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

80  int

num_nodes = nodes.size();

85  for

(

int i

= num_nodes - 1;

i

>= 0;

i

--) {

93  CHit

*hit1 = nodes[

i

].hit;

94  double

self_score = nodes[

i

].best_score;

95  for

(

int

j =

i

+ 1; j < num_nodes; j++) {

97  CHit

*hit2 = nodes[j].hit;

100

nodes[j].best_score + self_score > nodes[

i

].best_score) {

102

nodes[

i

].best_score = nodes[j].best_score + self_score;

103

nodes[

i

].path_next = &(nodes[j]);

110  if

(nodes[

i

].best_score > best_score) {

111

best_score = nodes[

i

].best_score;

112

best_node = &(nodes[

i

]);

152  for

(

int i

= 0;

i

< num_queries - 1;

i

++) {

154  for

(

int

j =

i

+ 1; j < num_queries; j++) {

162  while

(best_path !=

NULL

) {

186

printf(

"Saved Segments:\n"

);

189

printf(

"query %2d %3d - %3d query %2d %3d - %3d score %d\n"

,

int Size() const

Retrieve number of hits in list.

void MakeCanonical()

Sort the list in a canonical form: first swap the indices and ranges on all hits and subhits so that ...

void SetKeepHit(int index, bool keep)

Set whether a hit in the hitlist will be scheduled for deletion.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

void PurgeUnwantedHits()

Delete all hits scheduled to be deleted.

A generalized representation of a pairwise alignment.

int m_Score

Score of alignment.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

TRange m_SeqRange2

The range of offsets on the second sequence.

bool StrictlyBelow(const TThisType &r)

Test whether 'this' represents a sequence range strictly less than a given sequence range.

bool GetVerbose(void) const

Get verbose mode.

SGraphNode * x_FindBestPath(vector< SGraphNode > &nodes)

Find a maximum weight path in a directed acyclic graph.

struct CMultiAligner::SGraphNode SGraphNode

vector< CSequence > m_QueryData

void x_FindConsistentHitSubset(void)

Find consistent subset of pair-wise hits that can be used as alignment constraints.

CConstRef< CMultiAlignerOptions > m_Options

void x_FindAlignmentSubsets()

Interface for CMultiAligner.

#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.

#define INT4_MIN

Smallest (most negative) number represented by signed int.

struct SGraphNode * path_next

the optimal path node belongs to

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