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tweaked tests to support dashes in arg names
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@ -40,14 +40,14 @@ int main(int argc, char **argv)
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false, -10, "negative int");
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false, -10, "negative int");
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cmd.add( gapCreate );
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cmd.add( gapCreate );
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ValueArg<int> gapExtend("g","gapExtend",
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ValueArg<int> gapExtend("g","gap-Extend",
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"The cost for each extension of a gap", false, -2, "negative int");
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"The cost for each extension of a gap", false, -2, "negative int");
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cmd.add( gapExtend );
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cmd.add( gapExtend );
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SwitchArg dna("d","isDna","The input sequences are DNA", false);
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SwitchArg dna("d","isDna","The input sequences are DNA", false);
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cmd.add( dna );
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cmd.add( dna );
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ValueArg<string> scoringMatrixName("s","scoringMatrix",
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ValueArg<string> scoringMatrixName("s","scoring--Matrix",
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"Scoring Matrix name", false,"BLOSUM50","name string");
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"Scoring Matrix name", false,"BLOSUM50","name string");
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cmd.add( scoringMatrixName );
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cmd.add( scoringMatrixName );
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@ -453,7 +453,7 @@ inline Arg::Arg(const std::string& flag,
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if ( ( _name.substr( 0, Arg::flagStartString().length() ) == Arg::flagStartString() ) ||
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if ( ( _name.substr( 0, Arg::flagStartString().length() ) == Arg::flagStartString() ) ||
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( _name.substr( 0, Arg::nameStartString().length() ) == Arg::nameStartString() ) ||
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( _name.substr( 0, Arg::nameStartString().length() ) == Arg::nameStartString() ) ||
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( _name.find( " ", 0 ) != std::string::npos ) )
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( _name.find( " ", 0 ) != std::string::npos ) )
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throw(SpecificationException("Argument name cannot contain either '" +
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throw(SpecificationException("Argument name begin with either '" +
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Arg::flagStartString() + "' or '" +
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Arg::flagStartString() + "' or '" +
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Arg::nameStartString() + "' or space.",
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Arg::nameStartString() + "' or space.",
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toString() ) );
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toString() ) );
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@ -29,13 +29,13 @@ Where:
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-x <filename>, --filename1 <filename>
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-x <filename>, --filename1 <filename>
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Sequence 1 filename (FASTA format)
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Sequence 1 filename (FASTA format)
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-s <name string>, --scoringMatrix <name string>
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-s <name string>, --scoring--Matrix <name string>
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Scoring Matrix name
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Scoring Matrix name
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-d, --isDna
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-d, --isDna
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The input sequences are DNA
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The input sequences are DNA
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-g <negative int>, --gapExtend <negative int>
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-g <negative int>, --gap-Extend <negative int>
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The cost for each extension of a gap
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The cost for each extension of a gap
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-f <negative int>, --gapCreate <negative int>
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-f <negative int>, --gapCreate <negative int>
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