uk.ac.ebi.adfconverter.tools.converter
Class MAGEToADFConverter

java.lang.Object
  uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter

public class MAGEToADFConverter

extends java.lang.Object

Convert MAGE data file) in ADF objects This class converts a MAGE-OM object (MAGEJava) to an ADFJava object. The conversion happens only on Array design data.

Version:

1 09 September 2004

Author:

Pierre MARGUERITE

Field Summary

boolean

IsSimpleMicroArrayLayout

Constructor Summary

MAGEToADFConverter()
Default MAGEToADFConverter Constructor inits organization list

MAGEToADFConverter(java.util.Properties prop)
MAGEToADFConverter Constructor inits the converter with a list of properties

Method Summary

void	convertHeader(PhysicalArrayDesign mageobj) Retrieves a ADF header data from a Physical ArrayDesign Add data to the current ADFJava object corresponding to the mage data.
ADFJava	convertToADF(java.io.File magefile) Converts data from a MAGE-ML file to ADFJava.
ADFCompositeSequence	createCompositeSequence(ADFReporter reporter) In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

IsSimpleMicroArrayLayout

public boolean IsSimpleMicroArrayLayout

Constructor Detail

MAGEToADFConverter

public MAGEToADFConverter()

Default MAGEToADFConverter Constructor inits organization list

MAGEToADFConverter

public MAGEToADFConverter(java.util.Properties prop)

MAGEToADFConverter Constructor inits the converter with a list of properties

Parameters:

prop - configuration properties of the converter

Method Detail

convertHeader

public void convertHeader(PhysicalArrayDesign mageobj)
                   throws IncorrectFileStructure

Retrieves a ADF header data from a Physical ArrayDesign Add data to the current ADFJava object corresponding to the mage data. Header items are created adn data are added to the current headerTable.

Parameters:

mageobj - the Physical Array Design to retrieve data from.

Throws:

IncorrectFileStructure - if the file describing the ADF structure is incorrect

convertToADF

public ADFJava convertToADF(java.io.File magefile)
                     throws java.io.IOException,
                            IncorrectFileStructure

Converts data from a MAGE-ML file to ADFJava.

Parameters:

magefile - the MAGE-ML file to convert

Returns:

the ADFJava object corresponding to MAGE-ML data as ADF, if MAGE-ML data are correct or no datum is missing. null, otherwise

Throws:

java.io.IOException - if an error occurs during access to the MAGE-ML file

IncorrectFileStructure - if the structure file used to convert in ADF is incorrect

createCompositeSequence

public ADFCompositeSequence createCompositeSequence(ADFReporter reporter)
                                             throws IncorrectFileStructure

In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence

Parameters:

reporter - the ADFreporter which is associated the created compositesequence

Returns:

the ADF Composite Sequence corresponding to the MAGE CompositeSequence object.

Throws:

IncorrectFileStructure - if the ADF structure file is incorrect.