/*  Coclustering.h    Header file for coclustering, super class of all co-clustering algorithms     Copyright (c) 2005, 2006              by Hyuk Cho    Copyright (c) 2003, 2004    	      by Hyuk Cho, Yuqiang Guan, and Suvrit Sra                {hyukcho, yguan, suvrit}@cs.utexas.edu*/#if !defined(_COCLUSTERING_H_)#define _COCLUSTERING_H_#include <cmath>#include <vector>#include "Constants.h"#include "Tools.h"#include "RandomGenerator.h"#include "SparseMatrix.h"#include "DenseMatrix.h"#include "ExternalValidity.h"extern long memoryUsed;class Coclustering{  protected:    struct oneStep    {      int id;      int fromCluster;      int toCluster;      double change;    };     bool isShowingEachCluster;    bool isTakingReverse;    bool isHavingVariation;    bool isSilent;					// not used...    bool isComputingOneWayObjective;     bool isEmptyRowClusterReported;    bool isEmptyColClusterReported;    bool isAvoidingEmptyRowCluster;			// used for avoiding empty row cluster(s)    bool isAvoidingEmptyColCluster;			// used for avoiding empty col clusters(s)    bool *isReversed;        bool *isRowMarked;    bool *isColMarked;    bool hasReadRowSeedingFile;				// used for avoiding multiple readings    bool hasReadColSeedingFile;				// used for avoiding multiple readings        int numIteration;    int batchUpdateType;    int localSearchType;    double rowBatchUpdateThreshold;    double colBatchUpdateThreshold;    double rowLocalSearchThreshold;    double colLocalSearchThreshold;    int rowLocalSearchLength;    int colLocalSearchLength;    int rowV;    int colV;    int smoothingType;    int dumpLevel;    int dumpAccessMode;    int numRowCluster;    int numColCluster;    int numRow;    int numCol;    int numRowClass;    int numColClass;    int numEmptyRowCluster;    int numEmptyColCluster;    int numSingletonRowCluster;    int numSingletonColCluster;    int numReversedRow;    int numRowPermutation;		// -S m    int numColPermutation;		// -S m    vector<int> rowCLVec;		// used for permutation initialization    vector<int> colCLVec;		// used for permutation initialization    int *rowCL;    int *colCL;    int *rowCS;    int *colCS;    int *rowClassLabel;    int *colClassLabel;    int rowInitializationMethod;    int colInitializationMethod;    double objValue;    double objValue4RowCluster;    double objValue4ColCluster;    double rowPrecision;		// micro-averaged precision    double rowRecall;			// micro-averaged recall    double rowAccuracy;    double colPrecision;		// micro-averaged precision    double colRecall;			// micro-averaged recall    double colAccuracy;    double rowAnnealingFactor;    double colAnnealingFactor;    double rowSmoothingFactor;    double colSmoothingFactor;    double perturbationMagnitude;    double *twoNormOfEachRow;    double *twoNormOfEachCol;    double **Acompressed;    RandomGeneratorMT19937 randNumGenerator;    Matrix *myCCS;    Matrix *myCRS;    int rowSeedingOffsetType;    int colSeedingOffsetType;    int numRowSeedingSet;    int numColSeedingSet;    int rowSeedingAccessMode;    int colSeedingAccessMode;//    char *rowSeedingFilename;//    char *colSeedingFilename;//    char *coclusterFilename;    char rowSeedingFilename[FILENAME_LENGTH];    char colSeedingFilename[FILENAME_LENGTH];    char coclusterFilename[FILENAME_LENGTH];    char objectiveFilename[FILENAME_LENGTH];    char dumpFilename[FILENAME_LENGTH];    char statisticsFilename[FILENAME_LENGTH];    int coclusterOffsetType;    int coclusterLabelType;    int coclusterAccessMode;    int objectiveAccessMode;    int statisticsAccessMode;        void computeAcompressed();    void computeAcompressed(bool *isReversed);    void computeNumReversedRow();    void computeRowClusterSize();    void computeColClusterSize();    void doRowRandomInitialization();    void doColRandomInitialization();    void doRowRandomInitializationModified();    void doColRandomInitializationModified();    void doRowRandomInitializationDirect();    void doColRandomInitializationDirect();    virtual void doRowRandomPerturbInitialization() = 0;    virtual void doColRandomPerturbInitialization() = 0;    virtual void doRowFarthestInitialization() = 0;    virtual void doColFarthestInitialization() = 0;    void doSeedingInitializationI(char *seedingFilename);		// not used    void doSeedingInitializationII(char *seedingFilename);		// not used    void doRowCLVecInitialization();					// used for permutation initialization    void doColCLVecInitialization();					// used for permutation initialization    void doRowPermutationInitialization();				// used for permutation initialization    void doColPermutationInitialization();				// used for permutation initialization    void removeEmptyCluster();    void clearMark4Row();    void clearMark4Col();    void checkDumpLevel4Cocluster(ostream &os);    void checkDumpLevel4InitialObjectValue();    void checkDumpLevel4FinalObjectValue();    void checkDumpLevel4Centroid(double **centroid, int row, int col);    void checkDumpLevel4NumOfChange(char *token, int numChange);    void checkDumpLevel4ReversedRow();    void checkDumpLevel4BatchUpdate(char *token);    void checkDumpLevel4BatchUpdate(char *token, int num);    void checkDumpLevel4DeltaTrace(char *token, int id, int toCluster, double delta, double minDelta);    void checkDumpLevel4LocalSearch(char *token);    void checkDumpLevel4LocalSearch(char *token, int id, int from, int to, double change);    void checkDumpLevel4NumOfChain(char *token, int num, double *totalChange);    void checkDumpLevel4PingPong(char *token, int num);    void checkDumpLevel4Coclustering(ostream &os, int num, double value);    void chooseInitializationMethod();    std::ifstream rowSeedingFile;    std::ifstream colSeedingFile;  public:    Coclustering(Matrix *inputCCS, Matrix *inputCRS, commandLineArgument &myCLA);    virtual ~Coclustering();    std::ofstream coclusterFile;		// needed to be public because it's used in Cocluster    std::ofstream dumpFile;			// needed to be public because it's used in Cocluster    std::ofstream objectiveFile;		// needed to be public because it's used in Cocluster    std::ofstream statisticsFile;		// needed to be public because it's used in Cocluster    char *classPrefix;    void setSilent(bool s);			// not used...    void setSmoothingFactor(double smoothingFactor);    void setRowSmoothingFactor(double smoothingFactor);	// not used...    void setColSmoothingFactor(double smoothingFactor);	// not used...    virtual void doInitialization() = 0;    int getEmptyRC();    int getEmptyCC();    int getSingletonRC();    int getSingletonCC();    double getObjValue();    double getObjValue4RowCluster();    double getObjValue4ColCluster();    int getNumIteration();    int getNumReversedRow();    double getRowPrecision();    double getRowRecall();    double getRowAccuracy();    double getColPrecision();    double getColRecall();    double getColAccuracy();    void checkHavingReversedRow();    void updateVariable(double &minDistance, int &minCL, double tempDistance, int tempCL);    void updateVariable(double &minDistance, int &minCL, bool &tempIsReversed, double tempDistance, int tempCL, bool trueOrFalse);    void adjustClusterLabel(int value);    void validateRowCluster(int numRowClass, int *rowClassLabel);    void validateColCluster(int numColClass, int *colClassLabel);    virtual void doPingPong() = 0;    void writeCocluster();};#endif //!defined(_COCLUSTERING_H)