comparison blast_html.py @ 16:db7e4ee3be03

fix validation, reindent

15:648b3b7437da

    if not isinstance(hit, str):
        hit = hitid(hit)
    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
    if hsp != None:
        link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
    return jinja2.Markup(link)




class BlastVisualize:

            count = 0
            for i in range(self.query_length):
                if table[i] == last:
                    count += 1
                    continue
                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))
                last = table[i]
                count = 1
            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'none'))

            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))


    def queryscale(self):

16:db7e4ee3be03

    if not isinstance(hit, str):
        hit = hitid(hit)
    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
    if hsp != None:
        link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
    return link


# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
# I've removed the html escapes, since html escaping is already being performed by the template engine.

_base_js_escapes = (
    ('\\', r'\u005C'),
    ('\'', r'\u0027'),
    ('"', r'\u0022'),
    # ('>', r'\u003E'),
    # ('<', r'\u003C'),
    # ('&', r'\u0026'),
    # ('=', r'\u003D'),
    # ('-', r'\u002D'),
    # (';', r'\u003B'),
    # (u'\u2028', r'\u2028'),
    # (u'\u2029', r'\u2029')
)

# Escape every ASCII character with a value less than 32. This is
# needed a.o. to prevent parsers from jumping out of javascript
# parsing mode.
_js_escapes = (_base_js_escapes +
               tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))

@filter
def js_string_escape(value):
    """Escape javascript string literal escapes. Note that this only works
    within javascript string literals, not in general javascript
    snippets."""

    value = str(value)

    for bad, good in _js_escapes:
        value = value.replace(bad, good)

    return value



class BlastVisualize:

            count = 0
            for i in range(self.query_length):
                if table[i] == last:
                    count += 1
                    continue
                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
                last = table[i]
                count = 1
            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))

            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))


    def queryscale(self):