BaseFile             package:aroma.Base             R Documentation

_T_h_e _B_a_s_e_F_i_l_e _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     Package:  aroma.Base 
      *Class BaseFile*

     'Object'
      '~~|'
      '~~+--''BaseFile'

     *Directly known subclasses:*


     public static class *BaseFile*
      extends Object

_U_s_a_g_e:

     BaseFile(sections=NULL, ...)

_A_r_g_u_m_e_n_t_s:

sections: A 'list' BaseFileSection objects.

     ...: Not used.

_F_i_e_l_d_s _a_n_d _M_e_t_h_o_d_s:

     *Methods:*

         'appendSection'          Adds a section to this BASE file structure.
         'as.character'           Gets a string description of object.
         'as.list'                Gets a list representation of object.
         'equals'                 Checks if this object equals another.
         'getAllDataFiles'        Gets the names of a external data files used by a BASE file.
         'getSection'             Gets one section of this BASE file structure.
         'getSections'            Gets a subset or all BASE sections.
         'hasSerialBioAssaySets'  Checks if the bioassay sets have data in serial format.
         'isSerial'               Checks if a BASE file is in serial format or not.
         'length'                 -
         'nbrOfSections'          Gets the number of sections in this BASE file structure.
         'read'                   Static method to read a BASE file structure.
         'removeAllDataFiles'     Removes all external data files used by a BASE file structure.
         'removeSection'          Removes a section from a BASE file structure.
         'replaceSection'         Replaces a section in a BASE file structure.
         'seq'                    Gets an index sequence for the sections in this BASE file structure.
         'write'                  Writes this BASE file structure.

     *Methods inherited from Object*:
      $, $<-, [[, [[<-, as.character, attach, attachLocally,
     clearCache, clone, detach, equals, extend, finalize, gc,
     getEnvironment, getFields, getInstantiationTime,
     getStaticInstance, hasField, hashCode, ll, load, objectSize,
     print, registerFinalizer, save

_A_u_t_h_o_r(_s):

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

_E_x_a_m_p_l_e_s:

     # Read a simple BASE file structure (adopted from [2])
     filename <- system.file("data-ex", "baseExample.base", package="aroma.Base")
     base <- BaseFile$read(filename)
     print(base)

     # Write it back to file
     tmpfile <- tempfile()
     write(base, tmpfile)

     # Read the newly create file
     base2 <- BaseFile$read(tmpfile)
     file.remove(tmpfile)

     # Compare with the original structure
     stopifnot(equals(base, base2))

