/// <summary>
/// constructor taking a tokeniser to use
/// </summary>
/// <param name="tokeniserToUse">the tokeniser to use should a different tokeniser be required</param>
public MongeElkan(ITokeniser tokeniserToUse)
{
tokeniser = tokeniserToUse;
internalStringMetric = new SmithWatermanGotoh();
}
public void SetUp() {
LoadData();
# region SmithWaterman classes
// 0.5F and SubCostRange1ToMinus2 are the values used for the default constructor
mySmithWatermanDefault = new SmithWaterman();
mySmithWatermanCost = new SmithWaterman(0.5D);
mySmithWatermanCostFunction = new SmithWaterman(new SubCostRange1ToMinus2());
mySmithWatermanCostAndCostFunction = new SmithWaterman(0.5D, new SubCostRange1ToMinus2());
#endregion
// we also need to check running a different set of tests
#region SmithWatermanGotoh classes
mySmithWatermanGotohDefault = new SmithWatermanGotoh();
mySmithWatermanGotohGapCostFunction = new SmithWatermanGotoh(new AffineGapRange5To0Multiplier1());
mySmithWatermanGotohCostFunction = new SmithWatermanGotoh(new SubCostRange5ToMinus3());
mySmithWatermanGotohGapCostAndCostFunctions =
new SmithWatermanGotoh(new AffineGapRange5To0Multiplier1(), new SubCostRange5ToMinus3());
#endregion
#region SmithWatermanGotohWindowedAffine classes
mySWGWADefault = new SmithWatermanGotohWindowedAffine();
mySWGWAWindowSize = new SmithWatermanGotohWindowedAffine(100);
mySWGWAGapCostFunction = new SmithWatermanGotohWindowedAffine(new AffineGapRange5To0Multiplier1());
mySWGWAGapCostFunctionAndWindowSize = new SmithWatermanGotohWindowedAffine(new AffineGapRange5To0Multiplier1(), 100);
mySWGWAGapCostAndCostFunctions =
new SmithWatermanGotohWindowedAffine(new AffineGapRange5To0Multiplier1(), new SubCostRange5ToMinus3());
mySWGWAGapCostAndCostFunctionsAndWindowSize =
new SmithWatermanGotohWindowedAffine(new AffineGapRange5To0Multiplier1(), new SubCostRange5ToMinus3(), 100);
mySWGWACostFunction = new SmithWatermanGotohWindowedAffine(new SubCostRange5ToMinus3());
mySWGWACostFunctionAndWindowSize = new SmithWatermanGotohWindowedAffine(new SubCostRange5ToMinus3(), 100);
#endregion
}
/// <summary>
/// constructor taking a tokeniser to use
/// </summary>
/// <param name="tokeniserToUse">the tokeniser to use should a different tokeniser be required</param>
public MongeElkan(ITokeniser tokeniserToUse) {
tokeniser = tokeniserToUse;
internalStringMetric = new SmithWatermanGotoh();
}