///////////////////////////////////////////////////////////////////////////////
// Parse the command line arguments.
///////////////////////////////////////////////////////////////////////////////
bool bifold::parse( int argc, char** argv ) {
// Initialize arrays of flags without and with parameters.
const char* flagsNoParams[] = {
"-d", "-D", "--DNA",
"-i", "-I", "--intramolecular",
};
const char* flagsParams[] = {
"-l", "-L", "--loop",
"-m", "-M", "--maximum",
"-p", "-P", "--percent",
"-s", "-S", "--save",
"-t", "-T", "--temperature",
"-w", "-W", "--window"
};
// Initialize usage string.
string usageString =
"USAGE: bifold <seq file 1> <seq file 2> <ct file> [options]";
// Initialize required parameters string.
string seq1Help = "\
<seq file 1>\n\
The name of a file containing a first input sequence.\
";
string seq2Help = "\
<seq file 2>\n\
The name of a file containing a second input sequence.\
";
string ctHelp = "\
<ct file>\n\
The name of a CT file to which output will be written.\
";
string paramsString =
seq1Help + "\n\n" + seq2Help + "\n\n" + ctHelp;
// Initialize flags without parameters string.
string dnaHelp = "\
-d, -D, --DNA\n\
Specify that the sequence is DNA, and DNA parameters are to be used.\n\
Default is to use RNA parameters.\
";
string helpLabel = "\
-h, -H, --help\n\
Display the usage details message.\
";
string intramolecularHelp = "\
-i, -I, --intramolecular\n\
Forbid intramolecular pairs (pairs within the same strand).\n\
Default is to allow intramolecular pairs.\
";
string flagsNoParamsString =
dnaHelp + "\n\n" + helpLabel + "\n\n" + intramolecularHelp;
// Initialize the flags with parameters string.
string loopHelp = "\
-l, -L, --loop\n\
Specify a maximum internal/bulge loop size.\n\
Default is 30 unpaired nucleotides.\
";
string maxStructuresHelp = "\
-m, -M, --maximum\n\
Specify a maximum number of structures.\n\
Default is 20 structures.\
";
string percentHelp = "\
-p, -P, --percent\n\
Specify a maximum percent energy difference.\n\
Default is 10 percent (specified as 10, not 0.1).\
";
string saveHelp = "\
-s, -S, --save\n\
Specify the name of a save file, needed for dotplots and refolding.\n\
Default is not to generate a save file.\
";
string tempHelp = "\
-t, -T, --temperature\n\
Specify the temperature at which calculation takes place in Kelvin.\n\
Default is 310.15 K, which is 37 degrees C.\
";
string windowHelp = "\
-w, -W, --window\n\
Specify a window size.\n\
Default is 0 nucleotides.\
";
string flagsParamsString =
loopHelp + "\n\n" + maxStructuresHelp + "\n\n" + percentHelp + "\n\n" +
saveHelp + "\n\n" + tempHelp + "\n\n" + windowHelp;
// Initialize parser and check the command line.
ParseCommandLine* parser = new ParseCommandLine( argc, argv, 3,
6, flagsNoParams,
18, flagsParams );
parser->setUsageStrings( usageString.c_str(), paramsString.c_str(),
flagsNoParamsString.c_str(),
flagsParamsString.c_str() );
bool noError = parser->checkLine();
// If command line structure is OK, proceed with argument retrieval, parsing.
if( noError ) {
// Get required parameters.
seqFile1 = parser->getParameter( 1 );
seqFile2 = parser->getParameter( 2 );
ctFile = parser->getParameter( 3 );
// Set non-parameterized flag(s).
isRNA = !parser->containsInGroup( "-d -D --DNA" );
intramolecular = !parser->containsInGroup( "-i -I --intramolecular" );
// Set parameterized options
// If one of these options is not found on the command line, the action to
// set that option is skipped.
