def __init__(self, **kwd):
"""
A Fastsearch Index consists of a binary file with the fingerprints
and a pointer the actual molecule file.
"""
Binary.__init__(self, **kwd)
self.add_composite_file('molecule.fs',
is_binary=True,
description='OpenBabel Fastsearch Index')
self.add_composite_file('molecule.sdf',
optional=True,
is_binary=False,
description='Molecule File')
self.add_composite_file('molecule.smi',
optional=True,
is_binary=False,
description='Molecule File')
self.add_composite_file('molecule.inchi',
optional=True,
is_binary=False,
description='Molecule File')
self.add_composite_file('molecule.mol2',
optional=True,
is_binary=False,
description='Molecule File')
self.add_composite_file('molecule.cml',
optional=True,
is_binary=False,
description='Molecule File')
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
# Binary model
self.add_composite_file('model.hmm.h3m', is_binary=True)
# SSI index for binary model
self.add_composite_file('model.hmm.h3i', is_binary=True)
# Profiles (MSV part)
self.add_composite_file('model.hmm.h3f', is_binary=True)
# Profiles (remained)
self.add_composite_file('model.hmm.h3p', is_binary=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
"""The metadata"""
self.add_composite_file('imzml',
description='The imzML metadata component.',
is_binary=False)
"""The mass spectral data"""
self.add_composite_file(
'ibd',
description='The mass spectral data component.',
is_binary=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
self.add_composite_file(
'wiff',
description='AB SCIEX files in .wiff format. This can contain all needed information or only metadata.',
is_binary=True)
self.add_composite_file(
'wiff_scan',
description='AB SCIEX spectra file (wiff.scan), if the corresponding .wiff file only contains metadata.',
optional='True', is_binary=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
"""The header file. Provides information about dimensions, identification, and processing history."""
self.add_composite_file('hdr',
description='The Analyze75 header file.',
is_binary=False)
"""The image file. Image data, whose data type and ordering are described by the header file."""
self.add_composite_file('img',
description='The Analyze75 image file.',
is_binary=True)
"""The optional t2m file."""
self.add_composite_file('t2m',
description='The Analyze75 t2m file.',
optional='True',
is_binary=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
self.add_composite_file('shapefile.shp', description='Geometry File (shp)', is_binary=True, optional=False)
self.add_composite_file('shapefile.shx', description='Geometry index File (shx)', is_binary=True, optional=False)
self.add_composite_file('shapefile.dbf', description='Columnar attributes for each shape (dbf)', is_binary=True, optional=False)
# optional
self.add_composite_file('shapefile.prj', description='Projection description (prj)', is_binary=False, optional=True)
self.add_composite_file('shapefile.sbn', description='Spatial index of the features (sbn)', is_binary=True, optional=True)
self.add_composite_file('shapefile.sbx', description='Spatial index of the features (sbx)', is_binary=True, optional=True)
self.add_composite_file('shapefile.fbn', description='Read only spatial index of the features (fbn)', is_binary=True, optional=True)
self.add_composite_file('shapefile.fbx', description='Read only spatial index of the features (fbx)', is_binary=True, optional=True)
self.add_composite_file('shapefile.ain', description='Attribute index of the active fields in a table (ain)', is_binary=True, optional=True)
self.add_composite_file('shapefile.aih', description='Attribute index of the active fields in a table (aih)', is_binary=True, optional=True)
self.add_composite_file('shapefile.atx', description='Attribute index for the dbf file (atx)', is_binary=True, optional=True)
self.add_composite_file('shapefile.ixs', description='Geocoding index (ixs)', is_binary=True, optional=True)
