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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuAlignmentCollection_8hpp_source.html below:

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

1 #ifndef CU_ALIGNMENT_COLLECTION_HPP 2 #define CU_ALIGNMENT_COLLECTION_HPP 27 void

AddSequence(

CCdCore

* cd);

32 void clear

() {m_firstCd = 0; m_seqAligns.clear(); m_rowSources.clear();}

34 int

GetNumRows()

const

;

35 int

GetNumPendingRows()

const

;

36 int

GetAlignmentLength(

int row

=0)

const

;

40 string

GetDefline(

int row

)

const

;

41 bool

GetGI(

int row

TGi

& gi,

bool

ignorePDBs =

true

)

const

;

45 bool

IsPending(

int row

)

const

;

46 bool

wasMaster(

int row

)

const

;

47 void

removeRowSourcesForCD(

CCdCore

* cd);

48 void

addRowSources(

const

vector<int>& rows,

CCdCore

* cd,

bool

scoped=

true

);

54 int

getCDs(vector<CCdCore*>& cds);

56 int

getCDsInScope(vector<CCdCore*>& cds);

58 int

getCDsOutofScope(vector<CCdCore*>& cds);

59 bool

isCDInScope(

CCdCore

* cd)

const

;

60 bool

isRowInScope(

int row

)

const

;

61 CCdCore

* GetLeafDescendentCD(

int row

bool

includeSelf=

false

)

const

;

63 CCdCore

* GetSeniorMemberCD(

int row

bool

scopedOnly=

true

)

const

;

64 void

convertFromCDRows(

CCdCore

* cd,

const

vector<int>& cdRows,

set<int>

& colRows)

const

;

65 void

convertToCDRows(

const

vector<int>& colRows,

CDRowsMap

& cdRows)

const

;

68 void

getAllRowsForCD(

CCdCore

* cd, vector<int>& colRows)

const

;

69 bool

GetSpeciesForRow(

int row

string

& species)

const

;

71 int

GetRowsWithSameSeqID(

int

rowToMatch, vector<int>& rows,

bool

inclusive =

true

)

const

;

72 int

GetRowsWithSeqID(

const CRef< CSeq_id >

& SeqID, vector<int>& rows)

const

;

73 bool

IsStruct(

int row

);

74 bool

IsPdb(

int row

)

const

;

75 void

GetAllSequences(vector<string>& sequences);

76 string

GetSequenceForRow(

int row

);

77 void

GetAlignedResiduesForRow(

int row

char

*&);

78 void

GetAlignedResiduesForAll(

char

** & ppAlignedResidues,

bool

forceRecompute) ;

80 void

getNormalRowsNotInChild(vector<int>& childless,

bool

excludeMaster=

false

)

const

;

85 bool

AreNonOverlapping()

const

;

105 void

addPendingAlignment(

CCdCore

* cd,

bool

uniqueSeqId=

false

bool

scoped=

true

);

106 void

addNormalAlignment(

CCdCore

* cd,

bool

uniqueSeqId=

false

bool

scoped=

true

);

118 bool

setAlignment(

const CDFamily

& family);

120 void

setAlignment(

CCdCore

* cd,

bool

scoped=

true

);

123 bool

isBlockAligned()

const

;

126 bool

findParentalEquivalent(

const

cd_utils::BlockModel& bar,

int

& pRow,

bool

inputAsChild=

true

)

const

;

127 bool

findParentalCastible(

const

cd_utils::BlockModel& bar,

int

& pRow)

const

;

128 bool

locateChildRow(

const

cd_utils::BlockModel& childRow,

int

& pRow)

const

;

129 const

cd_utils::BlockModel& getBlockModel(

int row

)

const

;

131 bool

transferToCD(

CCdCore

* cd =0);

139 void

makeBlockTable();

int getNumFamilies() const

vector< CRef< CBioseq > > m_bioseqs

RowSourceTable m_rowSources

CRef< CSeq_align > getSeqAlign(int row) const

const RowSourceTable & GetRowSourceTable() const

void setNumFamilies(int num)

CCdCore * getFirstCD() const

vector< CRef< CSeq_align > > m_seqAligns

void AddAlignment(CCdCore *cd, CCdCore::AlignmentUsage alignUse)

vector< cd_utils::BlockModel > m_blockTable

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

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

#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

#define row(bind, expected)

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