void test_int_range ()
{
int inputs [] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 99, 999, -1, -3, -99, 234234 };
int outputs [] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10, 10, -1, -1, -1, 10 };
std::vector<int> results;
std::vector<int> in_v;
std::copy ( a_begin(inputs), a_end(inputs), std::back_inserter ( in_v ));
ba::clamp_range ( a_begin(inputs), a_end(inputs), std::back_inserter ( results ), -1, 10 );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( in_v.begin (), in_v.end (), std::back_inserter ( results ), -1, 10 );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( a_begin(inputs), a_end(inputs), std::back_inserter ( results ), 10, -1, intGreater );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( in_v.begin (), in_v.end (), std::back_inserter ( results ), 10, -1, intGreater );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( a_range(inputs), std::back_inserter ( results ), -1, 10 );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( in_v, std::back_inserter ( results ), -1, 10 );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( a_range(inputs), std::back_inserter ( results ), 10, -1, intGreater );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
ba::clamp_range ( in_v, std::back_inserter ( results ), 10, -1, intGreater );
BOOST_CHECK ( std::equal ( results.begin(), results.end (), outputs ));
results.clear ();
int junk[elementsof(inputs)];
ba::clamp_range ( inputs, junk, 10, -1, intGreater );
BOOST_CHECK ( std::equal ( b_e(junk), outputs ));
}
int compare_filenames(const std::string& a, const std::string& b)
{
utf8_const_iterator a_begin(a.begin()), a_end(a.end());
utf8_const_iterator b_begin(b.begin()), b_end(b.end());
utf8_const_iterator a_it(a_begin);
utf8_const_iterator b_it(b_begin);
for (; a_it != a_end && b_it != b_end; ) {
int a_chr = *a_it;
int b_chr = *b_it;
if ((a_chr >= '0') && (a_chr <= '9') && (b_chr >= '0') && (b_chr <= '9')) {
utf8_const_iterator a_it2 = a_it;
utf8_const_iterator b_it2 = b_it;
while (a_it2 != a_end && (*a_it2 >= '0') && (*a_it2 <= '9')) ++a_it2;
while (b_it2 != b_end && (*b_it2 >= '0') && (*b_it2 <= '9')) ++b_it2;
int a_num = std::strtol(std::string(a_it, a_it2).c_str(), NULL, 10);
int b_num = std::strtol(std::string(b_it, b_it2).c_str(), NULL, 10);
if (a_num != b_num)
return a_num - b_num < 0 ? -1: 1;
a_it = a_it2;
b_it = b_it2;
}
else if (is_path_separator(a_chr) && is_path_separator(b_chr)) {
++a_it;
++b_it;
}
else {
a_chr = std::tolower(a_chr);
b_chr = std::tolower(b_chr);
if (a_chr != b_chr)
return a_chr - b_chr < 0 ? -1: 1;
++a_it;
++b_it;
}
}
if (a_it == a_end && b_it == b_end)
return 0;
else if (a_it == a_end)
return -1;
else
return 1;
}
char *
ovOverlap::toString(char *str,
ovOverlapDisplayType type,
bool newLine) {
switch (type) {
case ovOverlapAsHangs:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_S32P" %6"F_U32P" %6"F_S32P" %7.6f%s%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
a_hang(), span(), b_hang(),
erate(),
(overlapIsDovetail()) ? "" : " PARTIAL",
(newLine) ? "\n" : "");
break;
case ovOverlapAsCoords:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %7.6f%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
span(),
a_bgn(), a_end(),
b_bgn(), b_end(),
erate(),
(newLine) ? "\n" : "");
break;
case ovOverlapAsRaw:
sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %7.6f %s %s %s%s",
a_iid, b_iid,
flipped() ? 'I' : 'N',
span(),
dat.ovl.ahg5, dat.ovl.ahg3,
dat.ovl.bhg5, dat.ovl.bhg3,
erate(),
dat.ovl.forOBT ? "OBT" : " ",
dat.ovl.forDUP ? "DUP" : " ",
dat.ovl.forUTG ? "UTG" : " ",
(newLine) ? "\n" : "");
break;
case ovOverlapAsCompat:
sprintf(str, "%8"F_U32P" %8"F_U32P" %c %6d %6d %5.2f %5.2f%s",
a_iid,
b_iid,
dat.ovl.flipped ? 'I' : 'N',
a_hang(), b_hang(),
erate() * 100.0,
erate() * 100.0,
(newLine) ? "\n" : "");
break;
case ovOverlapAsPaf:
// miniasm/map expects entries to be separated by tabs
// no padding spaces on names we don't confuse read identifiers
sprintf(str, "%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%c\t%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P" %s",
