libAMOS: msgtest.cc Source File

00001 #include "foundation_AMOS.hh" 00002 #include <fstream> 00003 #include <ctime> 00004 using namespace std; 00005 using namespace AMOS; 00006 00007 #define ITERS 500000 00008 00009 int main (int argc, char ** argv) 00010 { 00011 Message_t msg; 00012 Read_t red; 00013 Contig_t ctg; 00014 00015 double loopa = 0; 00016 double loopb = 0; 00017 clock_t clocka, clockb; 00018 00019 vector<Tile_t> tlevec; 00020 Tile_t tle; 00021 00022 tle . source = 33396; 00023 tle . offset = 512; 00024 tle . range = Range_t (12,832); 00025 tle . gaps . push_back (12); 00026 tle . gaps . push_back (30); 00027 tle . gaps . push_back (337); 00028 tle . gaps . push_back (508); 00029 tle . gaps . push_back (514); 00030 tle . gaps . push_back (789); 00031 00032 for ( int j = 0; j < 200; j ++ ) 00033 tlevec . push_back (tle); 00034 00035 try { 00036 00037 red . setIID (1); 00038 red . setEID ("str2"); 00039 red . setComment ("GBRAA01TF"); 00040 red . setSequence 00041 ("CCTTTGTGCTGGAAGGTGAATGCGGTGCGGCTGGTAACGGGCCGCGCGGGCGCAATCGGCGTCGTGATGGGCCGCAACAGCGAGTTTCACTTTGCCGAATTCATGCGCGGCATGGCCGAACGGCTGGGGCAGGACGAAGTGGACATTCTCGTCAGCCCCACCTCGCCGACCGGCAATGACGACGAGGTGCAGCTTTGTCACCGGCTGGCAACGAGCGGACGGGTGGATGCCGTTATCGTCACTTCCCCCAGGCCGAATGATGAACGCATCCGCATGTTGCACAAGCTCGGCATGCCGTTTCTGGTCCACGGGCGTTCGCAGATCGACATTCCCCATGCATGGCTTGATATCGACAATGAGAGCGCGGTCTATCATTCCACCGCACATCTGCTCGATCTTGGCCACAAGCGGATTGCGATGATCAACGGGCGCCATGGCTTCACCTTCTCGCTGCACCGCGACGCTGGCTATCGTAAGGCGCTTGAAAGCCGGGGAATCGACTTTGATCCCGACCTGGTGGAACATGGCGATTTCACCGATGAAATCGGCTATTGCCTCGCCCGCAAGCTTCTGGAACGCAATCCACGTCCAACGGCATTCGTCGCAGGCTCCATGATGACCGCGCTCGGCATCTACCGTGCCGCCCGCTCCTTCGGCCTTACGATCGGCAAGGATATTTCCGTCATCGCCCATGACGACGTGATCTCGTTCCTCAGCGCCGGTAATATGGGTGCCGTCGCTGACTGCGACACGCTCTTCAATGCGCGCGGCTGGCAAGCGATGCGCCGACCTTTTGATGGATATCCTCGATGGGCGCGCGCCCACCGAAATCCA", 00042 "9878<?JQONBB77:=EGMPDOHRNSTSTSTRSSSREMRSSRSSRSQSSLQLLLLMPPPRRSSSRRRRSSSRSSSRRSRRRRSRIJJJONLTTTTRRROLLLLLLTTTTTTTRRRRPPPSRRSTTTRSRRRSPOLOOLOSSSSRSSRSRPRPPPSPSTSTSQSQTRURSSSSSTTTTRRRSRRSRSSSURRRRSWSSRRRSSTSRRTTTTTTTTTPPSRPPSTTTTRSRUSSSSUSPPPPRSQRTTTTSSSRRRRRTRRSTRTTTRTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTPSPPPPPRRRTTTTTRSSSSRRSRRSTSTTTTTTTTRTTRSSSTRSRSRRSSSTTTRSSRSSSUSSQSSRSSSSRRRRRSRRTRTSRTSURTTTTTRSSSSSSTRTRRRSSRSSRTSPSPPPRTRRSSRRSTRRRSSRRRRTTTRRRUSRSSSTRSSSSRRLLLLOLNOTTTSRRRRSSSTTTTTTTTTTTWRRPPPPPPSTTTTWPPMSTPTTTTTTTTSTSRSRSSTTRSSSSTTTTTTTTPPPPKPPSRSSSTSSSSTSSRRSSSTTTTTRRSSTTSSRSSSSSTTTTTTTTTTTRTTTSRSSSSSTTTTRRRSSPPSPPPTTTTSRRPORSRPPPPLPPSSSSTTSSRSSSRPPNSSQRTTTTTSSPKKGMNPSSQSSRSSSSQLLIL?HSTQPSSPLRSQSSRSUQSMRSSUPRLLPGEPPSNMRPTYRRQPMMGGPMLQE?CENRNCRSLQRNTTKTKLQTXSRSRTTPRQXISRCONK<?IDTPPPDDIR?B<LALBDL@;LQQLCH?E=@IC<9F9?I;9;=8"); 00043 red . setFragment (1); 00044 red . setClearRange (Range_t(16,823)); 00045 red . setVectorClearRange (Range_t(16,823)); 00046 red . setQualityClearRange (Range_t(16,823)); 00047 00048 ctg . setIID (1); 00049 ctg . setEID ("str2"); 00050 ctg . setComment ("big contig"); 00051 00052 ctg . setSequence 00053 ("CCTTTGTGCTGGAAGGTGAATGCGGTGCGGCTGGTAACGGGCCGCGCGGGCGCAATCGGCGTCGTGATGGGCCGCAACAGCGAGTTTCACTTTGCCGAATTCATGCGCGGCATGGCCGAACGGCTGGGGCAGGACGAAGTGGACATTCTCGTCAGCCCCACCTCGCCGACCGGCAATGACGACGAGGTGCAGCTTTGTCACCGGCTGGCAACGAGCGGACGGGTGGATGCCGTTATCGTCACTTCCCCCAGGCCGAATGATGAACGCATCCGCATGTTGCACAAGCTCGGCATGCCGTTTCTGGTCCACGGGCGTTCGCAGATCGACATTCCCCATGCATGGCTTGATATCGACAATGAGAGCGCGGTCTATCATTCCACCGCACATCTGCTCGATCTTGGCCACAAGCGGATTGCGATGATCAACGGGCGCCATGGCTTCACCTTCTCGCTGCACCGCGACGCTGGCTATCGTAAGGCGCTTGAAAGCCGGGGAATCGACTTTGATCCCGACCTGGTGGAACATGGCGATTTCACCGATGAAATCGGCTATTGCCTCGCCCGCAAGCTTCTGGAACGCAATCCACGTCCAACGGCATTCGTCGCAGGCTCCATGATGACCGCGCTCGGCATCTACCGTGCCGCCCGCTCCTTCGGCCTTACGATCGGCAAGGATATTTCCGTCATCGCCCATGACGACGTGATCTCGTTCCTCAGCGCCGGTAATATGGGTGCCGTCGCTGACTGCGACACGCTCTTCAATGCGCGCGGCTGGCAAGCGATGCGCCGACCTTTTGATGGATATCCTCGATGGGCGCGCGCCCACCGAAATCCA", 00054 "9878<?JQONBB77:=EGMPDOHRNSTSTSTRSSSREMRSSRSSRSQSSLQLLLLMPPPRRSSSRRRRSSSRSSSRRSRRRRSRIJJJONLTTTTRRROLLLLLLTTTTTTTRRRRPPPSRRSTTTRSRRRSPOLOOLOSSSSRSSRSRPRPPPSPSTSTSQSQTRURSSSSSTTTTRRRSRRSRSSSURRRRSWSSRRRSSTSRRTTTTTTTTTPPSRPPSTTTTRSRUSSSSUSPPPPRSQRTTTTSSSRRRRRTRRSTRTTTRTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTPSPPPPPRRRTTTTTRSSSSRRSRRSTSTTTTTTTTRTTRSSSTRSRSRRSSSTTTRSSRSSSUSSQSSRSSSSRRRRRSRRTRTSRTSURTTTTTRSSSSSSTRTRRRSSRSSRTSPSPPPRTRRSSRRSTRRRSSRRRRTTTRRRUSRSSSTRSSSSRRLLLLOLNOTTTSRRRRSSSTTTTTTTTTTTWRRPPPPPPSTTTTWPPMSTPTTTTTTTTSTSRSRSSTTRSSSSTTTTTTTTPPPPKPPSRSSSTSSSSTSSRRSSSTTTTTRRSSTTSSRSSSSSTTTTTTTTTTTRTTTSRSSSSSTTTTRRRSSPPSPPPTTTTSRRPORSRPPPPLPPSSSSTTSSRSSSRPPNSSQRTTTTTSSPKKGMNPSSQSSRSSSSQLLIL?HSTQPSSPLRSQSSRSUQSMRSSUPRLLPGEPPSNMRPTYRRQPMMGGPMLQE?CENRNCRSLQRNTTKTKLQTXSRSRTTPRQXISRCONK<?IDTPPPDDIR?B<LALBDL@;LQQLCH?E=@IC<9F9?I;9;=8"); 00055 ctg . setReadTiling (tlevec); 00056 00057 clocka = clock( ); 00058 for ( int i = 0; i < ITERS; i ++ ) 00059 red . writeMessage (msg); 00060 clockb = clock( ); 00061 loopa = (double)(clockb - clocka); 00062 00063 clocka = clock( ); 00064 for ( int i = 0; i < ITERS; i ++ ) 00065 red . readMessage (msg); 00066 clockb = clock( ); 00067 loopb = (double)(clockb - clocka); 00068 00069 msg . setField ("eid", "hello"); 00070 msg . setField ("bla", "foo"); 00071 msg . write (cerr); 00072 00073 Message_t::const_iterator mi; 00074 cerr << "\nField List\n"; 00075 for ( mi = msg . begin( ); mi != msg . end( ); ++ mi ) 00076 cerr << Decode (mi -> first) << endl; 00077 00078 cerr << endl 00079 << "loopa: " << (double)loopa / CLOCKS_PER_SEC << " sec.\n" 00080 << "loopb: " << (double)loopb / CLOCKS_PER_SEC << " sec.\n" 00081 << "granu: " << CLOCKS_PER_SEC << " of a sec.\n"; 00082 } 00083 catch (Exception_t & e) { 00084 cerr << "ERROR: exception\n" << e; 00085 } 00086 00087 return 0; 00088 }