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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSeqSwapper.cpp Source File

45

m_cd(cd), m_clusteringThreshold(identityThreshold), m_replacingThreshold(identityThreshold), m_ac(cd,

CCdCore

::USE_ALL_ALIGNMENT)

53

vector< vector<int> * > clusters;

55

vector< pair<int, int> > replacementPairs;

57 LOG_POST

(

"Clustering is done (made "

<< clusters.size() <<

" clusters)"

);

58 LOG_POST

(

"Find replacements by BLAST in each cluster"

);

59 for

(

unsigned int i

= 0;

< clusters.size();

++)

61

vector<int>* cluster = clusters[

];

67 LOG_POST

(

"Done with BLAST in each cluster"

);

70

vector<int> selectedNormalRows;

72 for

(

unsigned int

p = 0; p < replacementPairs.size(); p++)

80 LOG_POST

(

"replacing "

<<nid<<

" with "

<<pid);

82 if

(replacementPairs[p].

first

== 0)

83

newMaster = replacementPairs[p].second - numNormal;

86

selectedNormalRows.push_back(replacementPairs[p].

first

);

87

usedPendings.

insert

(replacementPairs[p].second - numNormal);

91 if

(structures.

size

() > 0)

93 LOG_POST

(

"Adding "

<<structures.

size

()<<

" structures"

);

95

usedPendings.

insert

(*sit - numNormal);

107

rows.push_back(newMaster);

125 double

pid = ((double)identityThreshold)/100.0;

126 double

distTh = 1.0 - pid;

128

vector<SeqTreeIterator> nodes;

130 for

(

unsigned int i

= 0;

< nodes.size();

++)

132

vector<int>* rowids =

new

vector<int>;

134

clusters.push_back(rowids);

142 if

(cluster.size() == 0)

145

vector<int> normalLocal, normalNonLocal, pending;

146 bool

hasNormalPDB =

false

;

148 for

(

unsigned int i

= 0;

< cluster.size();

++)

152

pending.push_back(cluster[

]);

155

pending3D.

insert

(cluster[

]);

163

normalLocal.push_back(cluster[

]);

166

normalNonLocal.push_back(cluster[

]);

167 if

(seqId->

IsPdb

())

168

hasNormalPDB =

true

;

173 if

((normalLocal.size() != 0) && (pending.size() != 0))

175

vector< pair<int,int> > pairs;

177 for

(

unsigned int i

= 0;

< pairs.size();

++)

179

replacementPairs.push_back(pairs[

]);

181 if

(sit != pending3D.

end

())

183

pending3D.

erase

(sit);

189

!pending3D.

empty

() &&

190

!normalNonLocal.empty())

192

vector< pair<int,int> > pairsWith3D;

193

vector<int> pending3DVec;

195

pending3DVec.push_back(*sit);

197 if

(pairsWith3D.size() > 0)

199

structs.

insert

(pairsWith3D[0].second);

206 if

((normal.size() == 0) || (pending.size() == 0))

218 for

(

int n

= 0;

< (

int

) normal.size();

++)

222 for

(

int

p = 0; p < (

int

) pending.size(); p++)

224 if

(usedPendingIndice.

find

(p) == usedPendingIndice.

end

())

234 if

( maxIdIndex >= 0)

236

usedPendingIndice.

insert

(maxIdIndex);

237

pairs.push_back(pair<int, int>(normal[

], pending[maxIdIndex]));

247 for

(

int i

= 0;

< num;

++)

255 int

masterInPending = -1;

258

masterInPending = *newMaster;

266 if

(masterInPending >= 0)

267

rows.

insert

(masterInPending);

bool IsPdb(int row) const

CRef< CSeq_align > getSeqAlign(int row) const

bool IsPending(int row) const

bool GetSeqIDForRow(int row, CRef< CSeq_id > &SeqID) const

bool EraseTheseRows(const std::vector< int > &TossRows)

bool AddSeqAlign(CRef< CSeq_align > seqAlign)

void ErasePendingRows(set< int > &rows)

void setQueryRows(const vector< int > *rows)

double getPairwiseScore(int row1, int row2)

void setScoreType(CSeq_align::EScoreType scoreType)

bool blast(NotifierFunction notifier=0)

void setSubjectRows(const vector< int > *rows)

void findBestPairings(const vector< int > &normal, const vector< int > &pending, vector< pair< int, int > > &pairs)

int m_clusteringThreshold

void makeClusters(int identityThreshold, vector< vector< int > * > &clusters)

void findReplacements(vector< int > &cluster, vector< pair< int, int > > &replacementPairs, set< int > &structs)

void promotePendingRows(set< int > &rows, int *newMaster=0)

void findStructuralPendings(set< int > &rows)

void getDistantNodes(double dist, vector< SeqTreeIterator > &nodes)

void getSequenceRowid(const iterator &node, vector< int > &selections)

double getMaxDistanceToRoot()

static SeqTree * makeTree(AlignmentCollection *alignData, const TreeOptions &treeOptions)

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

bool ReMasterCdWithoutUnifiedBlocks(CCdCore *cd, int Row, bool resetFields=true)

@ ePercentIdentityRelaxed

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

const string AsFastaString(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.

void ResetPending(void)

Reset Pending data member.

bool IsPdb(void) const

Check if variant Pdb is selected.

bool IsLocal(void) const

Check if variant Local is selected.

unsigned int

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

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