uk.ac.ebi.adfconverter.data.adf
Class ADFJava

java.lang.Object
  uk.ac.ebi.adfconverter.data.adf.ADFJava

public class ADFJava

extends java.lang.Object

Root Object representing an ADF file/data set.s Composed of an header part, several features, reporters and CompositeSequences(optional) data The internal ADF representation is based on the ADF file structure. THe ADF files can be in tabular text format or Microsoft Excel Workbook format ADF files (spreadsheet):

• Header: containing metadata about the array
• FeatureReporter: with Feature and Reporter Data
• CompositeSequence (optional): with CompositeSequence data

Since:

8 sept. 2004

Version:

1

Author:

Pierre MARGUERITE

Field Summary

java.lang.String	application application representation the microarray application, the experiment is used for.
static java.lang.String	compositeFileExtension compositeFileExtension: default CompositeSequence text file extension
static java.lang.String	headerFileExtension adfFile: default header text file extension
static java.lang.String	reporterFileExtension reporterFileExtension: default feature reporter text file extension
static java.lang.String	workbookFileExtension workbookFileExtension: default Microsoft Excel Workbook file extension

Constructor Summary

ADFJava()
Default ADFJava Constructor Inits associated tables

ADFJava(CorrectableDataTable header)
testing purpose

ADFJava(CorrectableDataTable header, CorrectableDataTable features, CorrectableDataTable reporters, CorrectableDataTable CompositeSequences, CorrectableDataTable bioSequences, java.util.Hashtable ReporterGroupList, java.util.Hashtable CompositeSequenceList)
ADFJava class Constructor with associated elements (header, feature, reporter, CompositeSequence biosequence, and group lists.

Method Summary

void	clear() Clear the object
java.io.File	getADFFile() retrieves the ADF associated to the object
java.lang.String	getApplication() retrieves the application of the microarray layout
static java.util.ArrayList	getAuthorisedADFExtension() Retrieves the list of possible file extensions for ADF
CorrectableDataTable	getBiosequencesTable() retrieves the ADF biosequences table
java.util.Hashtable	getCompositeSequenceList() retrieves the ADF Composite Sequence List
CorrectableDataTable	getCompositeSequenceTable() retrieves the ADF compositeSequences table
CorrectableDataTable	getFeatureTable() retrieves the ADF feature table
CorrectableDataTable	getHeaderTable() retrieves the ADF header table
java.util.Hashtable	getReporterGroupList() retrieves the ADF Reporter Group List
CorrectableDataTable	getReporterTable() retrieves the ADF reporter table * @return the associated ADF reporter table
CorrectableDataTable	getTable(java.lang.String tableName) Retrieves a table following a given name

Methods inherited from class java.lang.Object

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

Field Detail

application

public java.lang.String application

application representation the microarray application, the experiment is used for.

compositeFileExtension

public static final java.lang.String compositeFileExtension

compositeFileExtension: default CompositeSequence text file extension

See Also:

Constant Field Values

headerFileExtension

public static final java.lang.String headerFileExtension

adfFile: default header text file extension

See Also:

Constant Field Values

reporterFileExtension

public static final java.lang.String reporterFileExtension

reporterFileExtension: default feature reporter text file extension

See Also:

Constant Field Values

workbookFileExtension

public static final java.lang.String workbookFileExtension

workbookFileExtension: default Microsoft Excel Workbook file extension

See Also:

Constant Field Values

Constructor Detail

ADFJava

public ADFJava()

Default ADFJava Constructor Inits associated tables

ADFJava

public ADFJava(CorrectableDataTable header)

testing purpose

Parameters:

header -

ADFJava

public ADFJava(CorrectableDataTable header,
               CorrectableDataTable features,
               CorrectableDataTable reporters,
               CorrectableDataTable CompositeSequences,
               CorrectableDataTable bioSequences,
               java.util.Hashtable ReporterGroupList,
               java.util.Hashtable CompositeSequenceList)

ADFJava class Constructor with associated elements (header, feature, reporter, CompositeSequence biosequence, and group lists.

Parameters:

header - the ADF Header table

features - the ADF Feature table

reporters - THe ADF reporter table

bioSequences - The biosequence table associated to reporters and CompositeSequences

CompositeSequences - The CompositeSequence table

ReporterGroupList - The Reporter group list

CompositeSequenceList - The CompositeSequence group listS

Method Detail

clear

public void clear()

Clear the object

getADFFile

public java.io.File getADFFile()

retrieves the ADF associated to the object

Returns:

a File object

getApplication

public java.lang.String getApplication()

retrieves the application of the microarray layout

Returns:

the application as string

getAuthorisedADFExtension

public static java.util.ArrayList getAuthorisedADFExtension()

Retrieves the list of possible file extensions for ADF

Returns:

an ArrayList object containing the extensions as String (without ".")

getBiosequencesTable

public CorrectableDataTable getBiosequencesTable()

retrieves the ADF biosequences table

Returns:

the associated BioSequence table

getCompositeSequenceList

public java.util.Hashtable getCompositeSequenceList()

retrieves the ADF Composite Sequence List

Returns:

the list of associated CompositeSequence groups

getCompositeSequenceTable

public CorrectableDataTable getCompositeSequenceTable()

retrieves the ADF compositeSequences table

Returns:

the associated ADF CompositeSequence table

getFeatureTable

public CorrectableDataTable getFeatureTable()

retrieves the ADF feature table

Returns:

the associated ADF Feature table

getHeaderTable

public CorrectableDataTable getHeaderTable()

retrieves the ADF header table

Returns:

the associated ADF header table

getReporterGroupList

public java.util.Hashtable getReporterGroupList()

retrieves the ADF Reporter Group List

Returns:

the list of associated Reporter groups

getReporterTable

public CorrectableDataTable getReporterTable()

retrieves the ADF reporter table * @return the associated ADF reporter table

getTable

public CorrectableDataTable getTable(java.lang.String tableName)

Retrieves a table following a given name

Parameters:

tableName - the name of the table to retrieve

Returns:

the CorrectableDataTable object called by the given name, if found. null otherwise