGenomeNode*));
if (!had_err) {
had_err = gt_feature_index_get_range_for_seqid(features,
&sequence_region_range,
seqid,
err);
}
if (!had_err) {
qry_range.start = (arguments->start == GT_UNDEF_UWORD ?
sequence_region_range.start :
arguments->start);
qry_range.end = (arguments->end == GT_UNDEF_UWORD ?
sequence_region_range.end :
arguments->end);
}
if (!had_err) {
if (arguments->verbose)
fprintf(stderr, "# of results: "GT_WU"\n", gt_array_size(results));
/* find and load style file */
if (!(sty = gt_style_new(err)))
had_err = -1;
if (gt_str_length(arguments->stylefile) == 0) {
gt_str_append_str(arguments->stylefile, defaultstylefile);
} else {
if (!had_err && gt_file_exists(gt_str_get(arguments->stylefile))) {
if (arguments->unsafe)
gt_style_unsafe_mode(sty);
}
else
{
had_err = -1;
gt_error_set(err, "style file '%s' does not exist!",
gt_str_get(arguments->stylefile));
}
}
if (!had_err)
had_err = gt_style_load_file(sty, gt_str_get(arguments->stylefile), err);
}
if (!had_err) {
/* create and write image file */
if (!(d = gt_diagram_new(features, seqid, &qry_range, sty, err)))
had_err = -1;
if (!had_err && arguments->flattenfiles)
gt_diagram_set_track_selector_func(d, flattened_file_track_selector,
NULL);
if (had_err || !(l = gt_layout_new(d, arguments->width, sty, err)))
had_err = -1;
if (!had_err)
had_err = gt_layout_get_height(l, &height, err);
if (!had_err) {
ii = gt_image_info_new();
if (strcmp(gt_str_get(arguments->format),"pdf")==0) {
canvas = gt_canvas_cairo_file_new(sty, GT_GRAPHICS_PDF,
arguments->width,
height, ii, err);
}
else if (strcmp(gt_str_get(arguments->format),"ps")==0) {
canvas = gt_canvas_cairo_file_new(sty, GT_GRAPHICS_PS,
arguments->width,
height, ii, err);
}
else if (strcmp(gt_str_get(arguments->format),"svg")==0) {
canvas = gt_canvas_cairo_file_new(sty, GT_GRAPHICS_SVG,
arguments->width,
height, ii, err);
}
else {
canvas = gt_canvas_cairo_file_new(sty, GT_GRAPHICS_PNG,
arguments->width,
height, ii, err);
}
if (!canvas)
had_err = -1;
if (!had_err) {
had_err = gt_layout_sketch(l, canvas, err);
}
if (!had_err) {
if (arguments->showrecmaps) {
GtUword i;
const GtRecMap *rm;
for (i = 0; i < gt_image_info_num_of_rec_maps(ii) ;i++) {
char buf[BUFSIZ];
rm = gt_image_info_get_rec_map(ii, i);
(void) gt_rec_map_format_html_imagemap_coords(rm, buf, BUFSIZ);
printf("%s, %s\n",
buf,
gt_feature_node_get_type(gt_rec_map_get_genome_feature(rm)));
}
}
if (arguments->use_streams) {
GtFile *outfile;
GtStr *str = gt_str_new();
gt_canvas_cairo_file_to_stream((GtCanvasCairoFile*) canvas, str);
outfile = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, file, "w+", err);
if (outfile) {
gt_file_xwrite(outfile, gt_str_get_mem(str), gt_str_length(str));
gt_file_delete(outfile);
} else {
had_err = -1;
}
gt_str_delete(str);
} else {
had_err = gt_canvas_cairo_file_to_file((GtCanvasCairoFile*) canvas,
file,
err);
}
}
}
}
/* free */
gt_free(seqid);
gt_canvas_delete(canvas);
gt_layout_delete(l);
gt_image_info_delete(ii);
gt_style_delete(sty);
gt_diagram_delete(d);
gt_array_delete(results);
gt_str_delete(defaultstylefile);
gt_feature_index_delete(features);
return had_err;
}
