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testSource.cpp

Go to the documentation of this file.

#include "gn/gnFASSource.h"
#include <iostream>


#include "gn/gnFilter.h"

int32 main( int32 argc, char* argv[])
{
        argc; argv;

        gnFASSource source;
        string sourceFile = "w:/developm/_data/cft073/v6/cft073v6.fas";
        cout << "Enter Source: ";
        cin >> sourceFile;
        cout << "Opening " << sourceFile << endl;
        if( !source.Open( sourceFile ) )
        {
                cout << "Failed to open " << sourceFile << endl;
                return 1;
        }

        cout << "Number of Contigs " << source.GetContigListLength() << endl;
        for( uint32 i=0; i < source.GetContigListLength(); ++i )
        {
                gnFileContig* fg = source.GetContig(i);
                cout << "\t" << fg->GetName() <<  endl;
                cout << "\t\t" << fg->GetSeqLength() << " : {" 
                        << fg->GetFileStartEnd().first << ", "
                        << fg->GetFileStartEnd().second << ": ";
                for( uint32 j=0; j<CONTIG_SECTION_SIZE; ++j )
                        cout << "(" << fg->GetSectStartEnd( (gnContigSection)j ).first << ","
                                << fg->GetSectStartEnd( (gnContigSection)j ).second << ") ";
                cout << "}" << endl;
                cout << "\t\t" << (fg->HasRepeatSeqGap()?"TRUE":"FALSE")
                        << " (" << fg->GetRepeatSeqGapSize().first << ","
                        << fg->GetRepeatSeqGapSize().second << ")" << endl;
        }

        uint32 seqLen = 75;
        gnSeqC* seq = new gnSeqC[seqLen+1];
        for( uint32 i=0; i < seqLen; ++i )
                seq[i] = '@';
        seq[seqLen] = 0;

        cout << "SeqRead(0, seq, " << seqLen << ", 0)" << endl;
        if( source.SeqRead( 158, seq, seqLen, 0 ) )
        {
                seq[seqLen] = 0;
                cout << seqLen << "> " << seq << endl;
        }
        else
                cout << "Read failed " << endl;
        return 0;
}

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