#include <realigneralgo.h>
Inheritance diagram for RealignerAlgo:
Public Member Functions | |
| RealignerAlgo (TrapperDoc *pDoc_, std::set< db_recno_t > &recnoList, AlgoParam *param) | |
| void | start () |
Definition at line 6 of file realigneralgo.h.
|
||||||||||||||||
|
Definition at line 9 of file realigneralgo.h. 00009 : 00010 RWAlgo(pDoc_, recnoList, param) {}
|
|
|
Implements RWAlgo. Definition at line 24 of file realigneralgo.cc. References RWAlgo::getMAl(). 00025 { 00026 bool debug_update = false; 00027 bool debug_alignment = false; 00028 bool draw = false; 00029 int type = 1; 00030 00031 // important parameters 00032 int bandSize = 8; 00033 double a_koeff = 0.5; 00034 00035 // create a realigner 00036 00037 al::Realigner<LayAlCont, alphabet> rea; 00038 00039 // initialize the realigner with bandSize, a_koeff an other things 00040 00041 rea.init_div(bandSize, debug_update, debug_alignment, type, draw, a_koeff); 00042 00043 00044 // construct and initialize the wrapper with the mal object 00045 00046 LayAlCont la(getMAl()); 00047 00048 // read alignment from stdin (doesn't work with MalWrapper) 00049 // al::read_layout_alignment<al::dna_alphabet>(la, cin); 00050 00051 // register the wrapped mal object in the realigner 00052 00053 std::pair<bool, bool> set_la_ok = rea.set_la(la); 00054 00055 // ofstream ut("alignment.my"); 00056 // // write alignment to stdout 00057 // al::write_layout_alignment<al::dna_alphabet>(la, ut); 00058 // cerr << "Written file!" << endl; 00059 00060 // do the actual realigning 00061 00062 // timer t0; 00063 00064 if (set_la_ok.first) { 00065 // t0.restart(); 00066 rea.realign_loop(); 00067 00068 // cerr << "realign_loop(): " << t0.elapsed() << "seconds" << endl; 00069 00070 } 00071 00072 }
|
1.4.4