Package CHEM :: Package ML :: Package features :: Module AggregateSpectrumExtractor :: Class AggregateSpectrumExtractor

Class AggregateSpectrumExtractor

BaseFeatureExtractor.BaseFeatureExtractor --+
                                            |
                                           AggregateSpectrumExtractor

Extension of simple SpectrumExtractor. Basically just does the simple SpectrumExtractor for all values of k (length of substrings to compare) from a minimum (default=1) up to the length of the strings.

Instance Methods

[hide private]

__init__(self)
Constructor.

loadOptions(self, options)
Load relevant options derived from an optparse.OptionParser into the state of this object.

__call__(self, aString)
Create a dictionary keyed by all the k-mers (k-length substrings) of aString, with values equal to the number of times that k-mer appears in aString.

objectDescription(self, obj)
Input is a string itself, so just return the first token

getNameID(self, obj)
See if a second token exists, otherwise, return sentinel value

Inherited from BaseFeatureExtractor.BaseFeatureExtractor: loadArgs, main, outputFeatures

Class Variables

[hide private]

minK = 1

Inherited from BaseFeatureExtractor.BaseFeatureExtractor: inputFunction, inputIter, outFile, parser

Method Details

[hide private]

init(self)
(Constructor)

Constructor. Initializes expected command-line options.

Overrides: BaseFeatureExtractor.BaseFeatureExtractor.__init__

loadOptions(self, options)

Load relevant options derived from an optparse.OptionParser into the state of this object.

Sub-classes should have this handle any of the options it added to the command-line parser via the constructor.

Overrides: BaseFeatureExtractor.BaseFeatureExtractor.loadOptions: (inherited documentation)

call(self, aString)
(Call operator)

Create a dictionary keyed by all the k-mers (k-length substrings) of aString, with values equal to the number of times that k-mer appears in aString.

Overrides: BaseFeatureExtractor.BaseFeatureExtractor.__call__

objectDescription(self, obj)

Input is a string itself, so just return the first token

Overrides: BaseFeatureExtractor.BaseFeatureExtractor.objectDescription

getNameID(self, obj)

See if a second token exists, otherwise, return sentinel value

Overrides: BaseFeatureExtractor.BaseFeatureExtractor.getNameID

Class AggregateSpectrumExtractor

__init__(self) (Constructor)

loadOptions(self, options)

__call__(self, aString) (Call operator)

objectDescription(self, obj)

getNameID(self, obj)

init(self)
(Constructor)

call(self, aString)
(Call operator)