testSource.cpp Source File

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# testSource.cpp

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    00001 #include "gn/gnFASSource.h"
    00002 #include <iostream>
    00003
    00004
    00005 #include "gn/gnFilter.h"
    00006
    00007 int32 main( int32 argc, char* argv[])
    00008 {
    00009         argc; argv;
    00010
    00011         gnFASSource source;
    00012         string sourceFile = "w:/developm/_data/cft073/v6/cft073v6.fas";
    00013         cout << "Enter Source: ";
    00014         cin >> sourceFile;
    00015         cout << "Opening " << sourceFile << endl;
    00016         if( !source.Open( sourceFile ) )
    00017         {
    00018                 cout << "Failed to open " << sourceFile << endl;
    00019                 return 1;
    00020         }
    00021
    00022         cout << "Number of Contigs " << source.GetContigListLength() << endl;
    00023         for( uint32 i=0; i < source.GetContigListLength(); ++i )
    00024         {
    00025                 gnFileContig* fg = source.GetContig(i);
    00026                 cout << "\t" << fg->GetName() <<  endl;
    00027                 cout << "\t\t" << fg->GetSeqLength() << " : {"
    00028                         << fg->GetFileStartEnd().first << ", "
    00029                         << fg->GetFileStartEnd().second << ": ";
    00030                 for( uint32 j=0; j<CONTIG_SECTION_SIZE; ++j )
    00031                         cout << "(" << fg->GetSectStartEnd( (gnContigSection)j ).first << ","
    00032                                 << fg->GetSectStartEnd( (gnContigSection)j ).second << ") ";
    00033                 cout << "}" << endl;
    00034                 cout << "\t\t" << (fg->HasRepeatSeqGap()?"TRUE":"FALSE")
    00035                         << " (" << fg->GetRepeatSeqGapSize().first << ","
    00036                         << fg->GetRepeatSeqGapSize().second << ")" << endl;
    00037         }
    00038
    00039         uint32 seqLen = 75;
    00040         gnSeqC* seq = new gnSeqC[seqLen+1];
    00041         for( uint32 i=0; i < seqLen; ++i )
    00042                 seq[i] = '@';
    00043         seq[seqLen] = 0;
    00044
    00045         cout << "SeqRead(0, seq, " << seqLen << ", 0)" << endl;
    00046         if( source.SeqRead( 158, seq, seqLen, 0 ) )
    00047         {
    00048                 seq[seqLen] = 0;
    00049                 cout << seqLen << "> " << seq << endl;
    00050         }
    00051         else
    00052                 cout << "Read failed " << endl;
    00053         return 0;
    00054 }