int main(int argc, char const ** argv)
{
ArgumentParser parser("arg_parse_demo");
setShortDescription(parser, "Just a demo of the new seqan::ArgumentParser!");
setVersion(parser, "0.1");
setDate(parser, "Mar 2012");
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fIIN\\fP \\fIOUT\\fP ");
addDescription(parser, "This is just a little demo to show what seqan::ArgumentParser is able to do.");
addDescription(parser, "\\fIIN\\fP is a multi-FASTA input.");
addDescription(parser, "\\fIOUT\\fP is a txt output.");
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUTFILE, "IN"));
addArgument(parser, ArgParseArgument(ArgParseArgument::OUTPUTFILE, "OUT"));
// allow only fasta files as input
setValidValues(parser, 0, "FASTA fa");
setValidValues(parser, 1, "txt");
addSection(parser, "Important Tool Parameters");
addOption(parser, ArgParseOption("", "id", "Sequence identity between [0.0:1.0]", ArgParseArgument::DOUBLE, "ID"));
setRequired(parser, "id", true);
setMinValue(parser, "id", "0.0");
setMaxValue(parser, "id", "1.0");
addSection(parser, "Miscellaneous");
addOption(parser, ArgParseOption("v", "verbose", "Turn on verbose output."));
addOption(parser, ArgParseOption("H", "hidden", "Super mysterious flag that will not be shown in the help screen or man-page."));
hideOption(parser, "H");
addTextSection(parser, "References");
addText(parser, "http://www.seqan.de");
ArgumentParser::ParseResult res = parse(parser, argc, argv);
if (res == ArgumentParser::PARSE_OK)
{
bool verbose = false;
getOptionValue(verbose, parser, "verbose");
std::cout << "Verbose: " << (verbose ? "on" : "off") << std::endl;
double identity = -1.0;
getOptionValue(identity, parser, "id");
std::cout << "Identity: " << identity << std::endl;
CharString inputFile, outputFile;
getArgumentValue(inputFile, parser, 0);
getArgumentValue(outputFile, parser, 1);
std::cout << "Input-File: " << inputFile << std::endl;
std::cout << "Output-File: " << outputFile << std::endl;
return 0;
}
else
{
return res == ArgumentParser::PARSE_ERROR; // 1 on errors, 0 otherwise
}
}
int half_sw_banded(const Ts1 &s1, const Ts2 &s2,
int match, int mismatch,
int indel,
const Tf &lizard_tail,
int max_indels = 6) {
using std::min;
using std::max;
using seqan::length;
using std::vector;
const int INF = 1005000;
if (max_indels == 0) {
return half_hamming(s1, s2, match, mismatch, lizard_tail);
}
int len1 = length(s1), len2 = length(s2); // Cache lengths because of length(s) computation maybe not O(1) e.g. for char*-strings
vector<int> base(2*max_indels + 1, -INF);
for (int i2 = max(0, len1 - max_indels); i2 <= min(len1 + max_indels, len2); ++i2) {
int ind = i2 + max_indels - len1;
base[ind] = lizard_tail(len2 - i2);
}
vector<int> new_base(2*max_indels + 1, -INF);
for (int i1 = len1 - 1; i1 >= 0; --i1) {
for (int i2 = i1 + max_indels; i2 >= i1 - max_indels; --i2) {
int inx = max_indels + i2 - i1;
if ((i2 < 0) || (i2 > len2)) {
new_base[inx] = -INF;
} else if (i2 == len2) {
new_base[inx] = lizard_tail(len1 - i1);
} else {
int m = (s1[i1] == s2[i2]) ? match : mismatch;
if (inx == 0)
new_base[inx] = max( { m + base[inx], indel + new_base[inx + 1]} );
else if (inx == 2*max_indels)
new_base[inx] = max( { m + base[inx], indel + base[inx - 1] } );
else
new_base[inx] = max( { m + base[inx], indel + base[inx - 1], indel + new_base[inx + 1]} );
}
}
std::swap(base, new_base);
}
return max(-INF, base[max_indels]); // Score is always finite due to possibility to align using mismatches
}
int half_hamming(const Ts1 &s1, const Ts2 &s2,
int match, int mismatch,
const Tf &lizard_tail) {
int len1 = length(s1), len2 = length(s2); // Cache lengths because of length(s) computation maybe not O(1) e.g. for char*-strings
size_t len = std::min<size_t>(len1, len2);
size_t res = 0;
for (size_t i = 0; i < len; ++i) {
res += (s1[i] == s2[i]) ? match : mismatch;
}
res += lizard_tail(std::abs(len1 - len2));
return res;
}
void add(const T &s, size_t id, const Tf &toIndex) {
if (!root) {
root.reset(new TrieNode);
}
typename TrieNode::pointer_type p = this->root.get();
for (size_t i = 0; i < length(s); ++i) {
size_t el = toIndex(s[i]);
assert((0 <= el) && (el < p->children.size()));
if (!p->children[el]) {
p->children[el] = new TrieNode();
}
p = p->children[el];
}
if (!p->ids) {
p->ids = new std::vector<size_t>;
}
p->ids->push_back(id);
}
int main(int argc, char const ** argv)
{
// Initialize ArgumentParser.
ArgumentParser parser("arg_parse_demo");
setCategory(parser, "Demo");
setShortDescription(parser, "Just a demo of the new seqan::ArgumentParser!");
setVersion(parser, "0.1");
setDate(parser, "Mar 2012");
// Add use and description lines.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fIIN\\fP \\fIOUT\\fP ");
addDescription(
parser,
"This is just a little demo to show what seqan::ArgumentParser is "
"able to do. \\fIIN\\fP is a multi-FASTA input file. \\fIOUT\\fP is a "
"txt output file.");
// Add positional arguments and set their valid file types.
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUTFILE, "IN"));
addArgument(parser, ArgParseArgument(ArgParseArgument::OUTPUTFILE, "OUT"));
setValidValues(parser, 0, "FASTA fa");
setValidValues(parser, 1, "txt");
// Add a section with some options.
addSection(parser, "Important Tool Parameters");
addOption(parser, ArgParseOption("", "id", "Sequence identity between [0.0:1.0]",
ArgParseArgument::DOUBLE, "ID"));
setRequired(parser, "id", true);
setMinValue(parser, "id", "0.0");
setMaxValue(parser, "id", "1.0");
// Adding a verbose and a hidden option.
addSection(parser, "Miscellaneous");
addOption(parser, ArgParseOption("v", "verbose", "Turn on verbose output."));
addOption(parser, ArgParseOption("H", "hidden", "Super mysterious flag that will not be shown in "
"the help screen or man page."));
hideOption(parser, "H");
// Add a Reference section.
addTextSection(parser, "References");
addText(parser, "http://www.seqan.de");
// Parse the arguments.
ArgumentParser::ParseResult res = parse(parser, argc, argv);
// Return if there was an error or a built-in command was triggered (e.g. help).
if (res != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR; // 1 on errors, 0 otherwise
// Extract and print the options.
bool verbose = false;
getOptionValue(verbose, parser, "verbose");
std::cout << "Verbose: " << (verbose ? "on" : "off") << std::endl;
double identity = -1.0;
getOptionValue(identity, parser, "id");
std::cout << "Identity: " << identity << std::endl;
CharString inputFile, outputFile;
getArgumentValue(inputFile, parser, 0);
getArgumentValue(outputFile, parser, 1);
std::cout << "Input-File: " << inputFile << std::endl;
std::cout << "Output-File: " << outputFile << std::endl;
return 0;
}