# This file was automatically generated by SWIG (http://www.swig.org).
# Version 1.3.36
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# Don't modify this file, modify the SWIG interface instead.

Modules
		AUREA.learner._dirac AUREA.learner.dirac new

Classes
		Dirac __builtin__.object BoolVector DoubleVector IntVector dirac_PySwigIterator   class BoolVector(__builtin__.object)       Methods defined here: __del__ lambda self __delitem__(*args) __delslice__(*args) __getitem__(*args) __getslice__(*args) __init__(self, *args) __iter__(self) __len__(*args) __nonzero__(*args) __repr__ = _swig_repr(self) __setitem__(*args) __setslice__(*args) append(*args) assign(*args) back(*args) begin(*args) capacity(*args) clear(*args) empty(*args) end(*args) erase(*args) front(*args) get_allocator(*args) insert(*args) iterator(*args) pop(*args) pop_back(*args) push_back(*args) rbegin(*args) rend(*args) reserve(*args) resize(*args) size(*args) swap(*args) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined) thisown The membership flag Data and other attributes defined here: __swig_destroy__ = <built-in function delete_BoolVector>   class Dirac     This is the python class that controls the execution of the  DIRAC algorithm. The format of the inputs are quite exhaustively described in the dirac.cpp file. If you are curious about DIRAC the algorithm please check out "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation" by James A. Eddy, et al Published in PLoS Computational Biology May 2010 | Volume 6 | Issue 5.     Methods defined here: __init__(self, data, numGenes, classSizes, geneNet, geneNetSize, numTopNetworks, netMap) addUnclassified(self, unclassifiedVector) Takes unclassified data vector and saves it classify(self) Returns 0 or 1. The netStart and netEnd are where in the rank templates and unclassified rank vector the gene network you are interested in is located.   Update: you can now set numTopNetworks in the constructor. Passing here should be deprecated. classify_network(self, network_index) Returns a tuple that contains (classified class [0 or 1], class one percent match,  class two percent match) uses C classify function crossValidate(self, k=10) Runs the C-based cross validation K-Fold testing of the given data, returns Matthews correlation coefficient. getNetworkRankSize(self, network_idx) Returns the size of a network segment of a rank based data structure (template or matrix) getNetworkRankStart(self, network_id) Returns the starting index of a network segment of a rank based data structure (template or matrix) getNetworkStart(self, network_id) Maps the gene network( relative to its position in geneNetSize) to the starting location of its data matrix entries. i.e finding the starting location of the gene indices in the data matrix tables for the 3rd gene would be getNetworkStart(3) getRankConservation(self) Returns a list of lists that contains the rank conservation score for each class and gene network [     rcs for     [gn1.class1,gn1.class2],     [gn2.class1,gn2.class2],     ...,     [gnn.class1,gn2.class2] ] getRankDifference(self, numNets=None) Returns a list of tuples containing (sum of matches, gene_index, distance) in sorted order getRankMatchingScores(self) Returns a list of lists  {(2 * num genenetworks) x (number of samples)} containing the rank matching scores which describe how well a sample matches a template. [       rms of rt.c1.gN1 vs [c1.sa1.gN1, c1.sa2,gN1, ... c2.san.gN1],           rt.c2.gN1 vs [c1.sa1.gN1, c1.sa2,gN1, ... c2.san.gN1],             ...,           rt.c2.gNn vs [c1.sa1.gNn, c1.sa2,gNn, ... c2.san.gNn],            ] getRankMatrix(self) Returns the rankMatrix as a list of Bools [     [class1.sample1.genenet1.gene1,  sample1.genenet1.gene2 , ... sample1.gnN,gN]     [class1.sample2.genenet1.gene1, sample2.geneNet1.gene2, ...]     ...     [class2.samplen.genenet1.gene1, ...]   ] getRankTemplates(self) Returns the rank templates for class1 class2 [     [class 1 rt by geneNetwork order]     [class 2 rt by geneNetwork order] ] getTopNetworks(self) returns a list of the top networks(by name) as determined by get rank difference getUnclassifiedRankTemplate(self, geneNetwork) Builds the rank template for the unclassified vector for the subset defined by the gene network at genestart that goes to geneEnd nChooseTwo(self, n) testAll(self) Some testing for debugging purposes train(self) This is the method that performs the training from the provided data vecToList(self, vector, numRows) Takes a vector and turns it into a list of lists with the inner lists having len(numRows)   class DoubleVector(__builtin__.object)       Methods defined here: __del__ lambda self __delitem__(*args) __delslice__(*args) __getitem__(*args) __getslice__(*args) __init__(self, *args) __iter__(self) __len__(*args) __nonzero__(*args) __repr__ = _swig_repr(self) __setitem__(*args) __setslice__(*args) append(*args) assign(*args) back(*args) begin(*args) capacity(*args) clear(*args) empty(*args) end(*args) erase(*args) front(*args) get_allocator(*args) insert(*args) iterator(*args) pop(*args) pop_back(*args) push_back(*args) rbegin(*args) rend(*args) reserve(*args) resize(*args) size(*args) swap(*args) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined) thisown The membership flag Data and other attributes defined here: __swig_destroy__ = <built-in function delete_DoubleVector>   class IntVector(__builtin__.object)       Methods defined here: __del__ lambda self __delitem__(*args) __delslice__(*args) __getitem__(*args) __getslice__(*args) __init__(self, *args) __iter__(self) __len__(*args) __nonzero__(*args) __repr__ = _swig_repr(self) __setitem__(*args) __setslice__(*args) append(*args) assign(*args) back(*args) begin(*args) capacity(*args) clear(*args) empty(*args) end(*args) erase(*args) front(*args) get_allocator(*args) insert(*args) iterator(*args) pop(*args) pop_back(*args) push_back(*args) rbegin(*args) rend(*args) reserve(*args) resize(*args) size(*args) swap(*args) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined) thisown The membership flag Data and other attributes defined here: __swig_destroy__ = <built-in function delete_IntVector>   class dirac_PySwigIterator(__builtin__.object)       Methods defined here: __add__(*args) __del__ lambda self __eq__(*args) __iadd__(*args) __init__(self, *args, **kwargs) __isub__(*args) __iter__(self) __ne__(*args) __repr__ = _swig_repr(self) __sub__(*args) advance(*args) copy(*args) decr(*args) distance(*args) equal(*args) incr(*args) next(*args) previous(*args) value(*args) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined) thisown The membership flag Data and other attributes defined here: __swig_destroy__ = <built-in function delete_dirac_PySwigIterator>

Functions
		BoolVector_swigregister(...) DoubleVector_swigregister(...) IntVector_swigregister(...) classify(...) crossValidate(...) dirac_PySwigIterator_swigregister(...) runDirac(...)