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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuCdCore_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/structure/cd_utils/cuCdCore.hpp Source File

63

USE_NORMAL_ALIGNMENT=0,

74 void

SetAccession(

string

Accession,

int

Version);

75 void

SetAccession(

string

Accession);

80 bool

HasCddId(

const CCdd_id

id

)

const

;

83 string

GetLongDescription();

85 int

GetNumRows()

const

;

86 int

GetNumSequences()

const

;

87 int

GetNumRowsWithSequences()

const

;

88 int

GetAlignmentLength()

const

;

89 int

GetPSSMLength()

const

;

91 int

GetNumBlocks()

const

;

92 bool

GetCDBlockLengths(vector<int>& lengths)

const

;

93 bool

GetBlockStartsForRow(

int

rowIndex, vector<int>& starts)

const

;

96 int

GetSeqIndexForRowIndex(

int

rowIndex)

const

;

97 int

GetMasterSeqIndex()

const

;

102 int

GetAllRowIndicesForSeqId(

const CRef<CSeq_id>

& SeqID, list<int>& rows)

const

;

103 int

GetAllRowIndicesForSeqId(

const CRef<CSeq_id>

& SeqID, vector<int>& rows)

const

;

107 bool

GetGI(

int

Row,

TGi

& GI,

bool

ignorePDBs =

true

);

111 bool

Get_GI_or_PDB_String_FromAlignment(

int

RowIndex,

std::string

& Str,

bool

Pad,

int Len

)

const

;

113 string

GetSpeciesForRow(

int

Row);

114 string

GetSequenceStringByRow(

int

rowId);

120 TGi

GetGIFromSequenceList(

int

SeqIndex)

const

;

121 string

GetDefline(

int

SeqIndex)

const

;

123 string

GetSequenceStringByIndex(

int

SeqIndex);

124 string

GetSpeciesForIndex(

int

SeqIndex);

137 bool

HasSeqId(

const CRef<CSeq_id>

& ID,

int

& RowIndex)

const

;

140 bool

GetSeqIDForRow(

int

Pair,

int

DenDiagRow,

CRef<CSeq_id>

& SeqID)

const

;

141 bool

GetSeqIDFromAlignment(

int

RowIndex,

CRef<CSeq_id>

& SeqID)

const

;

148 bool

GetSeqIDForIndex(

int

SeqIndex,

CRef<CSeq_id>

& SeqID)

const

;

150 const

list< CRef< CSeq_id > >& GetSeqIDs(

int

SeqIndex)

const

;

153 bool

EraseOtherRows(

const

std::vector<int>& KeepRows);

154 bool

EraseTheseRows(

const

std::vector<int>& TossRows);

155 void

EraseSequence(

int

SeqIndex);

156 void

EraseSequences();

157 void

ErasePendingRows(

set<int>

& rows);

158 void

ErasePendingRow(

int row

);

161 bool

Has3DMaster()

const

;

162 int

Num3DAlignments()

const

;

163 bool

GetRowsForMmdbId(

int

mmdbId, list<int>& rows)

const

;

164 bool

GetRowsWithMmdbId(vector<int>& rows)

const

;

165 bool

GetMmdbId(

int

SeqIndex,

int

id

)

const

;

175 bool

SynchronizeMaster3D(

bool

checkRow1WhenConsensusMaster =

true

);

181 int

MapPositionToOtherRow(

int

thisRow,

int

thisPos,

int

otherRow)

const

;

186 bool

IsSeqAligns()

const

;

190 const

list< CRef< CSeq_align > >& GetSeqAligns()

const

;

191

list< CRef< CSeq_align > >& GetSeqAligns();

196 bool

UsesConsensusSequenceAsMaster()

const

;

197 bool

HasConsensusSequence()

const

;

198 int

GetRowsWithConsensus(vector<int>& consensusRows)

const

;

199 bool

FindConsensusInSequenceList(vector<int>* indices =

NULL

)

const

;

218 bool

AddOthername(

const string

& othername);

219 bool AddTitle

(

const string

& title);

221 bool AddSource

(

const string

source

bool

removeExistingSources =

true

);

222 bool

AddCreateDate();

230 unsigned int

GetTitles(vector<string>& titles)

const

;

233 bool

RemoveCddDescrsOfType(

int

cddDescrChoice);

237 bool

AllResiduesInRangeAligned(

int

rowId,

int

from,

int

to)

const

;

238 bool

AlignAnnotsValid(

string

* err =

NULL

)

const

;

239 int

GetNumAlignmentAnnotations();

240 string

GetAlignmentAnnotationDescription(

int

Index);

244 bool

GetClassicalParentId(

const CCdd_id

*& parentId)

const

;

245 string

GetClassicalParentAccession(

int

& Version)

const

;

246 string

GetClassicalParentAccession()

const

;

CCdCore(const CCdCore &value)

size_t GetNumPending() const

CCdCore & operator=(const CCdCore &value)

int GetLowerBound(const CRef< CSeq_align > &seqAlign, bool onMaster)

int GetUpperBound(const CRef< CSeq_align > &seqAlign, bool onMaster)

const int PENDING_ROW_START

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

#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.

#define NCBI_CDUTILS_EXPORT

const TPending & GetPending(void) const

Get the Pending member data.

CRef< CDate_std > GetUpdateDate(string_view str, Parser::ESource source)

void AddComment(CSeq_feat &feat, const string &comment)

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

#define row(bind, expected)

static CRef< CSeqdesc > AddSource(CRef< CSeq_entry > entry, string taxname)

static void AddTitle(CRef< CSeq_entry > entry, string defline)

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