Esempio n. 1
0
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;
}
Esempio n. 2
0
static int canvas_lua_delete(lua_State *L)
{
  GtCanvas **canvas;
  canvas = check_canvas(L, 1);
  gt_canvas_delete(*canvas);
  return 0;
}
Esempio n. 3
0
static int gt_sketch_page_runner(GT_UNUSED int argc,
                                 const char **argv,
                                 int parsed_args,
                                 void *tool_arguments,
                                 GtError *err)
{
  SketchPageArguments *arguments = tool_arguments;
  int had_err = 0;
  GtFeatureIndex *features = NULL;
  GtRange qry_range, sequence_region_range;
  GtStyle *sty = NULL;
  GtStr *prog, *gt_style_file;
  GtDiagram *d = NULL;
  GtLayout *l = NULL;
  GtBioseq *bioseq = NULL;
  GtCanvas *canvas = NULL;
  const char *seqid = NULL, *outfile;
  unsigned long start, height, num_pages = 0;
  double offsetpos, usable_height;
  cairo_surface_t *surf = NULL;
  cairo_t *cr = NULL;
  GtTextWidthCalculator *twc;
  gt_error_check(err);

  features = gt_feature_index_memory_new();

  if (cairo_version() < CAIRO_VERSION_ENCODE(1, 8, 6))
    gt_warning("Your cairo library (version %s) is older than version 1.8.6! "
               "These versions contain a bug which may result in "
               "corrupted PDF output!", cairo_version_string());

  /* get style */
  sty = gt_style_new(err);
  if (gt_str_length(arguments->stylefile) == 0)
  {
    prog = gt_str_new();
    gt_str_append_cstr_nt(prog, argv[0],
                          gt_cstr_length_up_to_char(argv[0], ' '));
    gt_style_file = gt_get_gtdata_path(gt_str_get(prog), err);
    gt_str_delete(prog);
    gt_str_append_cstr(gt_style_file, "/sketch/default.style");
  }
  else
  {
    gt_style_file = gt_str_ref(arguments->stylefile);
  }
  had_err = gt_style_load_file(sty, gt_str_get(gt_style_file), err);

  outfile = argv[parsed_args];
  if (!had_err)
  {
    /* get features */
    had_err = gt_feature_index_add_gff3file(features, argv[parsed_args+1], err);
     if (!had_err && gt_str_length(arguments->seqid) == 0) {
      seqid = gt_feature_index_get_first_seqid(features);
      if (seqid == NULL)
      {
        gt_error_set(err, "GFF input file must contain a sequence region!");
        had_err = -1;
      }
    }
    else if (!had_err
               && !gt_feature_index_has_seqid(features,
                                              gt_str_get(arguments->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);
  }

  /* set text */
  if (gt_str_length(arguments->text) == 0)
  {
    gt_str_delete(arguments->text);
    arguments->text = gt_str_new_cstr(argv[parsed_args+1]);
  }

  if (!had_err)
  {
    /* set display range */
    gt_feature_index_get_range_for_seqid(features, &sequence_region_range,
                                         seqid);
    qry_range.start = (arguments->range.start == GT_UNDEF_ULONG ?
                         sequence_region_range.start :
                         arguments->range.start);
    qry_range.end   = (arguments->range.end == GT_UNDEF_ULONG ?
                         sequence_region_range.end :
                         arguments->range.end);

    /* set output format */
    if (strcmp(gt_str_get(arguments->format), "pdf") == 0)
    {
      surf = cairo_pdf_surface_create(outfile,
                                      mm_to_pt(arguments->pwidth),
                                      mm_to_pt(arguments->pheight));
    }
    else if (strcmp(gt_str_get(arguments->format), "ps") == 0)
    {
      surf =  cairo_ps_surface_create(outfile,
                                      mm_to_pt(arguments->pwidth),
                                      mm_to_pt(arguments->pheight));
    }
    gt_log_log("created page with %.2f:%.2f dimensions\n",
                                                  mm_to_pt(arguments->pwidth),
                                                  mm_to_pt(arguments->pheight));

    offsetpos = TEXT_SPACER + arguments->theight + TEXT_SPACER;
    usable_height = mm_to_pt(arguments->pheight)
                              - arguments->theight
                              - arguments->theight
                              - 4*TEXT_SPACER;

    if (gt_str_length(arguments->seqfile) > 0) {
      bioseq = gt_bioseq_new(gt_str_get(arguments->seqfile), err);
    }

    cr = cairo_create(surf);
    cairo_set_font_size(cr, 8);
    twc = gt_text_width_calculator_cairo_new(cr, sty);
    for (start = qry_range.start; start <= qry_range.end;
         start += arguments->width)
    {
      GtRange single_range;
      GtCustomTrack *ct = NULL;
      const char *seq;
      single_range.start = start;
      single_range.end = start + arguments->width;

      if (had_err)
        break;

      d = gt_diagram_new(features, seqid, &single_range, sty, err);
      if (!d) {
        had_err = -1;
        break;
      }
      if (bioseq) {
        seq = gt_bioseq_get_sequence(bioseq, 0);
        ct = gt_custom_track_gc_content_new(seq,
                                      gt_bioseq_get_sequence_length(bioseq, 0),
                                      800, 70, 0.4, true);
        gt_diagram_add_custom_track(d, ct);
      }

      l = gt_layout_new_with_twc(d, mm_to_pt(arguments->width), sty, twc, err);
      had_err = gt_layout_get_height(l, &height, err);
      if (!had_err) {
        if (gt_double_smaller_double(usable_height - 10 - 2*TEXT_SPACER
              - arguments->theight, offsetpos + height))
        {
            draw_header(cr, gt_str_get(arguments->text), argv[parsed_args+1],
                        seqid, num_pages, mm_to_pt(arguments->pwidth),
                        mm_to_pt(arguments->pheight),
                        arguments->theight);
          cairo_show_page(cr);
          offsetpos = TEXT_SPACER + arguments->theight + TEXT_SPACER;
          num_pages++;
        }
        canvas = gt_canvas_cairo_context_new(sty,
                                             cr,
                                             offsetpos,
                                             mm_to_pt(arguments->pwidth),
                                             height,
                                             NULL,
                                             err);
        if (!canvas)
          had_err = -1;
        offsetpos += height;
        if (!had_err)
          had_err = gt_layout_sketch(l, canvas, err);
      }
      gt_canvas_delete(canvas);
      gt_layout_delete(l);
      gt_diagram_delete(d);
      if (ct)
        gt_custom_track_delete(ct);
    }
    draw_header(cr, gt_str_get(arguments->text), argv[parsed_args+1], seqid,
                num_pages, mm_to_pt(arguments->pwidth),
                mm_to_pt(arguments->pheight),
                arguments->theight);
    cairo_show_page(cr);
    num_pages++;
    gt_log_log("finished, should be %lu pages\n", num_pages);
    gt_text_width_calculator_delete(twc);
    cairo_destroy(cr);
    cairo_surface_flush(surf);
    cairo_surface_finish(surf);
    cairo_surface_destroy(surf);
    cairo_debug_reset_static_data();
    if (bioseq)
      gt_bioseq_delete(bioseq);
    gt_style_delete(sty);
    gt_str_delete(gt_style_file);
    gt_feature_index_delete(features);
  }
  return had_err;
}
Esempio n. 4
0
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;
}