testSource.cpp Source File

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 }