libpbihdf-dev 0~20151014+gitbe5d1bf-2 / usr / include / pbihdf / HDFRegionTableWriter.hpp

#ifndef _BLASR_HDF_REGION_TABLE_WRITER_HPP_
#define _BLASR_HDF_REGION_TABLE_WRITER_HPP_

#include <string>

#include "Enumerations.h"
#include "reads/RegionTable.hpp"
#include "HDFFile.hpp"
#include "HDFArray.hpp"
#include "HDF2DArray.hpp"
#include "HDFAtom.hpp"


using namespace H5;
using namespace std;


class HDFRegionTableWriter {
public:
	HDFFile regionTableFile;

	HDF2DArray<int> regions;
	HDFAtom<vector<string> > regionTypes;
	HDFAtom<vector<string> > regionDescriptions;
	HDFAtom<vector<string> > regionSources;
	HDFAtom<vector<string> > columnNames;
	int curRow;
	int nRows;
	HDFGroup *parentGroupPtr, pulseDataGroup;

    void CreateGroupStructure() {

        regionTableFile.rootGroup.AddGroup("PulseData");
        if (pulseDataGroup.Initialize(regionTableFile.rootGroup, "PulseData") == 0) {
            cout << "Could not create group PulseData. This is a bug." << endl;
            exit(1);
        }
        parentGroupPtr = &pulseDataGroup;
        regions.Initialize(pulseDataGroup, "Regions", RegionAnnotation::NCOLS);

    }

    int Create(string fileName) {
        H5File newFile(fileName.c_str(), H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, FileAccPropList::DEFAULT);  
        regionTableFile.hdfFile.openFile(fileName.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);    
        regionTableFile.rootGroup.Initialize(regionTableFile.hdfFile, "/");
        CreateGroupStructure();
    }

    HDFRegionTableWriter() {
        curRow = 0;
        nRows  = 0;
        parentGroupPtr = NULL;
    }

    int Initialize(HDFGroup &parentGroupP) {
        /*
         * Initialize in an existing file.
         */
        parentGroupPtr = &parentGroupP;
        return Initialize();
    }

    int Initialize(string &regionTableFileName, 
            const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
        /*
         * Initialize access to the HDF file.
         */
        try {
            regionTableFile.Open(regionTableFileName, H5F_ACC_TRUNC, fileAccPropList);
        }
        catch (Exception &e) {
            cout << e.getDetailMsg() << endl;
            return 0;
        }
        CreateGroupStructure();
        return 1;
    }

    int Initialize() {

        if (regions.Initialize(*parentGroupPtr, "Regions", RegionAnnotation::NCOLS) == 0) {
            return 0;
        }
        nRows = regions.GetNRows();


        curRow = 0;
        return 1;
    }

    void Finalize(vector<string> &columnNamesVect, 
            vector<string> &regionTypesVect,
            vector<string> &regionDescriptionsVect,
            vector<string> &regionSourcesVect) {
        //
        // Make sure data has been written to the dataset.  If not, the
        // dataset will not exist and creating the attributes will fail.
        //
        if (curRow > 0) {
            regionTypes.Create(regions.dataset, "RegionTypes", regionTypesVect);
            columnNames.Create(regions.dataset, "ColumnNames", columnNamesVect);
            regionDescriptions.Create(regions.dataset, "RegionDescriptions", regionDescriptionsVect);
            regionSources.Create(regions.dataset,  "RegionSources", regionSourcesVect);
        }
    }

    void WriteRows(vector<RegionAnnotation> &annotations) {
        int i;
        for (i = 0; i < annotations.size(); i++) {
            Write(annotations[i]);
        }
    }

    int Write(RegionAnnotation &annotation, int at=-1) {
        if (at == -1) {
            regions.WriteRow(annotation.row, annotation.NCOLS);
            ++curRow;
        }
        else {

        }
        return 1;
    }	

    void Close() {
        regions.Close();
        //
        // Check to see if this is external
        //
        if (parentGroupPtr == &pulseDataGroup) {
            pulseDataGroup.Close();
        }
        regionTableFile.rootGroup.Close();
    }

};


#endif