Uses of Class
de.zimek.proteinfeatures.protein.Protein

Packages that use Protein

de.zimek.proteinfeatures	Provides the main class for creating features for proteins in arff-format.
de.zimek.proteinfeatures.attributeAssigner
de.zimek.proteinfeatures.attributeAssigner.composition
de.zimek.proteinfeatures.attributeAssigner.dingAttributes
de.zimek.proteinfeatures.attributeAssigner.distribution
de.zimek.proteinfeatures.parser

Uses of Protein in de.zimek.proteinfeatures

Methods in de.zimek.proteinfeatures that return Protein

protected Protein[]

ArffFileCreator.filterClasses(Protein[] proteins) Returns only the proteins having at least minimumSupport.

Methods in de.zimek.proteinfeatures with parameters of type Protein

void	ArffFileCreator.printArffFile(Protein[] proteins, java.io.PrintStream out) Prints an arff file for the given proteins according to the current settings to the given PrintStream.
void	ArffFileCreator.setCoveredClasses(Protein[] proteins) Sets the covered classes according to the classes occuring in the given array of proteins.
protected Protein[]	ArffFileCreator.filterClasses(Protein[] proteins) Returns only the proteins having at least minimumSupport.
java.lang.String	ArffFileCreator.getDataLine(Protein protein) Returns a String providing the data-entry-line in arff-format for the given protein, at last the class according to the current set class-level in scop- or cath-notation and a newline.

Uses of Protein in de.zimek.proteinfeatures.attributeAssigner

Methods in de.zimek.proteinfeatures.attributeAssigner with parameters of type Protein

protected double[]	ProteinLength.attributes(Protein protein)
java.lang.String[]	ArffAttributeAssigner.getAttribute(Protein protein) Returns the attribute-list in arff format (comma separated).
protected double[]	AutoCorrelationFunction.attributes(Protein protein) Returns a list of attributes of length m according to the currently set AAIndex.
protected double[]	MotifAssigner.attributes(Protein protein)
protected double[]	AbstractGroupTransitionAssigner.attributes(Protein protein)
protected int	AbstractGroupAssigner.getGroupIndex(Protein protein, int index) Returns the group-index for the given index of the protein, with respect to the group.
protected abstract double[]	AbstractArffRealAttributeAssigner.attributes(Protein protein) Returns the attributes according to the actual attribute-assigner.
java.lang.String[]	AbstractArffRealAttributeAssigner.getAttribute(Protein protein)

Uses of Protein in de.zimek.proteinfeatures.attributeAssigner.composition

Methods in de.zimek.proteinfeatures.attributeAssigner.composition with parameters of type Protein

protected double[]

AbstractGroupCompositionAssigner.attributes(Protein protein)

Uses of Protein in de.zimek.proteinfeatures.attributeAssigner.dingAttributes

Methods in de.zimek.proteinfeatures.attributeAssigner.dingAttributes with parameters of type Protein

protected double[]

DingAttribute.attributes(Protein protein)

Uses of Protein in de.zimek.proteinfeatures.attributeAssigner.distribution

Methods in de.zimek.proteinfeatures.attributeAssigner.distribution with parameters of type Protein

protected double[]

AbstractGroupDistributionAssigner.attributes(Protein protein)

Uses of Protein in de.zimek.proteinfeatures.parser

Methods in de.zimek.proteinfeatures.parser that return Protein

Protein[]	AstralDBParser.parse(java.io.File in)
Protein[]	ManifoldParser.parse(java.io.File in)
Protein	ManifoldParser.parseSingleProtein(java.io.File in) Parses the proteins as given in the MANIFOLD directory.
Protein[]	McGuffinParser.parse(java.io.File in)
Protein	McGuffinParser.parseSingleProtein(java.io.File in)
Protein[]	Parser.parse(java.io.File in)

Methods in de.zimek.proteinfeatures.parser with parameters of type Protein

static void	AbstractParser.print(Protein[] proteins, java.io.PrintStream out)
static void	AbstractParser.printForMotifScan(Protein[] proteins, java.io.PrintStream out) Prints all proteins to the given PrintStream in format convenient for motifScan.