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How to use highlight_regions method in Testify

Best Python code snippet using Testify_python

highlight_manager.py

Source:highlight_manager.py

1import sublime2from .color_scheme_manager import *3from .minimal_region_set import *4class HighlightManager():5    def __init__(self, view, settings):6        self.view = view7        self.key_base = "regex_highlight_"8        self.settings = settings9    def highlight(self):10        color_dictionary, colors = self._get_highlight_dictionary()11        if self.settings.get("prompt_new_color_scheme"):12            color_scheme_manager = ColorSchemeManager("User/ColorScheme")13            color_scheme_manager.create_user_custom_theme(colors)14        self._highlight_regex(color_dictionary)15    def _get_highlight_dictionary(self):16        view = self.view17        settings = self.settings18        regex_list = settings.get("regex")19        region_set = MinimalRegionSet()20        region_dictionary = {}21        color_dictionary = {}22        colors = []23        self.solid_underline_regions = []24        self.squiggly_underline_regions = []25        self.stippled_underline_regions = []26        # Find all entries that match a pattern27        for obj in regex_list:28            if "syntax" in obj:29                applicable = False30                view_syntax = view.settings().get('syntax')31                if view_syntax:32                    for syn in obj["syntax"]:33                        if syn in view_syntax:34                            applicable = True35                if not applicable:36                    continue37            if "syntax_ignore" in obj:38                applicable = True39                view_syntax = view.settings().get('syntax')40                if view_syntax:41                    for syn in obj["syntax_ignore"]:42                        if syn in view_syntax:43                            applicable = False44                if not applicable:45                    continue46            if "pattern" in obj and len(obj["pattern"]) > 0:47                if "ignore_case" in obj and obj["ignore_case"]:48                    regions = view.find_all(obj["pattern"], sublime.IGNORECASE)49                else:50                    regions = view.find_all(obj["pattern"])51            elif "pattern_scope" in obj:52                regions = view.find_by_selector(obj["pattern_scope"])53            else:54                continue55            if "ignored_scopes" in obj:56                scope = obj["ignored_scopes"].lower();57                regions = [region for region in regions if len([sel_scope for sel_scope in view.scope_name(region.begin()).split() if sel_scope in scope]) == 0]58            if "color_scope" in obj:59                color = obj["color_scope"]60            elif "color" in obj:61                colors.append(obj["color"])62                color = "highlight.color." + obj["color"].upper()63            else:64                color = "entity.name.class"65            solid_underline = False66            squiggly_underline = False67            stippled_underline = False68            if "underline" in obj and obj["underline"]:69                solid_underline = True70                if int(sublime.version()) >= 3014:71                    if "underline_style" in obj:72                        if obj["underline_style"].lower() == "squiggly":73                            squiggly_underline = True74                            solid_underline = False75                        elif obj["underline_style"].lower() == "stippled":76                            stippled_underline = True77                            solid_underline = False78            if len(regions) > 0:79                region_set.add_all(regions)80                for region in regions:81                    if solid_underline:82                        self.solid_underline_regions.append(region)83                    elif squiggly_underline:84                        self.squiggly_underline_regions.append(region)85                    elif stippled_underline:86                        self.stippled_underline_regions.append(region)87                    region_dictionary[str(region)] = color88        # Create a dictionary of only the entries to be colored,89        # and their associated color90        regions = region_set.to_array()91        for region in regions:92            color = region_dictionary[str(region)]93            if color in color_dictionary:94                color_dictionary[color].append(region)95            else:96                color_dictionary[color] = [region]97        return color_dictionary, colors98    def _highlight_regex(self, color_dictionary):99        version = int(sublime.version())100        view = self.view101        key_base = self.key_base102        counter = 0103        for color, regions in color_dictionary.items():104            highlight_regions = []105            solid_underline_regions = []106            stippled_underline_regions = []107            squiggly_underline_regions = []108            for region in regions:109                if region in self.solid_underline_regions:110                    if version < 3014:111                        highlight_regions += self._underline(region)112                    else:113                        solid_underline_regions.append(region)114                elif region in self.squiggly_underline_regions:115                    squiggly_underline_regions.append(region)116                elif region in self.stippled_underline_regions:117                    stippled_underline_regions.append(region)118                else:119                    highlight_regions.append(region)120            if len(highlight_regions) > 0:121                view.add_regions(key_base + str(counter),122                                 highlight_regions, color, "",123                                 sublime.DRAW_EMPTY_AS_OVERWRITE)124                counter += 1125            if version >= 3014:126                underline_standard = sublime.DRAW_NO_FILL | sublime.DRAW_NO_OUTLINE127                if len(solid_underline_regions) > 0:128                    view.add_regions(key_base + str(counter),129                                     solid_underline_regions, color, "",130                                     underline_standard | sublime.DRAW_SOLID_UNDERLINE)131                    counter += 1132                if len(squiggly_underline_regions) > 0:133                    view.add_regions(key_base + str(counter),134                                     squiggly_underline_regions, color, "",135                                     underline_standard | sublime.DRAW_SQUIGGLY_UNDERLINE)136                    counter += 1137                if len(stippled_underline_regions) > 0:138                    view.add_regions(key_base + str(counter),139                                     stippled_underline_regions, color, "",140                                     underline_standard | sublime.DRAW_STIPPLED_UNDERLINE)141                    counter += 1142    def _underline(self, region):143        ret_regions = []144        begin = region.begin()145        end = region.end()146        while begin < end:147            ret_regions.append(sublime.Region(begin, begin))148            begin += 1149        return ret_regions150    def remove_highlight(self):151        view = self.view152        key_base = self.key_base153        counter = 0154        while True:155            temp = view.get_regions(key_base + str(counter))156            if len(temp) > 0:157                view.erase_regions(key_base + str(counter))158                counter += 1159            else:...

