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MAl_addon Class Reference

#include <MAl_addon.h>

Collaboration diagram for MAl_addon:

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List of all members.

Public Member Functions

 MAl_addon (MAl *m)
 ~MAl_addon ()
int get_min_col ()
int get_max_col ()
int get_num_rows ()
char get_most_freq_base_on_col (int col)
int get_num_bases_on_col (int col, char base)
size_t get_num_DNPs_on_col (int col)
char get_entry (int row, int col)
int get_qual (int row, int col)
void set_DNP (int row, int col, bool status, int dnpID, int type)
bool is_DNP (int row, int col)
int get_row_start (int row)
int get_row_end (int row)

Private Attributes

MAl * mal
size_t min_col
size_t max_col
map< char, int > base_index
vector< char > index_base
vector< cons_struct > consensus

Classes

struct  cons_struct

Detailed Description

Definition at line 8 of file MAl_addon.h.

Constructor & Destructor Documentation

MAl_addon::MAl_addon (  MAl *  m  ) 
 

Definition at line 7 of file MAl_addon.cc.

References base_index, consensus, MAl_Readonly::get_base_global(), MAl_Readonly::get_beginGood_global(), MAl_Readonly::get_endGood_global(), MAl_Readonly::get_num_seq(), index_base, is_DNP(), mal, max_col, and min_col.

00007                              : mal(m)
00008 {
00009   //Base index stuff
00010   base_index[ 'a' ] = 0;
00011   index_base.push_back('a');
00012   
00013   base_index[ 't' ] = 1;
00014   index_base.push_back('t');
00015 
00016   base_index[ 'g' ] = 2;
00017   index_base.push_back('g');
00018 
00019   base_index[ 'c' ] = 3;
00020   index_base.push_back('c');
00021   
00022   base_index[ '-' ] = 4;
00023   index_base.push_back('-');
00024 
00025   base_index[ '*' ] = 5;
00026   index_base.push_back('*');
00027 
00028   base_index[ 'x' ] = 6;
00029   index_base.push_back('x');
00030 
00031   base_index[ 'n' ] = 7;
00032   index_base.push_back('n');
00033 
00034   //Min and max col, and bookeeping of cons
00035   min_col = numeric_limits<size_t>::max();
00036   max_col = 0;
00037   
00038   for( size_t i = 0; i < mal->get_num_seq(); i++ ) {
00039     if (mal->get_beginGood_global( i ) < min_col ) {
00040       min_col = mal->get_beginGood_global( i );
00041     }
00042     if (mal->get_endGood_global( i ) > max_col ) {
00043       max_col = mal->get_endGood_global( i );
00044     }
00045     
00046     if ( max_col > consensus.size() ) {
00047 
00048       for( size_t j = consensus.size(); j < max_col; j++ ) {
00049         consensus.push_back( cons_struct() );      
00050       }
00051 
00052     }
00053 //     cerr<<"i: "<<i<<endl;
00054 //     cerr<<"mal->get_beginGood_global( i ): "<<mal->get_beginGood_global( i )<<endl;
00055 //     cerr<<"mal->get_endGood_global( i ): "<<mal->get_endGood_global( i )<<endl;
00056 //     cerr<<"mal->get_seq_begin_global( i ): "<<mal->get_seq_begin_global( i )<<endl;
00057 //     cerr<<"mal->get_seq_end_global( i ): "<<mal->get_seq_end_global( i )<<endl;
00058     for( size_t j = mal->get_beginGood_global( i ); 
00059          j < mal->get_endGood_global( i ); j++ ) {
00060       
00061 
00062       assert( base_index[ mal->get_base_global(i,j) ] < 8 );
00063 
00064       consensus[ j ].num[ base_index[ mal->get_base_global(i,j) ] ]++;
00065       if ( is_DNP(i, j) ) {
00066         consensus[ j ].num_DNPs++;
00067       }
00068       
00069     }
00070     
00071   }
00072   assert( max_col == consensus.size() );
00073   
00074 
00075   //Set cons bases
00076   for( size_t i = min_col; i < consensus.size(); i++ ) {
00077     int max(0);
00078 
00079     for( size_t j = 0; j < 8; j++ ) {
00080       if ( consensus[ i ].num[ j ] > max ) {
00081         max = consensus[ i ].num[ j ];
00082         consensus[ i ].cons = index_base[ j ];
00083       }
00084 
00085     }
00086     assert( max > 0 );
00087     
00088   }
00089 
00090 }

MAl_addon::~MAl_addon (   ) 
 

Definition at line 91 of file MAl_addon.cc.

00092 {
00093   
00094 }

Member Function Documentation

char MAl_addon::get_entry (  int  row,
int  col
) 
 

Definition at line 126 of file MAl_addon.cc.

References MAl_Readonly::get_base_global(), and mal.

Referenced by DNPclass::pick_base_row_and_qual_columns(), and DNPclass::set_DNPs().

