BioDataSet.h

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#ifndef BIODATASET_H
#define BIODATASET_H


#include "BioUtilities.h"
#include "BioStatistics.h"
#include "BioProbeSet.h"
#include "BioSampleSet.h"

class BioDataSet
{
protected:
        BioDataSet(); // Default Constructor - NOT TO BE USED, hence PRIVATE;
        vector<BioProbeSet> probeData_;
        vector<string>sampleNames_;
public:

        BioDataSet(vector<string>&  sampleNames, vector<BioProbeSet>& prbData);
        BioProbeSet getProbeSet(int probeIndex);

        BioProbeSet getAverageOfProbeSets(string probeIndexPattern);

        int getNumberOfSamples();

        int getNumberOfProbes();

        int getSampleIndex(string sampleName);

        int getProbeIndex(string probeReference);

        BioSampleSet getSampleSet(int sampleIndex);

        BioSampleSet getAverageOfSampleSets( string sampleIndexPattern);

        BioDataSet getMultipleProbeSets(string indexString);

        BioDataSet getMultipleSampleSets(string indexString);

        float getSampleRMSD( int sampleIndex1, int sampleIndex2);

        float getProbeRMSD( int probeIndex1, int probeIndex2);

        float getProbeCorrelationCoefficient( int probeIndex1, int probeIndex2);

        float getSampleCorrelationCoefficient( int sampleIndex1, int sampleIndex2);

        vector<int> getProbeIndexListExcludingAllNullProbes();
        vector<int> getControlProbeIndexList();
        vector<int> getAllNullProbeIndexList();
        vector<int> getCleanProbeIndexList();
        vector<int> getAllNullSampleIndexList();
        vector<int> getCleanSampleIndexList();

        BioDataSet getNormalizedDataSet();
        float getMean();
        float getMaximum();
        float getMinimum();
        float getStandardDeviation();
        float getMedian();
        
        BioDataSet getCleanDataSet();
        BioDataSet getDataSetExcludingControlProbes();
        
};

#endif