int
main( int argc, char const *argv[] ) {
sf::Time sf_time;
std::cout << "Kick Ass!\n";
Greeter greeter = Greeter( 3 );
FoldedGreeter fd_greeter = FoldedGreeter( 3 );
greeter.PrintSingleGreetings();
std::cout << "\n";
greeter.PrintMultipleGreetings();
std::cout << "\n";
fd_greeter.PrintSingleGreetings();
std::cout << "\n";
fd_greeter.PrintMultipleGreetings();
return 0;
}
/* parse the command line arguments */
bool EludeCaller::ParseOptions(int argc, char** argv) {
ostringstream intro;
intro << Greeter() << endl << "Usage:" << endl;
intro << " elude [-t \"train data file\" ] [-l \"retention model\"] " << endl;
intro << "Where input file is the file including the test data; output file" << endl;
intro << "the output will be written (ensure to have read and write access on the file)." << endl;
CommandLineParser cmd(intro.str());
// define available options
cmd.defineOption("v",
"verbose",
"Set verbosity of output: 0 = no processing info, 5 = all, default is 2.",
"level");
cmd.defineOption("t",
"train",
"Specifies the file including the training data.",
"filename");
cmd.defineOption("e",
"evaluate",
"Specifies the file including the test data.",
"filename");
cmd.defineOption("s",
"save-model",
"Specifies the file in which the model will be saved.",
"filename");
cmd.defineOption("l",
"load-model",
"Specifies a file including a SVR model to be loaded.",
"filename");
cmd.defineOption("o",
"out",
"File to save the ions.",
"filename");
cmd.defineOption("a",
"auto",
"The SVR model is selected automatically from the library.",
"",
TRUE_IF_SET);
cmd.defineOption("b",
"lib-path",
"Specifies the path to the library.",
"filename");
cmd.defineOption("d",
"append",
"Append current model to library.",
"",
TRUE_IF_SET);
cmd.defineOption("j",
"no_linear_adjust",
"The model will NOT be linearly adjusted.",
"",
TRUE_IF_SET);
cmd.defineOption("c",
"lts-coverage",
"Specifies the fraction of data used in calibrating a model via LTS. "
"This option is not valid when the -j option is used.",
"value");
cmd.defineOption("u",
"unique",
"Remove all redundant peptides from the test set",
"",
TRUE_IF_SET);
cmd.defineOption("k",
"common",
"Remove the peptides from the train that are also in the test set",
"",
TRUE_IF_SET);
cmd.defineOption("y",
"no-in-source",
"Specifies that in source fragments should be removed from the test set."
"This option can be used only when the test set includes retention time.",
"",
TRUE_IF_SET);
cmd.defineOption("i",
"save-in-source",
"The file where the detected in source fragments are stored",
"filename");
cmd.defineOption("z",
"enzyme",
"The enzyme used for digestion. Possible values {NO_ENZYME,TRYPSIN,CHYMOTRYPSIN,ELASTASE}."
"By default: TRYPSIN",
"value");
cmd.defineOption("x",
"remove-non-enzymatic",
"All non enzymatic peptides will be removed from both train and test."
"The option is available only when the sequence is given as A.XXX.B",
"",
TRUE_IF_SET);
cmd.defineOption("r",
"retention-index",
"File to save the trained retention index.",
"filename");
cmd.defineOption("f",
"context-format",
"The peptides are given in the format A.XXX.B, where XXX is the"
"peptide sequence and A and B are the previous and next amino acid"
"in the protein sequence. If the peptide is at the beginning (end)"
"of the protein, then A(B) will be -.",
"",
TRUE_IF_SET);
cmd.defineOption("g",
"test-rt",
"The test file includes rt. In this case the in source-fragments in"
"the test data can be detected and various performance measures for"
"the test data will be displayed.",
"",
TRUE_IF_SET);
cmd.defineOption("p",
"ignore-ptms",
"If there are ptms in the test set that were not present when "
"training the model, they will be ignored and the index value of "
"the unmodified amino acid is used ",
"",
TRUE_IF_SET);
cmd.defineOption("n",
"index-only",
"Calculate only the hydrophobicity index",
"",
TRUE_IF_SET);
cmd.defineOption("w",
"supress-print",
"Supress the final printing of the predictions ",
"",
TRUE_IF_SET);
cmd.parseArgs(argc, argv);
// process options
if (cmd.optionSet("v")) {
Globals::getInstance()->setVerbose(cmd.getInt("v", 0, 10));
}
if (cmd.optionSet("t")) {
train_file_ = cmd.options["t"];
}
if (cmd.optionSet("e")) {
test_file_ = cmd.options["e"];
}
if (cmd.optionSet("s")) {
save_model_file_ = cmd.options["s"];
}
if (cmd.optionSet("l")) {
load_model_file_ = cmd.options["l"];
}
if (cmd.optionSet("o")) {
output_file_ = cmd.options["o"];
}
if (cmd.optionSet("a")) {
automatic_model_sel_ = true;
}
if (cmd.optionSet("b")) {
library_path_ = cmd.options["b"];
int n = library_path_.length();
if (library_path_[n - 1] != '\\' && library_path_[n - 1] != '/') {
library_path_ += "/";
}
}
if (cmd.optionSet("d")) {
append_model_ = true;
}
if (cmd.optionSet("j")) {
linear_calibration_ = false;
}
if (cmd.optionSet("c")) {
double coverage = cmd.getDouble("c", 0.0, 1.0);
LTSRegression::setCoverage(coverage);
}
if (cmd.optionSet("u")) {
remove_duplicates_ = true;
}
if (cmd.optionSet("k")) {
remove_common_peptides_ = true;
}
if (cmd.optionSet("y")) {
remove_in_source_ = true;
}
if (cmd.optionSet("i")) {
in_source_file_ = cmd.options["i"];
}
if (cmd.optionSet("z")) {
SetEnzyme(cmd.options["z"]);
}
if (cmd.optionSet("x")) {
remove_non_enzymatic_ = true;
}
if (cmd.optionSet("r")) {
index_file_ = cmd.options["r"];
}
if (cmd.optionSet("f")) {
context_format_ = true;
}
if (cmd.optionSet("g")) {
test_includes_rt_ = true;
}
if (cmd.optionSet("p")) {
RetentionFeatures::set_ignore_ptms(true);
ignore_ptms_ = true;
}
if (cmd.optionSet("n")) {
only_hydrophobicity_index_ = true;
}
if (cmd.optionSet("w")) {
supress_print_ = true;
}
return true;
}