00127 {
00128   return mal->get_base_global( row, col );
00129 }

int MAl_addon::get_max_col (   ) 
 

Definition at line 101 of file MAl_addon.cc.

References max_col.

Referenced by DNPclass::evaluate_DNP_candidate_positions(), DNPclass::find_DNP_candidate_positions(), and ConsAlgo::start().

00102 {
00103   return max_col;
00104 }

int MAl_addon::get_min_col (   ) 
 

Definition at line 96 of file MAl_addon.cc.

References min_col.

Referenced by DNPclass::find_DNP_candidate_positions(), and ConsAlgo::start().

00097 {
00098   return min_col;
00099 }

char MAl_addon::get_most_freq_base_on_col (  int  col  ) 
 

Definition at line 111 of file MAl_addon.cc.

References consensus.

Referenced by DNPclass::column_is_candidate(), and ConsAlgo::start().

00112 {
00113   return consensus[ col ].cons;
00114 }

int MAl_addon::get_num_bases_on_col (  int  col,
char  base
) 
 

Definition at line 116 of file MAl_addon.cc.

References base_index, and consensus.

Referenced by DNPclass::column_is_candidate().

00117 {
00118   return consensus[ col ].num[ base_index[ base ] ];
00119 }

size_t MAl_addon::get_num_DNPs_on_col (  int  col  ) 
 

Definition at line 121 of file MAl_addon.cc.

References consensus.

Referenced by ConsAlgo::start().

00122 {
00123   return consensus[ col ].num_DNPs;
00124 }

int MAl_addon::get_num_rows (   ) 
 

Definition at line 106 of file MAl_addon.cc.

References MAl_Readonly::get_num_seq(), and mal.

Referenced by DNPclass::pick_base_row_and_qual_columns().

00107 {
00108   return mal->get_num_seq();
00109 }

int MAl_addon::get_qual (  int  row,
int  col
) 
 

Definition at line 131 of file MAl_addon.cc.

References MAl_Readonly::get_qual_global(), and mal.

Referenced by DNPclass::pick_base_row_and_qual_columns(), and DNPclass::set_DNPs().

00132 {
00133   return mal->get_qual_global( row, col );  
00134 }

int MAl_addon::get_row_end (  int  row  ) 
 

Definition at line 153 of file MAl_addon.cc.

References MAl_Readonly::get_endGood_global(), and mal.

Referenced by DNPclass::pick_base_row_and_qual_columns().

00154 {
00155   return mal->get_endGood_global( row );
00156 }

int MAl_addon::get_row_start (  int  row  ) 
 

Definition at line 148 of file MAl_addon.cc.

References MAl_Readonly::get_beginGood_global(), and mal.

Referenced by DNPclass::pick_base_row_and_qual_columns().

00149 {
00150   return mal->get_beginGood_global( row );
00151 }

bool MAl_addon::is_DNP (  int  row,
int  col
) 
 

Definition at line 143 of file MAl_addon.cc.

References MAl_Readonly::is_DNP_global(), and mal.

Referenced by MAl_addon(), and DNPclass::set_DNPs().

00144 {
00145   return mal->is_DNP_global( row, col );
00146 }

void MAl_addon::set_DNP (  int  row,
int  col,
bool  status,
int  dnpID,
int  type
) 
 

Definition at line 137 of file MAl_addon.cc.

References mal, MAl::set_DNP_global(), MAl::set_DNP_ID_global(), and MAl::set_DNP_type_global().

Referenced by DNPclass::set_DNPs().

00138 {
00139   mal->set_DNP_global( row, col, status );
00140   mal->set_DNP_ID_global( row, col, dnpID );
00141   mal->set_DNP_type_global( row, col, type );
00142 }

Member Data Documentation

map<char, int> MAl_addon::base_index [private]
 

Definition at line 48 of file MAl_addon.h.

Referenced by get_num_bases_on_col(), and MAl_addon().

vector<cons_struct> MAl_addon::consensus [private]
 

Definition at line 50 of file MAl_addon.h.

Referenced by get_most_freq_base_on_col(), get_num_bases_on_col(), get_num_DNPs_on_col(), and MAl_addon().

vector<char> MAl_addon::index_base [private]
 

Definition at line 49 of file MAl_addon.h.

Referenced by MAl_addon().

MAl* MAl_addon::mal [private]
 

Definition at line 45 of file MAl_addon.h.

Referenced by get_entry(), get_num_rows(), get_qual(), get_row_end(), get_row_start(), is_DNP(), MAl_addon(), and set_DNP().

size_t MAl_addon::max_col [private]
 

Definition at line 47 of file MAl_addon.h.

Referenced by get_max_col(), and MAl_addon().

size_t MAl_addon::min_col [private]
 

Definition at line 46 of file MAl_addon.h.

Referenced by get_min_col(), and MAl_addon().

The documentation for this class was generated from the following files:
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