diff --git a/examples/test7.cpp b/examples/test7.cpp index 71f1610..89e788f 100644 --- a/examples/test7.cpp +++ b/examples/test7.cpp @@ -2,6 +2,7 @@ #include using namespace TCLAP; +using namespace std; int main(int argc, char** argv) { @@ -30,6 +31,43 @@ int main(int argc, char** argv) UnlabeledMultiArg intArg("times","Number of times to print",iallowed); cmd.add( intArg ); + // Ignore the names and comments! These args mean nothing (to this + // program) and are here solely to take up space. + ValueArg gapCreate("f","gapCreate", "The cost of creating a gap", + false, -10, "negative int"); + cmd.add( gapCreate ); + + ValueArg gapExtend("g","gapExtend", + "The cost for each extension of a gap", false, -2, "negative int"); + cmd.add( gapExtend ); + + SwitchArg dna("d","isDna","The input sequences are DNA", false); + cmd.add( dna ); + + ValueArg scoringMatrixName("s","scoringMatrix", + "Scoring Matrix name", false,"BLOSUM50","name string"); + cmd.add( scoringMatrixName ); + + ValueArg seq1Filename ("f","filename1", + "Sequence 1 filename (FASTA format)", false,"","filename"); + cmd.add( seq1Filename ); + + ValueArg seq2Filename ("F","filename2", + "Sequence 2 filename (FASTA format)", false,"","filename"); + cmd.add( seq2Filename ); + + ValueArg lowerBound("b","lowerBound", "lower percentage bound", + false,1.0,"float lte 1"); + cmd.add( lowerBound ); + + ValueArg upperBound("u","upperBound", "upper percentage bound", + false,1.0,"float lte 1"); + cmd.add( upperBound ); + + ValueArg limit("l","limit","Max number of alignments allowed", + false, 1000,"int"); + cmd.add( limit ); + // Parse the args. cmd.parse( argc, argv );