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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuBlock_8hpp_source.html below:

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

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26 Block

(

int

start,

int len

int id

);

33 bool

contain(

const Block

& rhs)

const

;

34 bool

isIntersecting(

const Block

& rhs)

const

;

35 bool

intersect(

Block

& rhs)

const

;

43 int getEnd

()

const

{

return

m_start + m_len -1;}

44 void setEnd

(

int

end) { m_len = end - m_start + 1;}

45 int getId

()

const

{

return

m_id;}

46 void setId

(

int id

) {m_id = id;}

47 Block

extend (

int

nExt,

int

cExt)

const

;

48 void

extendSelf (

int

nExt,

int

cExt);

49 void

addOffset(

int

nExt);

55 bool isValid

()

const

{

return

m_len > 0 && m_start >= 0;}

76 void

addBlock(

Block

& block);

87

pair<DeltaBlockModel*, bool> intersect(

const BlockModel

)

const

;

96 void

findIntersectingBlocks(

const Block

& target, vector<int>&

result

)

const

;

100 int

getBlockNumber(

int

pos)

const

;

101 const

vector<Block>&

getBlocks

()

const

{

return

m_blocks;}

113 bool

completeModelExtendsIntoUnallowedGappedRegion(

const BlockModel

& completeModel,

int

sequenceLength,

const

vector<int>* commonBlockExt =

NULL

)

const

;

114 int

getLastAlignedPosition()

const

;

115 int

getFirstAlignedPosition()

const

;

116 int

getTotalBlockLength()

const

;

117 int

getGapToNTerminal(

int

bn)

const

;

118 int

getGapToCTerminal(

int

bn,

int len

=-1)

const

;

119 bool

isValid(

int

seqLen,

int

& errBlock)

const

;

121 void

addOffset(

int

nExt);

127 bool mask

(

const

vector<Block>& maskBlocks);

130 void

clipToRange(

unsigned int min

unsigned max

);

164 int

mapToMaster(

int

slavePos)

const

;

165 int

mapToSlave(

int

masterPos)

const

;

166 bool

isValid()

const

;

175 bool mask

(

const

vector<Block>& maskBlocks,

bool

maskBasedOnMaster);

182 void

extendMidway(

int

blockNum);

ncbi::TMaskedQueryRegions mask

const vector< Block > & getBlocks() const

CRef< CSeq_id > getSeqId() const

vector< Block > & getBlocks()

void setSeqId(CRef< CSeq_id > seqId)

bool operator<(const Block rhs) const

set< Block > SortedBlocks

string DeltaBlockModelToString(const DeltaBlockModel &dbm)

multiset< DeltaBlock > DeltaBlockModel

bool operator==(const CEquivRange &A, const CEquivRange &B)

string operator+(const CCgiEntry &e, const string &s)

CVect2< T > operator-(const CVect2< T > &v)

#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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_CDUTILS_EXPORT

static std::string toString(boost::unit_test::const_string bstr)

Int4 delta(size_t dimension_, const Int4 *score_)

bool operator<(const DeltaBlock &rhs) const

static DP_BlockInfo * blocks

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