uk.ac.ebi.adfconverter.common.tools.file.reader
Class DataFileReader

java.lang.Object
  uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf
      uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader

public class DataFileReader

extends DataFileReaderIntf

This class converts data from a file in a DataTable in Java, for manipulation

Version:

1

Author:

Pierre MARGUERITE

See Also:

DataTable

Constructor Summary

DataFileReader(java.io.File aFile)
constructor for converting a data file in data table in memory

DataFileReader(java.io.File aFile, boolean hasHeader)
constructor for converting a data file in data table in memory

Method Summary

void	close() Closes file access/ reading
DataTable	getData() Retrieves data from file
DataTable	getData(int fileFormat) Retrieves data from file in a given file format, specifying file format type
DataTable	getData(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int orientation, int type) Retrieves data from file with a specific character encoding
DataRow	getHorizontalDataRow() Retrieves the next datarow in the horizontal datable.
DataTable	getHorizontalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape) Retrieves data from file with a specific character encoding in a vertical orientation of data
DataTable	getHorizontalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Retrieves data from file with a specific character encoding in a horizontal orientation of data
DataTableHeader	getHorizontalHeader() Retrieves the header of a horizontal data table contained in a file
DataTable	getVerticalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape) Retrieves data from file with a specific character encoding in a vertical orientation of data
DataTable	getVerticalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Retrieves data from file with a specific character encoding in a vertical orientation of data
DataTable	horizontalToVerticalTable(DataTable table) ConvertTable from table obtained from a file in the correct data orientation
boolean	open(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type

Methods inherited from class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf

containsHeader, containsHeader, getFile, setSheet, setSheet

Methods inherited from class java.lang.Object

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

Constructor Detail

DataFileReader

public DataFileReader(java.io.File aFile)

constructor for converting a data file in data table in memory

Parameters:

aFile - a file object of a file containing data

DataFileReader

public DataFileReader(java.io.File aFile,
                      boolean hasHeader)

constructor for converting a data file in data table in memory

Parameters:

aFile - a file object of a file containing data

hasHeader - a boolean indicating if the first row is considered as the table header

Method Detail

close

public void close()

Closes file access/ reading

Specified by:

close in class DataFileReaderIntf

getData

public DataTable getData()
                  throws java.io.IOException,
                         IncorrectFile,
                         IncorrectDataFile

Retrieves data from file

Specified by:

getData in class DataFileReaderIntf

Returns:

the data contained in the data file as DataTable

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type, incorrect file structure)

getData

public DataTable getData(int fileFormat)
                  throws java.io.IOException,
                         IncorrectFile,
                         IncorrectDataFile

Retrieves data from file in a given file format, specifying file format type

Specified by:

getData in class DataFileReaderIntf

Parameters:

fileFormat - the file format

Returns:

the data contained in the data file as DataTable

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type, incorrect file structure)

getData

public DataTable getData(java.lang.String enc,
                         java.lang.String delimiter,
                         java.lang.String escape,
                         int orientation,
                         int type)
                  throws java.io.IOException,
                         IncorrectFile,
                         IncorrectDataFile

Retrieves data from file with a specific character encoding

Specified by:

getData in class DataFileReaderIntf

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

the retrieved data table from the data file

Throws:

java.io.IOException

IncorrectFile

IncorrectDataFile

See Also:

authorizes file format
Description of Data Content Typical Filename Extensions MIME type/subtype Text and Text-Related Types HTML text data (RFC 1866) html htm text/html Plain text: documents; program listings txt c c++ pl cc h text/plain Excel spreadsheet (Microsoft) xls, xlc, xll, xlm, xlw application/vnd.ms-excel application/x-msexcel application/ms-excel application/msexcel application/x-excel *

getHorizontalDataRow

public DataRow getHorizontalDataRow()
                             throws java.io.IOException,
                                    IncorrectDataFile

Retrieves the next datarow in the horizontal datable. Must be call after calling once open method

Specified by:

getHorizontalDataRow in class DataFileReaderIntf

Returns:

the next retrieved DataRow, if existing. null, otherwise.

Throws:

java.io.IOException

IncorrectDataFile

getHorizontalDataTable

public DataTable getHorizontalDataTable(java.lang.String enc,
                                        java.lang.String delimiter,
                                        java.lang.String escape)
                                 throws java.io.IOException,
                                        IncorrectFile,
                                        IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Specified by:

getHorizontalDataTable in class DataFileReaderIntf

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

getHorizontalDataTable

public DataTable getHorizontalDataTable(java.lang.String enc,
                                        java.lang.String delimiter,
                                        java.lang.String escape,
                                        int type)
                                 throws java.io.IOException,
                                        IncorrectFile,
                                        IncorrectDataFile

Retrieves data from file with a specific character encoding in a horizontal orientation of data

Specified by:

getHorizontalDataTable in class DataFileReaderIntf

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

See Also:

DataTable

getHorizontalHeader

public DataTableHeader getHorizontalHeader()
                                    throws java.io.IOException,
                                           IncorrectDataFile

Retrieves the header of a horizontal data table contained in a file

Specified by:

getHorizontalHeader in class DataFileReaderIntf

Returns:

the retrieved DataTableHeader, if the table contains an header. null, otherwise.

Throws:

java.io.IOException

IncorrectDataFile

getVerticalDataTable

public DataTable getVerticalDataTable(java.lang.String enc,
                                      java.lang.String delimiter,
                                      java.lang.String escape)
                               throws java.io.IOException,
                                      IncorrectFile,
                                      IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Specified by:

getVerticalDataTable in class DataFileReaderIntf

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

getVerticalDataTable

public DataTable getVerticalDataTable(java.lang.String enc,
                                      java.lang.String delimiter,
                                      java.lang.String escape,
                                      int type)
                               throws java.io.IOException,
                                      IncorrectFile,
                                      IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Specified by:

getVerticalDataTable in class DataFileReaderIntf

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

java.io.IOException - if an error occurs during file access

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

See Also:

DataTable

horizontalToVerticalTable

public DataTable horizontalToVerticalTable(DataTable table)

ConvertTable from table obtained from a file in the correct data orientation

Parameters:

table - the table to change orientation

Returns:

the table in the correct orientation TODO conversion for table without header

open

public boolean open(java.lang.String enc,
                    java.lang.String delimiter,
                    java.lang.String escape,
                    int type)

Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type

Specified by:

open in class DataFileReaderIntf

Parameters:

enc -

delimiter -

escape -

type -

Returns:

true, if the file is opened correctly.

See Also:

DataTable