src/algo/align/nw/nw_spliced_aligner16.cpp File Reference

#include <ncbi_pch.hpp>
#include "messages.hpp"
#include <algo/align/nw/nw_spliced_aligner16.hpp>
#include <algo/align/nw/align_exception.hpp>

Include dependency graph for nw_spliced_aligner16.cpp:

Go to the source code of this file.

Defines

#define NW_NDON_EVAL(st_idx)
#define NW_SIG_EVAL(st_idx)
#define NW_DON_EVAL(st_idx)

Functions

const unsigned char g_topidx (splice_type_count_16-1)

Variables

const unsigned char g_nwspl_donor [splice_type_count_16][2]
const unsigned short g_nwspl_donor_16 [splice_type_count_16]
 16-bit donor table
const unsigned char g_nwspl_acceptor [splice_type_count_16][2]
const unsigned short g_nwspl_acceptor_16 [splice_type_count_16]
const unsigned char kMaskFc = 0x01
const unsigned char kMaskEc = 0x02
const unsigned char kMaskE = 0x04
const unsigned char kMaskD = 0x08

Define Documentation

#define NW_DON_EVAL (  st_idx   ) 
 

Value:

if( (v1 == g_nwspl_donor_16[st_idx]) &&  \
                        (V > vBestDonor[st_idx])){  \
                        size_t tl = jTail[st_idx]++; \
                        jAllDonors[st_idx][tl] = j; \
                        vAllDonors[st_idx][tl] = V; \
                    } \

#define NW_NDON_EVAL (  st_idx   ) 
 

Value:

{ \
                size_t jt = jTail[st_idx]; \
                size_t jh = jHead[st_idx]; \
                if ((jt > jh) && \
                    (j - jAllDonors[st_idx][jh] >= m_IntronMinSize))  { \
                                                                        \
                    if (vAllDonors[st_idx][jh] > vBestDonor[st_idx]) {  \
                        vBestDonor[st_idx] = vAllDonors[st_idx][jh];    \
                        jBestDonor[st_idx] = jAllDonors[st_idx][jh];    \
                    } \
            ++jHead[st_idx]; \
                } \
                }

#define NW_SIG_EVAL (  st_idx   ) 
 

Value:

v_best_d = vBestDonor[st_idx]; \
                    if ((v1 == g_nwspl_acceptor_16[st_idx]) && \
                        (v_best_d > kInfMinus)) \
                    { \
                        vAcc = v_best_d + m_Wi[st_idx]; \
                        if (vAcc > V) { \
                            V = vAcc; intron_length = j - jBestDonor[st_idx]; \
                        } \
                    }

Function Documentation

const unsigned char @0::g_topidx (  splice_type_count_16-  1  )  [static]
 

Variable Documentation

const unsigned char g_nwspl_acceptor[splice_type_count_16][2] [static]
 

Initial value:

 {
        {'A','G'}, {'A','G'}, {'A','C'}, {'?','?'}
    }

Definition at line 57 of file nw_spliced_aligner16.cpp.

const unsigned short g_nwspl_acceptor_16[splice_type_count_16] [static]
 

Initial value:

 {
        ('A' << 8) | 'G',  
        ('A' << 8) | 'G',  
        ('A' << 8) | 'C',  
        ('?' << 8) | '?'   
    }

Definition at line 61 of file nw_spliced_aligner16.cpp.

const unsigned char g_nwspl_donor[splice_type_count_16][2] [static]
 

Initial value:

 {
        {'G','T'}, {'G','C'}, {'A','T'}, {'?','?'}
    }

Definition at line 45 of file nw_spliced_aligner16.cpp.

const unsigned short g_nwspl_donor_16[splice_type_count_16] [static]
 

Initial value:

 {
        ('G' << 8) | 'T',   
        ('G' << 8) | 'C',   
        ('A' << 8) | 'T',   
        ('?' << 8) | '?'    
    }
16-bit donor table

Definition at line 50 of file nw_spliced_aligner16.cpp.

const unsigned char kMaskD = 0x08
 

Definition at line 792 of file nw_spliced_aligner16.cpp.

const unsigned char kMaskE = 0x04
 

Definition at line 791 of file nw_spliced_aligner16.cpp.

const unsigned char kMaskEc = 0x02
 

Definition at line 790 of file nw_spliced_aligner16.cpp.

const unsigned char kMaskFc = 0x01
 

Definition at line 789 of file nw_spliced_aligner16.cpp.

Generated on Wed Dec 9 07:41:00 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:18:29 2009 by modify_doxy.py rev. 173732