smueller
Class SymbolicRepresentationAlignment

java.lang.Object
  cross.commands.fragments.AFragmentCommand
      smueller.SymbolicRepresentationAlignment

All Implemented Interfaces:

cross.commands.fragments.IFragmentCommand, cross.commands.ICommand<cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>,cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>>, cross.datastructures.workflow.IWorkflowElement, cross.event.IEventSource<cross.datastructures.workflow.IWorkflowResult>, cross.IConfigurable, cross.io.xml.IXMLSerializable, Serializable

public class SymbolicRepresentationAlignment
extends cross.commands.fragments.AFragmentCommand

Author:

Soeren Mueller, smueller@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

SymbolicRepresentationAlignment()

Method Summary

cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>	apply(cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> t)
void	configure(org.apache.commons.configuration.Configuration cfg)
static OneAffineAlignment	getAl()
static int	getAlphabetgr()
static BreakPoints	getBpois()
String	getDescription()
static DistanceMatrix	getDistmatrix()
static int	getFenstergr()
static double	getGapinit()
static SortedJavArrays	getSorti()
static Standardizer	getStand()
cross.datastructures.workflow.WorkflowSlot	getWorkflowSlot()
static void	main(String[] args)
void	saveToCSV(cross.datastructures.fragments.IFileFragment pwdist, ArrayDouble.D2 distances, ArrayChar.D2 names)

Methods inherited from class cross.commands.fragments.AFragmentCommand

addListener, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResults, addWorkflowResults, appendXML, canEqual, createBlockingCompletionService, createCompletionService, createNonBlockingCompletionService, createWorkFragment, createWorkFragments, equals, fireEvent, getProgress, getWorkflow, hashCode, initProgress, initSubCommand, mapToInput, postProcess, removeListener, setProgress, setWorkflow, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SymbolicRepresentationAlignment

public SymbolicRepresentationAlignment()

Method Detail

getAl

public static OneAffineAlignment getAl()

getAlphabetgr

public static int getAlphabetgr()

getBpois

public static BreakPoints getBpois()

getDistmatrix

public static DistanceMatrix getDistmatrix()

getFenstergr

public static int getFenstergr()

getGapinit

public static double getGapinit()

getSorti

public static SortedJavArrays getSorti()

getStand

public static Standardizer getStand()

main

public static void main(String[] args)

apply

public cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> apply(cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> t)

configure

public void configure(org.apache.commons.configuration.Configuration cfg)

Specified by:

configure in interface cross.IConfigurable

Overrides:

configure in class cross.commands.fragments.AFragmentCommand

getDescription

public String getDescription()

Specified by:

getDescription in class cross.commands.fragments.AFragmentCommand

getWorkflowSlot

public cross.datastructures.workflow.WorkflowSlot getWorkflowSlot()

saveToCSV

public void saveToCSV(cross.datastructures.fragments.IFileFragment pwdist,
                      ArrayDouble.D2 distances,
                      ArrayChar.D2 names)