Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/traceback_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/traceback.cpp Source File

(m_Script.empty()) {

(last_op.

== op_type) {

(

= tback_range.

();

<= tback_range.

();

++) {

(tback[

]) {

TScriptOps::iterator itr(

.begin());

(link_start + itr->num_ops > tback_range.

())

link_start += itr->num_ops;

curr_tback = tback_range.

();

curr_tback <= tback_range.

()) {

num_ops =

(tback_range.

() - curr_tback + 1,

link_start + itr->num_ops - curr_tback);

new_script.

(itr->op_type, num_ops);

curr_tback += num_ops;

link_start += itr->num_ops;

go_past_seq1_gap)

q = start_offsets.first;

s = start_offsets.second;

TScriptOps::iterator itr(

.begin());

(s + itr->num_ops > seq2_target) {

(go_past_seq1_gap ==

) {

q--; s--; curr_tback--;

curr_tback += itr->num_ops;

curr_tback += itr->num_ops;

(s + itr->num_ops > seq2_target) {

curr_tback += seq2_target - s;

q += seq2_target - s;

curr_tback += itr->num_ops;

curr_tback += itr->num_ops;

new_offsets.first = q;

new_offsets.second = s;

new_tback = curr_tback;

go_past_seq2_gap)

q = start_offsets.first;

s = start_offsets.second;

TScriptOps::iterator itr(

.begin());

curr_tback += itr->num_ops;

(q + itr->num_ops > seq1_target) {

curr_tback += seq1_target - q;

s += seq1_target - q;

curr_tback += itr->num_ops;

(q + itr->num_ops > seq1_target) {

(go_past_seq2_gap ==

) {

q--; s--; curr_tback--;

curr_tback += itr->num_ops;

curr_tback += itr->num_ops;

new_offsets.first = q;

new_offsets.second = s;

new_tback = curr_tback;

**seq2_pssm,

gap_open,

gap_extend)

q = start_offsets.first;

s = start_offsets.second;

TScriptOps::iterator itr(

.begin());

(link_start + itr->num_ops > tback_range.

())

(itr->op_type) {

link_start += itr->num_ops;

(itr->op_type) {

s += tback_range.

() - link_start;

s += tback_range.

() - link_start;

q += tback_range.

() - link_start;

q += tback_range.

() - link_start;

curr_tback <= tback_range.

()) {

num_ops =

(tback_range.

() - curr_tback + 1,

link_start + itr->num_ops - curr_tback);

(itr->op_type) {

score += gap_open + num_ops * gap_extend;

(

= 0;

< num_ops;

++) {

score += seq2_pssm[s +

][c];

score += gap_open + num_ops * gap_extend;

curr_tback += num_ops;

link_start += itr->num_ops;

vector<TOffsetPair> region_list;

q = start_offsets.first;

s = start_offsets.second;

TScriptOps::iterator itr(

.begin());

(itr->op_type) {

int TOffset

Basic data type for offsets into a sequence.

pair< TOffset, TOffset > TOffsetPair

Basic type specifying a range on a sequence.

Interface for the traceback from blast hits.

void VerifyScript(TRange seq1_range, TRange seq2_range)

Validate that the alignment described by the CEditScript has the same size for each sequence as the i...

int GetScore(TRange tback_range, TOffsetPair start_offsets, CSequence &seq1, int **seq2_pssm, int gap_open, int gap_extend)

Compute the score associated with (a portion of) an alignment Assumes that seq1 is a sequence and tha...

void FindOffsetFromSeq2(TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq2_target, TOffset &new_tback, bool go_past_seq1_gap)

Given a subject offset, find the corresponding query offset.

TScriptOps m_Script

The list of edit operations in the current edit script.

CEditScript()

Generate empty traceback.

void FindOffsetFromSeq1(TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq1_target, TOffset &new_tback, bool go_past_seq2_gap)

Given a query offset, find the corresponding subject offset.

CEditScript MakeEditScript(TRange tback_range)

Return an edit script corresponding to a subset of the complete traceback available.

vector< TOffsetPair > ListMatchRegions(TOffsetPair start_offsets)

Compile a list of regions in the current edit script that contain substitutions.

void AddOps(EGapAlignOpType op_type, int num_ops)

Add a new edit operation to the current list.

Class for representing protein sequences.

unsigned char GetLetter(int pos) const

Access the sequence letter at a specified position.

EGapAlignOpType

Operation types within the edit script.

@ eGapAlignIns

Insertion: a gap in subject.

@ eGapAlignSub

Substitution.

@ eGapAlignDel

Deletion: a gap in query.

vector< ETranscriptSymbol > TTranscript

int TSignedSeqPos

Type for signed sequence position.

int32_t Int4

4-byte (32-bit) signed integer

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

TLen GetLen(void) const

Get the Len member data.

vector< TSignedSeqPos > TStarts

TDim GetDim(void) const

Get the Dim member data.

TDim GetDim(void) const

Get the Dim member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

unsigned int

A callback function used to compare two keys in a database.

Runlength-encoded representation of a traceback operation.

int num_ops

number of such operations

EGapAlignOpType op_type

type of operation

Edit script: linked list of correspondencies between two sequences.

Int4 * num

Array of number of operations.

Int4 size

Size of above arrays.

EGapAlignOpType * op_type

Array of type of operation.

Interface for CEditScript class.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4