// If one throws an error, an error message is shown and parsing continues,
// so all errors are shown if there are more than one.
bool flagSet = true;
// Maximum loop size option
flagSet = parser->setOption( maxLoop, "-l -L --loop",
"Invalid maximum loop size given." );
if( flagSet == false ) { noError = false; }
// Maximum number of structures option
flagSet = parser->setOption( maxStructures, "-m -M --maximum",
"Invalid number of structures given." );
if( flagSet == false ) { noError = false; }
// Percent difference option
flagSet = parser->setOption( percent, "-p -P --percent",
"Invalid percent difference given.", ">= 0" );
if( flagSet == false ) { noError = false; }
// Save file option
const char* saveString = "";
flagSet = parser->setOption( saveString, "-s -S --save",
"Error creating save file name.", false );
if( flagSet == false ) { noError = false; }
saveFile = saveString;
// Temperature option
flagSet = parser->setOption( temperature, "-t -T --temperature",
"Invalid temperature given.", ">= 0" );
if( flagSet == false ) { noError = false; }
// Window size option
flagSet = parser->setOption( windowSize, "-w -W --window",
"Invalid window size.", ">= 0" );
if( flagSet == false ) { noError = false; }
}
// Delete the parser and return the error state.
delete parser;
return noError;
}
///////////////////////////////////////////////////////////////////////////////
// Parse the command line arguments.
///////////////////////////////////////////////////////////////////////////////
bool AllSub::parse( int argc, char** argv ) {
// Initialize arrays of flags without and with parameters.
const char* flagsNoParams[] = {
"-d", "-D", "--DNA"
};
const char* flagsParams[] = {
"-a", "-A", "--absolute",
"-c", "-C", "--constraint",
"-p", "-P", "--percent",
"-t", "-T", "--temperature"
};
// Initialize usage string.
string usageString =
"USAGE: AllSub <seq file> <ct file> [options]";
// Initialize required parameters string.
string seqHelp = "\
<seq file>\n\
The name of a file containing an input sequence.\
";
string ctHelp = "\
<ct file>\n\
The name of a CT file to which output will be written.\
";
string paramsString =
seqHelp + "\n\n" + ctHelp;
// Initialize flags without parameters string.
string dnaHelp = "\
-d, -D, --DNA\n\
Specify that the sequence is DNA, and DNA parameters are to be used.\n\
Default is to use RNA parameters.\
";
string helpLabel = "\
-h, -H, --help\n\
Display the usage details message.\
";
string flagsNoParamsString =
dnaHelp + "\n\n" + helpLabel;
// Initialize flags with parameters string.
string absoluteHelp = "\
-a, -A, --absolute\n\
Specify a maximum absolute energy difference.\n\
Default is determined by the length of the sequence.\
";
string constraintHelp = "\
-c, -C, --constraint\n\
Specify a constraints file to be applied.\n\
Default is to have no constraints applied.\
";
string percentHelp = "\
-p, -P, --percent\n\
Specify a maximum percent energy difference.\n\
Default is determined by the length of the sequence.\
";
string tempHelp = "\
-t, -T, --temperature\n\
Specify the temperature at which calculation takes place in Kelvin.\n\
Default is 310.15 K, which is 37 degrees C.\
";
string flagsParamsString =
absoluteHelp + "\n\n" + constraintHelp + "\n\n" + percentHelp + "\n\n" +
tempHelp;
// Initialize parser and check the command line.
ParseCommandLine* parser = new ParseCommandLine( argc, argv, 2,
3, flagsNoParams,
12, flagsParams );
parser->setUsageStrings( usageString.c_str(), paramsString.c_str(),
flagsNoParamsString.c_str(),
flagsParamsString.c_str() );
bool noError = parser->checkLine();
// If command line structure is OK, proceed with argument retrieval, parsing.
if( noError ) {
// Get required parameters.
seqFile = parser->getParameter( 1 );
ctFile = parser->getParameter( 2 );
// Set non-parameterized flag(s).
isRNA = !parser->containsInGroup( "-d -D --DNA" );
// Set parameterized options
// If one of these options is not found on the command line, the action to
// set that option is skipped.
// If one throws an error, an error message is shown and parsing continues,
// so all errors are shown if there are more than one.
bool flagSet = true;
// Absolute energy difference option
flagSet =
parser->setOption( absolute, "-a -A --absolute",
"Invalid absolute energy difference given.", ">= 0" );
if( flagSet == false ) { noError = false; }
// Constraint file option
const char* constraintString = "";
flagSet = parser->setOption( constraintString, "-c -C --constraint",
"Constraint file not found.", true );
constraintFile = constraintString;
if( flagSet == false ) { noError = false; }
// Percent difference option
flagSet = parser->setOption( percent, "-p -P --percent",
"Invalid percent difference given.", ">= 0" );
if( flagSet == false ) { noError = false; }
// Temperature option
flagSet = parser->setOption( temperature, "-t -T --temperature",
"Invalid temperature given.", ">= 0" );
if( flagSet == false ) { noError = false; }
}
// Delete the parser and return the error state.
delete parser;
return noError;
}