class CdfHeader:
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf_header = self.affy._fusionCDFHeaderAutoClass()
def get_num_probe_sets(self):
return self.cdf_header.getNumProbeSets()
def get_num_qc_probe_sets(self):
return self.cdf_header.getNumQCProbeSets()
def get_reference(self):
return self.cdf_header.getReference()
def get_cols(self):
return self.cdf_header.getCols()
def get_rows(self):
return self.cdf_header.getRows()
def clear(self):
self.cdf_header.clear()
def get_format_version(self):
return self.cdf_header.getFormatVersion()
def get_guid(self):
return self.cdf_header.getGUID()
def get_integrity_md5(self):
return self.cdf_header.getIntegrityMd5()
class CdfProbeInformation:
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf_probe_information = self.affy._fusionCDFProbeInformationAutoClass()
def get_list_index(self):
return self.cdf_probe_information.getListIndex()
def get_expos(self):
return self.cdf_probe_information.getExpos()
def get_x(self):
return self.cdf_probe_information.getX()
def get_y(self):
return self.cdf_probe_information.getY()
def get_pbase(self):
self.cdf_probe_information.getPBase()
def get_tbase(self):
self.cdf_probe_information.getTBase()
def get_probe_length(self):
return self.cdf_probe_information.getProbeLength()
def get_probe_grouping(self):
return self.cdf_probe_information.getProbeGrouping()
def clear(self):
self.cdf_probe_information.clear()
class CdfProbeGroupInformation:
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf_probe_group_information = self.affy._fusionCDFProbeGroupInformationAutoClass()
def get_num_lists(self):
return self.cdf_probe_group_information.getNumLists()
def get_num_cells(self):
return self.cdf_probe_group_information.getNumCells()
def get_start(self):
return self.cdf_probe_group_information.getStart()
def get_stop(self):
return self.cdf_probe_group_information.getStop()
def get_probe_set_index(self):
return self.cdf_probe_group_information.getProbeSetIndex()
def get_group_index(self):
return self.cdf_probe_group_information.getGroupIndex()
def get_name(self):
return self.cdf_probe_group_information.getName()
def get_num_cells_per_list(self):
return self.cdf_probe_group_information.getNumCellsPerList()
def get_direction(self):
return self.cdf_probe_group_information.getDirection()
def get_wobble_situation(self):
return self.cdf_probe_group_information.getWobbleSituation()
def get_allele_code(self):
return self.cdf_probe_group_information.getAlleleCode()
def get_channel(self):
return self.cdf_probe_group_information.getChannel()
def get_rep_type(self):
return self.cdf_probe_group_information.getRepType()
def get_cell(self, index, probe):
self.cdf_probe_group_information.getCell(index, probe.cdf_probe_information)
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf = self.affy._fusionCDFDataAutoClass()
self.read_ok = False
class CdfFileParser:
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf = self.affy._fusionCDFDataAutoClass()
self.read_ok = False
def open_cdf_file(self, file_name):
j_file_name = self.affy.String(file_name)
self.set_file_name(j_file_name)
self.read()
####
# WRAPPER METHODS
def get_header(self):
header = CdfHeader()
header.cdf_header = self.cdf.getHeader()
return header
def set_file_name(self, file_name):
self.cdf.setFileName(file_name)
def read(self):
self.read_ok = self.cdf.read()
def get_probe_set_information(self, index, info):
self.cdf.getProbeSetInformation(index, info.cdf_probe_set_information)
def get_probe_set_name(self, index):
return self.cdf.getProbeSetName(index)
def get_file_name(self):
return self.cdf.getFileName()
def get_error(self):
return self.cdf.getError()
def get_chip_type(self):
return self.cdf.getChipType()
def prepare_gcos_objects_for_reading(self):
self.cdf.prepareGCOSObjectsForReading()
def read_header(self):
return self.cdf.readHeader()
def exists(self):
return self.cdf.exists()
def is_xda_compatible_file(self):
return self.cdf.isXDACompatibleFile()
def get_probe_set_type(self, index):
return self.cdf.getProbeSetType(index)
def clear(self):
self.cdf.clear()
def get_chip_types(self):
return self.cdf.getChipTypes()
def get_guid(self):
return self.cdf.getGUID()
def get_integrity_md5(self):
return self.cdf.getIntegrityMd5()
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf_header = self.affy._fusionCDFHeaderAutoClass()
def __init__(self):
self.affy = AffyMetrixCdfWrapper()
self.cdf_probe_group_information = self.affy._fusionCDFProbeGroupInformationAutoClass()