highlights.py

Source:highlights.py

1from coolbox.utilities import (2    opener, ReadBed,3    Interval, IntervalTree,4    rgb2hex,5    get_logger, GenomeRange,6    to_gr7)8from .base import Coverage9log = get_logger(__name__)10class _Highlights(object):11    DEFAULT_COLOR = '#ff5d0f'12    def fetch_data(self, gr: GenomeRange, **kwargs):13        gr = to_gr(gr)14        if gr.chrom not in list(self.interval_tree):15            gr.change_chrom_names()16        return [17            (region.begin, region.end, region.data)18            for region in sorted(19                self.interval_tree[gr.chrom][gr.start - 10000 : gr.end + 10000]20            )21        ]22    def plot(self, ax, gr: GenomeRange, **kwargs):23        regions = self.fetch_data(gr, **kwargs)24        for (start, end, color) in regions:25            if self.properties['color'] != 'bed_rgb':26                color = self.properties['color']27            if type(color) is not str:28                color = rgb2hex(*color)29            ax.axvspan(start, end, color=color, alpha=self.properties['alpha'])30            if self.properties['border_line'] == 'yes':31                # plot border line32                ymin, ymax = ax.get_ylim()33                ax.vlines([start, end], ymin, ymax,34                          linestyle=self.properties['border_line_style'],35                          linewidth=self.properties['border_line_width'],36                          color=self.properties['border_line_color'],37                          alpha=self.properties['border_line_alpha'])38class HighLightsFromFile(Coverage, _Highlights):39    """40    High light regions coverage, read the regions from the file.41    Parameters42    ----------43    file_ : str44        Path to the file.45    color : str, optional46        High light region color,47        use 'bed_rgb' for specify color from the file, default 'bed_rgb'.48    alpha : float, optional49        High light region alpha value, default 0.1.50    border_line : bool, optional51        Plot border line or not, default True.52    border_line_style : str, optional53        Border line style, default 'dashed'.54    border_line_width : float, optional55        Border line width, default 1.0.56    border_line_color : str, optional57        Border line color, default '#000000'58    border_line_alpha : float, optional59        Border line alpha value, default 0.860    name : str, optional61        The name of thr Coverage.62    """63    def __init__(self, file_, **kwargs):64        properties_dict = {65            "file": file_,66            "color": "bed_rgb",67            "alpha": 0.1,68            "border_line": True,69            "border_line_style": "dashed",70            "border_line_width": 0,71            "border_line_color": "#000000",72            "border_line_alpha": 0.8,73        }74        properties_dict.update(kwargs)75        super().__init__(properties_dict)76        self.interval_tree = self.__process_bed()77    def __process_bed(self):78        bed = ReadBed(opener(self.properties['file']))79        if self.properties['color'] == 'bed_rgb' and bed.file_type not in ['bed12', 'bed9']:80            log.warning("*WARNING* Color set to 'bed_rgb', but bed file does not have the rgb field. The color has "81                        "been set to {}".format(HighLights.DEFAULT_COLOR))82            self.properties['color'] = HighLights.DEFAULT_COLOR83        interval_tree = {}84        for intval in bed:85            if intval.chromosome not in interval_tree:86                interval_tree[intval.chromosome] = IntervalTree()87            if self.properties['color'] == 'bed_rgb':88                color = intval.rgb89            else:90                color = self.properties['color']91            interval_tree[intval.chromosome].add(Interval(intval.start, intval.end, color))92        return interval_tree93class HighLights(Coverage, _Highlights):94    """95    High light region.96    Parameters97    ----------98    highlight_regions : list of {str, tuple}99        A list of regions for highlights, region can be expressed as a tuple or string.100        region tuple like:101        [('chr1', 100000, 120000), ('chr2', 130000, 150000)]102        region string format: `chr:start-end` like:103        ['chr1:100000-120000', 'chr2:130000-150000'].104    color : str, optional105        High light region color, default HighLights.DEFAULT_COLOR.106    alpha : float, optional107        High light region alpha value, default 0.5108    border_line : bool, optional109        Plot border line or not, default True.110    border_line_style : str, optional111        Border line style, default 'dashed'112    border_line_width : float, optional113        Border line width, default 1.0114    border_line_color : str, optional115        Border line color, default '#000000'116    border_line_alpha : float, optional117        Border line alpha value, default 0.8118    name : str, optional119        The name of thr Coverage.120    """121    DEFAULT_COLOR = "#ff9c9c"122    def __init__(self, highlight_regions, **kwargs):123        if not isinstance(highlight_regions, list):124            highlight_regions = [highlight_regions]125        properties_dict = {126            "highlight_regions": highlight_regions,127            "color": HighLights.DEFAULT_COLOR,128            "alpha": 0.25,129            "border_line": True,130            "border_line_style": "dashed",131            "border_line_width": 0,132            "border_line_color": "#000000",133            "border_line_alpha": 0.8,134        }135        properties_dict.update(kwargs)136        super().__init__(properties_dict)137        self.interval_tree = self.__intervaltree_from_list(self.properties['highlight_regions'])138    # TODO  may be duplicate of vlines's method139    def __intervaltree_from_list(self, region_list):140        from intervaltree import IntervalTree141        itree = {}142        for r in region_list:143            if isinstance(r, str):144                grange = GenomeRange(r)145            elif isinstance(r, tuple):146                grange = GenomeRange(r[0], r[1], r[2])147            elif isinstance(r, GenomeRange):148                grange = r149            else:150                raise ValueError("position must be a tuple or string.")151            chr_ = grange.chrom152            itree.setdefault(chr_, IntervalTree())153            itree[chr_][grange.start:grange.end + 1] = grange...

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