void* gt_diagram_unit_test_sketch_func(void *data) { int had_err = 0; GtLayout *l = NULL; GtUword height; GtCanvas *c = NULL; GtDiagramTestShared *sh = (GtDiagramTestShared*) data; l = gt_layout_new(sh->d, 1000, sh->sty, sh->err); if (!l) had_err = -1; if (!had_err) had_err = gt_layout_get_height(l, &height, sh->err); if (!had_err) { c = gt_canvas_cairo_file_new(sh->sty, GT_GRAPHICS_PNG, 1000, height, NULL, sh->err); if (!c) had_err = -1; } if (!had_err) { had_err = gt_layout_sketch(l, c, sh->err); } if (had_err) sh->errstatus = 1; gt_layout_delete(l); gt_canvas_delete(c); return NULL; }
static int layout_lua_new(lua_State *L) { GtLayout **layout; GtDiagram **diagram; unsigned int width; GtStyle *style; GtError *err; diagram = check_diagram(L, 1); width = luaL_checkint(L, 2); /* create layout */ style = gt_lua_get_style_from_registry(L); layout = lua_newuserdata(L, sizeof (GtLayout*)); gt_assert(layout); err = gt_error_new(); *layout = gt_layout_new(*diagram, width, style, err); if (gt_error_is_set(err)) return gt_lua_error(L, err); gt_error_delete(err); luaL_getmetatable(L, LAYOUT_METATABLE); lua_setmetatable(L, -2); return 1; }
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; }
int main(int argc, char *argv[]) { const char *style_file, *png_file, *gff3_file; char *seqid; GtStyle *style; GtBioseq *bioseq; GtFeatureIndex *feature_index; GtRange range; GtDiagram *diagram; GtLayout *layout; GtCanvas *canvas; GtCustomTrack *custom; GtUword height, windowsize; GtError *err; if (argc != 9) { fprintf(stderr, "Usage: %s style_file PNG_file GFF3_file Seq_file seqid" " start end windowsize\n", argv[0]); return EXIT_FAILURE; } style_file = argv[1]; png_file = argv[2]; gff3_file = argv[3]; /* initialize */ gt_lib_init(); /* create error object */ err = gt_error_new(); /* create style */ if (!(style = gt_style_new(err))) handle_error(err); /* load style file */ if (gt_style_load_file(style, style_file, err)) handle_error(err); /* create feature index */ feature_index = gt_feature_index_memory_new(); /* add GFF3 file to index */ if (gt_feature_index_add_gff3file(feature_index, gff3_file, err)) handle_error(err); /* create diagram for first sequence ID in feature index */ seqid = argv[5]; if (gt_feature_index_get_range_for_seqid(feature_index, &range, seqid, err)) handle_error(err); sscanf(argv[6], "%lu", &range.start); sscanf(argv[7], "%lu", &range.end); sscanf(argv[8], "%lu", &windowsize); diagram = gt_diagram_new(feature_index, seqid, &range, style, err); if (gt_error_is_set(err)) handle_error(err); /* load sequence for GC plot */ bioseq = gt_bioseq_new(argv[4], err); if (gt_error_is_set(err)) handle_error(err); /* create custom track with GC plot for first sequence in file, window size 1000, 40px height and average line at 16.5% */ custom = gt_custom_track_gc_content_new(gt_bioseq_get_sequence(bioseq, 0), gt_bioseq_get_sequence_length(bioseq, 0), windowsize, 70, 0.165, true); gt_diagram_add_custom_track(diagram, custom); /* create layout with given width, determine resulting image height */ layout = gt_layout_new(diagram, 600, style, err); if (gt_error_is_set(err)) handle_error(err); if (gt_layout_get_height(layout, &height, err)) handle_error(err); /* create PNG canvas */ canvas = gt_canvas_cairo_file_new(style, GT_GRAPHICS_PNG, 600, height, NULL, err); if (!canvas) handle_error(err); /* sketch layout on canvas */ if (gt_layout_sketch(layout, canvas, err)) handle_error(err); /* write canvas to file */ if (gt_canvas_cairo_file_to_file((GtCanvasCairoFile*) canvas, png_file, err)) handle_error(err); /* free */ gt_custom_track_delete(custom); gt_bioseq_delete(bioseq); gt_canvas_delete(canvas); gt_layout_delete(layout); gt_diagram_delete(diagram); gt_feature_index_delete(feature_index); gt_style_delete(style); gt_error_delete(err); /* perform static data cleanup */ gt_lib_clean(); return EXIT_SUCCESS; }
int main(int argc, char *argv[]) { const char *style_file, *png_file, *gff3_file; char *seqid; GtStyle *style; GtFeatureIndex *feature_index; GtRange range; GtDiagram *diagram; GtLayout *layout; GtCanvas *canvas; GtUword height; GtError *err; if (argc != 4) { fprintf(stderr, "Usage: %s style_file PNG_file GFF3_file\n", argv[0]); return EXIT_FAILURE; } style_file = argv[1]; png_file = argv[2]; gff3_file = argv[3]; /* initialize */ gt_lib_init(); /* create error object */ err = gt_error_new(); /* create style */ if (!(style = gt_style_new(err))) handle_error(err); /* load style file */ if (gt_style_load_file(style, style_file, err)) handle_error(err); /* create feature index */ feature_index = gt_feature_index_memory_new(); /* add GFF3 file to index */ if (gt_feature_index_add_gff3file(feature_index, gff3_file, err)) handle_error(err); /* create diagram for first sequence ID in feature index */ if (!(seqid = gt_feature_index_get_first_seqid(feature_index, err))) { if (gt_error_is_set(err)) handle_error(err); } if (gt_feature_index_get_range_for_seqid(feature_index, &range, seqid, err)) handle_error(err); diagram = gt_diagram_new(feature_index, seqid, &range, style, err); gt_free(seqid); if (gt_error_is_set(err)) handle_error(err); /* create layout with given width, determine resulting image height */ layout = gt_layout_new(diagram, 600, style, err); if (!layout) handle_error(err); if (gt_layout_get_height(layout, &height, err)) handle_error(err); /* create PNG canvas */ canvas = gt_canvas_cairo_file_new(style, GT_GRAPHICS_PNG, 600, height, NULL, err); if (!canvas) handle_error(err); /* */ gt_layout_set_track_ordering_func(layout, rev_order_func, "foooo"); /* sketch layout on canvas */ if (gt_layout_sketch(layout, canvas, err)) handle_error(err); /* write canvas to file */ if (gt_canvas_cairo_file_to_file((GtCanvasCairoFile*) canvas, png_file, err)) handle_error(err); /* free */ gt_canvas_delete(canvas); gt_layout_delete(layout); gt_diagram_delete(diagram); gt_feature_index_delete(feature_index); gt_style_delete(style); gt_error_delete(err); /* perform static data cleanup */ gt_lib_clean(); return EXIT_SUCCESS; }