# 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._tsp new

Classes
		TSP __builtin__.object DoubleVector IntVector tsp_PySwigIterator   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 TSP     Top Scoring Pairs class.   This class runs the top scoring pairs algorithm described in The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA I mutations by Lin et al in BMC Bioinformatics 2009, 10:256 http://www.biomedcentral.com/1471-2105/10/256   TSP was originally introduces by Geman,D. et al. (2004) Classifying  gene expression proles from pairwise mRNA comparisons.  Statistical Applications in Genetics and Molecular Biology Vol 3 [2004], Issue 1 Article 19.  This code uses slightly modified code from  https://jshare.johnshopkins.edu/dnaiman1/public_html/rxa/ which is  the code described in the above mentioned paper.     Methods defined here: __init__(self, data, numGenes, classSizes, filter) Initializes the object.  data is an IntVector containing the microarray data and should be generated by the dataPackager class.  numGenes is an integer containing the number of genes/probes per sample     in the data table classSizes is an intvector containing the size of the 2 classes,      class 1 and class 2 respectively. filter (a two item IntVector) causes only the genes with the wilcoxon scores >=  the the filterth best wilcoxon scores to be considered addUnclassified(self, unclassifiedVector) classify(self) crossValidate(self, k=10) Runs the C-based cross validation K-fold testing of the given data, returns the Matthews correlation coefficient [-1.0, 1.0]. getMaxScores(self) Returns a list of the top scoring pairs indices train(self) Trains on the given data.   class tsp_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_tsp_PySwigIterator>

Functions
		DoubleVector_swigregister(...) IntVector_swigregister(...) crossValidate(...) runTSP(...) tsp_PySwigIterator_swigregister(...)