halo.userinterface.cmdline
Class CmdFilterData

java.lang.Object
  extended by halo.userinterface.cmdline.CmdFilterData

public class CmdFilterData
extends java.lang.Object

Serves as interface between Data manipulation tools and command line input

Author:
Stefanie Kaufmann

Field Summary
static java.lang.String rPath
           
static java.lang.String uracilOutput
           
 
Constructor Summary
CmdFilterData()
           
 
Method Summary
static void extractFlags(java.lang.String[] input)
          Takes the input options and sets all necessary variables accordingly
static boolean isValid()
          Checks whether all needed values are set
static void main(java.lang.String[] args)
          Main method which calls all necessary methods to get from a given options array to a finished output file
static Normalization performNormalization(Data data)
          Performs normalization on a given Data object with the previously specified method
static Data prepareData(java.lang.String[] input)
          Creates a data object from the information given as options array
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

uracilOutput

public static java.lang.String uracilOutput

rPath

public static java.lang.String rPath
Constructor Detail

CmdFilterData

public CmdFilterData()
Method Detail

isValid

public static boolean isValid()
Checks whether all needed values are set

Returns:
true if every essential flag was used in the input, false otherwise

extractFlags

public static void extractFlags(java.lang.String[] input)
                         throws InvalidFlagException
Takes the input options and sets all necessary variables accordingly

Parameters:
input - The options
Throws:
InvalidFlagException

prepareData

public static Data prepareData(java.lang.String[] input)
                        throws InvalidFlagException
Creates a data object from the information given as options array

Parameters:
input - The options
Returns:
The created Data object
Throws:
InvalidFlagException

performNormalization

public static Normalization performNormalization(Data data)
Performs normalization on a given Data object with the previously specified method

Parameters:
data - The data object
Returns:
The normalization object

main

public static void main(java.lang.String[] args)
Main method which calls all necessary methods to get from a given options array to a finished output file

Parameters:
args - Parameter list