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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/segmask_8cpp_source.html below:

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

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47  throw

runtime_error(

"Failed to allocate SegParameters structure"

);

63  if

( !

data

.IsProtein() ) {

64  throw

logic_error(

"SEG can only filter protein sequences"

);

68  throw

logic_error(

"SEG expects protein sequences in ncbistdaa format"

);

76  static_cast<Int4>

(sequence.size()), 0,

81  throw

runtime_error(

"SEG internal error (check that input is protein) "

+

NStr::IntToString

(status));

84

unique_ptr<TMaskList> retval(

new TMaskList

);

92  return

retval.release();

BLAST filtering functions.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

Int2 SeqBufferSeg(Uint1 *sequence, Int4 length, Int4 offset, SegParameters *sparamsp, BlastSeqLoc **seg_locs)

Runs seg on a protein sequence in ncbistdaa.

SegParameters * SegParametersNewAa(void)

Allocated SeqParameter struct for proteins and fills with default values.

void SegParametersFree(SegParameters *sparamsp)

Free SegParameters structure.

TMaskList * operator()(const objects::CSeqVector &data)

Function performing the actual dusting.

struct SegParameters * m_SegParameters

Parameters to SEG algorithm.

vector< pair< TSeqPos, TSeqPos > > TMaskList

Type representing a list of masked segments.

CSegMasker(int window=kSegWindow, double locut=kSegLocut, double hicut=kSegHicut)

Object constructor.

~CSegMasker()

Object destructor.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ e_Ncbistdaa

consecutive codes for std aas

double value_type

The numeric datatype used by the parser.

Used to hold a set of positions, mostly used for filtering.

struct BlastSeqLoc * next

next in linked list

Int4 window

initial window size to trigger further work.

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