a_iid,
(g->gkStore_getRead(a_iid)->gkRead_sequenceLength()), a_bgn(), a_end(),
flipped() ? '-' : '+',
b_iid,
(g->gkStore_getRead(b_iid)->gkRead_sequenceLength()), flipped() ? b_end() : b_bgn(), flipped() ? b_bgn() : b_end(),
(uint32)floor(span() == 0 ? (1-erate() * (a_end()-a_bgn())) : (1-erate()) * span()),
span() == 0 ? a_end() - a_bgn() : span(),
255,
(newLine) ? "\n" : "");
break;
}
return(str);
}
void link_check::inspect(
const string & library_name,
const path & full_path, // example: c:/foo/boost/filesystem/path.hpp
const string & contents ) // contents of file to be inspected
{
if (contents.find( "boostinspect:" "nounlinked" ) != string::npos)
m_paths[ relative_to( full_path, search_root_path() ) ] |= m_nounlinked_errors;
bool no_link_errors =
(contents.find( "boostinspect:" "nolink" ) != string::npos);
// build bookmarks databases
bookmarks.clear();
bookmarks_lowercase.clear();
string::const_iterator a_start( contents.begin() );
string::const_iterator a_end( contents.end() );
boost::match_results< string::const_iterator > a_what;
boost::match_flag_type a_flags = boost::match_default;
if(!is_css(full_path))
{
string previous_id;
while( boost::regex_search( a_start, a_end, a_what, html_bookmark_regex, a_flags) )
{
// a_what[0] contains the whole string iterators.
// a_what[1] contains the tag iterators.
// a_what[2] contains the attribute name.
// a_what[4] contains the bookmark iterators.
if (a_what[4].matched)
{
string tag( a_what[1].first, a_what[1].second );
boost::algorithm::to_lower(tag);
string attribute( a_what[2].first, a_what[2].second );
boost::algorithm::to_lower(attribute);
string bookmark( a_what[4].first, a_what[4].second );
bool name_following_id = ( attribute == "name" && previous_id == bookmark );
if ( tag != "meta" && attribute == "id" ) previous_id = bookmark;
else previous_id.clear();
if ( tag != "meta" && !name_following_id )
{
bookmarks.insert( bookmark );
// std::cout << "******************* " << bookmark << '\n';
// w3.org recommends case-insensitive checking for duplicate bookmarks
// since some browsers do a case-insensitive match.
string bookmark_lowercase( bookmark );
boost::algorithm::to_lower(bookmark_lowercase);
std::pair<bookmark_set::iterator, bool> result
= bookmarks_lowercase.insert( bookmark_lowercase );
if (!result.second)
{
++m_duplicate_bookmark_errors;
int ln = std::count( contents.begin(), a_what[3].first, '\n' ) + 1;
error( library_name, full_path, "Duplicate bookmark: " + bookmark, ln );
}
}
}
a_start = a_what[0].second; // update search position
a_flags |= boost::match_prev_avail; // update flags
a_flags |= boost::match_not_bob;
}
}
// process urls
string::const_iterator start( contents.begin() );
string::const_iterator end( contents.end() );
boost::match_results< string::const_iterator > what;
boost::match_flag_type flags = boost::match_default;
if(!is_css(full_path))
{
while( boost::regex_search( start, end, what, html_url_regex, flags) )
{
// what[0] contains the whole string iterators.
// what[1] contains the element type iterators.
// what[3] contains the URL iterators.
if(what[3].matched)
{
string type( what[1].first, what[1].second );
boost::algorithm::to_lower(type);
// TODO: Complain if 'link' tags use external stylesheets.
do_url( string( what[3].first, what[3].second ),
library_name, full_path, no_link_errors,
type == "a" || type == "link", contents.begin(), what[3].first );
}
start = what[0].second; // update search position
flags |= boost::match_prev_avail; // update flags
flags |= boost::match_not_bob;
}
}
while( boost::regex_search( start, end, what, css_url_regex, flags) )
{
// what[0] contains the whole string iterators.
// what[2] contains the URL iterators.
if(what[2].matched)
{
do_url( string( what[2].first, what[2].second ),
library_name, full_path, no_link_errors, false,
contents.begin(), what[3].first );
}
start = what[0].second; // update search position
flags |= boost::match_prev_avail; // update flags
flags |= boost::match_not_bob;
}
}
