GenomicMatrix.py

import cgDataV2.Exceptions
from cgDataV2.GenomicMatrixMetadata import GenomicMatrixMetadata

import sys

class GenomicMatrix(object):
    """GenomicMatrix objects contain sets of experimental observations.
    They operate on files that are structured as matrices, with the
    rows representing probes and the columns representing samples.
    Each cell, representing the intersection of one probe and one
    sample, represents one single experimental observation
    """
#    __format__ = {
#        "name" : "genomicMatrix",
#        "type" : "type",
#        "form" : "matrix",
#        "rowType" : "probeMap",
#        "colType" : "sampleMap",
#        "valueType" : "float",
#        "nullString" : "NA",
#        "links" : {
#            "dataSubType" : {}
#            }
#        }

    def __init__(self, genomicMatrixMetadata):
        """Given a genomic matrix metadata object, load and return the
        corresponding GenomicMatrix object.  Upon creation, the new
        object is validated, and if it fails validation, a
        ValidationFailed exception is thrown """
        pass

    def __validate(self):
        """Validate this GenomicMatrix. If unsuccessful, throw a ValidationFailed
        exception.
        """
        pass

    def compareProbeIds(id1, id2):
        """Return the results of a lexical comparison between the two probe IDs"""
        pass
    
    def getValue(self, probe, sample):
        """Get the data value for the indicated probe and sample"""
        pass

    def nProbes(self):
        """Return the number of probes in this GenomicMatrix"""
        pass

    def nSamples(self):
        """Return the number of samples in this GenomicMatrix"""

    def observationsByProbe(self, probe):
        """Given a probe, return a vector of the experimental observations
        from the GenomicMatrix for this probe

        Question: would it be most useful if the data was returned as a
        vector or a dictionary keyed by sample?
        """
        pass

    def observationsBySample(self, sample):
        """Given the name of a sample from the GenomicMatrix, return the
        set of experimental observations for this sample.

        Question: would it be most useful if the data was returned as a
        vector or a dictionary keyed by probe?
        """
        pass

    def probeList(self):
        """Return the list of probes represented in this GenomicMatrix
        """
        pass

    def sampleList(self):
        """Return the list of samples represented in this GenonicMatrix"""
        pass

    def setValue(self, probe, sample, newValue):
        """Update the value stored for the indicated probe and sample
        """
        pass

    def sort(self, cmp=compareProbeIds):
        """Sort the genomic matrix according to the indicated comparison
        function"""
        pass
    
    def write(self, filename):
        """Write the GenomicMatrix object to the indicated filename"""
        pass