Examples with ArgumentDefinition net.sourceforge.ondex.args.ArgumentDefinition used on opensource projects

Example 1 with ArgumentDefinition

use of net.sourceforge.ondex.args.ArgumentDefinition in project knetbuilder by Rothamsted.

the class Parser method getArgumentDefinitions.

public ArgumentDefinition<?>[] getArgumentDefinitions() {
    StringArgumentDefinition taxId = new StringArgumentDefinition(ArgumentNames.TAXID_ARG, ArgumentNames.TAXID_ARG_DESC, false, null, true);
    FileArgumentDefinition inputDir = new FileArgumentDefinition(FileArgumentDefinition.INPUT_DIR, "directory with generif files", true, true, true, false);
    return new ArgumentDefinition<?>[] { taxId, inputDir };
}

Example 2 with ArgumentDefinition

use of net.sourceforge.ondex.args.ArgumentDefinition in project knetbuilder by Rothamsted.

the class Parser method getArgumentDefinitions.

@Override
public ArgumentDefinition<?>[] getArgumentDefinitions() {
    FileArgumentDefinition arg1 = new FileArgumentDefinition("firstInputFile", "The first OXL input file.", true, true, false);
    FileArgumentDefinition arg2 = new FileArgumentDefinition("secondInputFile", "The second OXL input file.", true, true, false);
    return new ArgumentDefinition<?>[] { arg1, arg2 };
}

Example 3 with ArgumentDefinition

use of net.sourceforge.ondex.args.ArgumentDefinition in project knetbuilder by Rothamsted.

the class NT2ProteinBLASTxAlignmentMapping method getArgumentDefinitions.

@Override
public ArgumentDefinition<?>[] getArgumentDefinitions() {
    Set<ArgumentDefinition<?>> extendedDefinition = new HashSet<ArgumentDefinition<?>>();
    extendedDefinition.add(new FileArgumentDefinition(PROGRAM_DIR_ARG, PROGRAM_DIR_DESC, true, true, true));
    return extendedDefinition.toArray(new ArgumentDefinition<?>[extendedDefinition.size()]);
}

Example 4 with ArgumentDefinition

use of net.sourceforge.ondex.args.ArgumentDefinition in project knetbuilder by Rothamsted.

the class Mapping method getArgumentDefinitions.

public ArgumentDefinition<?>[] getArgumentDefinitions() {
    Set<ArgumentDefinition<?>> extendedDefinition = new HashSet<ArgumentDefinition<?>>();
    // Add blast program params
    extendedDefinition.add(new RangeArgumentDefinition<Float>(E_VALUE_ARG, E_VALUE_DESC, true, 0.000001F, 0f, Float.MAX_VALUE, Float.class));
    extendedDefinition.add(new RangeArgumentDefinition<Integer>(BITSCORE_ARG, BITSCORE_DESC, true, 200, 0, Integer.MAX_VALUE, Integer.class));
    extendedDefinition.add(new StringArgumentDefinition(TAX_ID_ARG, TAX_ID_ARG_DESC, false, null, true));
    extendedDefinition.add(new SequenceTypeArgumentDefinition(SEQ_TYPE_ARG, true, ATT_AMINO_ACID_SEQ));
    extendedDefinition.add(new FileArgumentDefinition(PROGRAM_DIR_ARG, PROGRAM_DIR_DESC, true, true, true));
    extendedDefinition.add(new SequenceAlignmentProgramArgumentDefinition(SEQ_ALIGNMENT_PROG_ARG, true, SequenceAlignmentProgramArgumentDefinition.DECYPHER));
    extendedDefinition.add(new RangeArgumentDefinition<Float>(OVERLAP_ARG, OVERLAP_DESC, false, 0.25F, 0F, Float.MAX_VALUE, Float.class));
    extendedDefinition.add(new RangeArgumentDefinition<Integer>(CUTOFF_ARG, CUTOFF_DESC, false, 5, 0, Integer.MAX_VALUE, Integer.class));
    return extendedDefinition.toArray(new ArgumentDefinition<?>[extendedDefinition.size()]);
}

Example 5 with ArgumentDefinition

use of net.sourceforge.ondex.args.ArgumentDefinition in project knetbuilder by Rothamsted.

the class Transformer method getArgumentDefinitions.

@Override
public ArgumentDefinition<?>[] getArgumentDefinitions() {
    StringMappingPairArgumentDefinition conceptAnToRegex = new StringMappingPairArgumentDefinition(anConceptArg, anConceptDesc, false, null, true);
    StringArgumentDefinition conceptAnSquareRoot = new StringArgumentDefinition(squareRootConceptArg, squareRootConceptDesc, false, null, true);
    StringArgumentDefinition conceptAnCubeRoot = new StringArgumentDefinition(cubeRootConceptArg, cubeRootConceptDesc, false, null, true);
    StringMappingPairArgumentDefinition relationAnToRegex = new StringMappingPairArgumentDefinition(anRelationArg, anRelationDesc, false, null, true);
    StringArgumentDefinition relationAnSquareRoot = new StringArgumentDefinition(squareRootRelationArg, squareRootRelationDesc, false, null, true);
    StringArgumentDefinition relationAnCubeRoot = new StringArgumentDefinition(cubeRootRelationArg, cubeRootRelationDesc, false, null, true);
    return new ArgumentDefinition<?>[] { conceptAnToRegex, conceptAnSquareRoot, relationAnToRegex, relationAnSquareRoot, conceptAnCubeRoot, relationAnCubeRoot };
}