data
Class LocalizationDataReader

java.lang.Object
  extended by data.LocalizationDataReader

public class LocalizationDataReader
extends Object

Reads localization data from a file or stream. The following data format is assumed:

PROTEINNAME[tab]loc1,loc2,loc3 The protein identifier and the localizations are seperated by a TAB, each localization information is then seperated by commas.

This class is not instantiatable.

Author:
Jan Krumsiek

Method Summary
static LocalizationData readLocalizationData(File file)
          Reads localization data from a given file.
static LocalizationData readLocalizationData(File file, String organism)
          Reads localization data from a given file.
static LocalizationData readLocalizationData(InputStream stream)
          Reads localization data from an input stream
static LocalizationData readLocalizationData(InputStream stream, String organism)
          Reads localization data from an input stream
static LocalizationData readLocalizationData(String file)
          Reads localization data from a given file.
static LocalizationData readLocalizationData(String file, String organism)
          Reads localization data from a given file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

readLocalizationData

public static LocalizationData readLocalizationData(String file)
                                             throws IOException
Reads localization data from a given file.

Parameters:
file - file from which the localization data will be read
Returns:
localization data object
Throws:
IOException - if the file could not be read
ProCopeException - if the data format is invalid

readLocalizationData

public static LocalizationData readLocalizationData(String file,
                                                    String organism)
                                             throws IOException
Reads localization data from a given file.

Parameters:
file - file from which the localization data will be read
organism - specify an organism identifier for the new proteins or null for no organism (see also: ProteinManager)
Returns:
localization data object
Throws:
IOException - if the file could not be read
ProCopeException - if the data format is invalid

readLocalizationData

public static LocalizationData readLocalizationData(File file)
                                             throws IOException
Reads localization data from a given file.

Parameters:
file - file from which the localization data will be read
Returns:
localization data object
Throws:
IOException - if the file could not be read
ProCopeException - if the data format is invalid

readLocalizationData

public static LocalizationData readLocalizationData(File file,
                                                    String organism)
                                             throws IOException
Reads localization data from a given file.

Parameters:
file - file from which the localization data will be read
organism - specify an organism identifier for the new proteins or null for no organism (see also: ProteinManager)
Returns:
localization data object
Throws:
IOException
ProCopeException - if the data format is invalid
IOException - if the file could not be read

readLocalizationData

public static LocalizationData readLocalizationData(InputStream stream)
Reads localization data from an input stream

Parameters:
stream - stream from which the localization data will be read
Returns:
localization data object
Throws:
ProCopeException - if the data format is invalid

readLocalizationData

public static LocalizationData readLocalizationData(InputStream stream,
                                                    String organism)
Reads localization data from an input stream

Parameters:
stream - stream from which the localization data will be read
organism - specify an organism identifier for the new proteins or null for no organism (see also: ProteinManager)
Returns:
localization data object
Throws:
ProCopeException - if the data format is invalid