self.add_composite_file('shapefile.mxs', description='Geocoding index in ODB format (mxs)', is_binary=True, optional=True)
self.add_composite_file('shapefile.shp.xml', description='Geospatial metadata in XML format (xml)', is_binary=False, optional=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
def __init__(self, **kwd):
"""Initialize binary datatype"""
Binary.__init__(self, **kwd)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
self.add_composite_file('analysis.baf',
description='analysis.baf file.',
optional='False',
is_binary=True)
self.add_composite_file('analysis.baf_idx',
description='analysis.baf file.',
optional='False',
is_binary=True)
self.add_composite_file('analysis.baf_xtr',
description='analysis.baf file.',
optional='False',
is_binary=True)
self.add_composite_file('analysis.content',
description='analysis.content file.',
optional='False',
is_binary=True)
self.add_composite_file(
'analysis.0.DataAnalysis.method',
description='analysis.0.DataAnalysis.method file.',
optional='False',
is_binary=True)
self.add_composite_file('analysis.0.result_c',
description='analysis.0.result_c file.',
optional='False',
is_binary=True)
self.add_composite_file('calib.bin',
description='calib.bin file.',
optional='False',
is_binary=True)
self.add_composite_file(
'desktop.ini',
description='desktop.ini file that contains some metadata.',
optional='True',
is_binary=False)
self.add_composite_file('ms-waters-pda.hss',
description='ms-waters-pda.hss file.',
optional='False',
is_binary=False)
self.add_composite_file('*.hdx',
description='any .hdx file.',
optional='False',
is_binary=True)
self.add_composite_file('*.u2',
description='any .u2 file.',
optional='False',
is_binary=True)
self.add_composite_file('*.und',
description='any .und file.',
optional='False',
is_binary=True)
self.add_composite_file('*.m',
description='any .m folder.',
optional='False',
is_binary=True)
self.add_composite_file('*.m/DataAnalysis.Method',
description='DataAnalysis.Method file.',
optional='False',
is_binary=True)
self.add_composite_file('*.m/desktop.ini',
description='*.m/desktop.ini file.',
optional='True',
is_binary=False)
self.add_composite_file('*.m/hystar.method',
description='*.m/hystar.method file.',
optional='True',
is_binary=True)
self.add_composite_file(
'*.m/microTOFQAcquisition.method',
description='*.m/microTOFQAcquisition.method file.',
optional='False',
is_binary=True)
self.add_composite_file('*.m/submethods.xml',
description='*.m/submethods.xml file.',
optional='False',
is_binary=True)
self.add_composite_file('*.mcf',
description='any .mcf file.',
optional='False',
is_binary=True)
self.add_composite_file('*.mcf_idx',
description='any .mcf_idx file.',
optional='False',
is_binary=True)
self.add_composite_file('Storage.mcf_idx',
description='Storage.mcf_idx file.',
optional='False',
is_binary=True)
self.add_composite_file(
'SampleInfo.xml',
description='SampleInfo.xml file that contains some metadata.',
optional='False',
is_binary=False)
self.add_composite_file('NuGenesisTemplate.txt',
description='NuGenesisTemplate.txt file.',
optional='True',
is_binary=False)
self.add_composite_file('LCParms.txt',
description='LCParms.txt file.',
optional='False',
is_binary=False)
self.add_composite_file('HS_columns.xmc',
description='HS_columns.xmc file.',
optional='False',
is_binary=True)
self.add_composite_file('BackgroundLineNeg.ami',
description='BackgroundLineNeg.ami file.',
optional='True',
is_binary=True)
self.add_composite_file('BackgroundUV.ami',
description='BackgroundUV.ami file.',
optional='True',
is_binary=True)
self.add_composite_file('Calibrator.ami',
description='Calibrator.ami file.',
optional='False',
is_binary=True)
self.add_composite_file('DensViewNeg.ami',
description='DensViewNeg.ami file.',
optional='True',
is_binary=True)
self.add_composite_file('DensViewNegBgnd.ami',
description='DensViewNegBgnd.ami file.',
optional='True',
is_binary=True)
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
log.info('Creating cummeRbund CuffDataDB')
