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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__sort_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/align/util/align_sort.hpp Source File

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1 #ifndef GPIPE_COMMON___ALIGN_SORT__HPP 2 #define GPIPE_COMMON___ALIGN_SORT__HPP 55  const string

&tmp_path =

"/tmp"

,

56  size_t

memory_limit = 0,

61  typedef

pair<string, double>

TItem

;

80  void

MergeSortedFiles(

const

vector<string> &input_files,

82  bool

remove_input_files =

false

,

83  bool

filtered =

false

);

94 

{

return

m_Extractor.count; }

126  return

predicate(k2.first, k1.first);

virtual size_t GetCountProcessed() const =0

virtual size_t GetCountEmitted() const =0

virtual ~IAlignSortedOutput()

virtual void Write(const TAlignment &aln)=0

SAlignExtractor m_Extractor

void SortAlignments(const list< CRef< objects::CSeq_align > > &aligns, list< CRef< objects::CSeq_align > > &sorted)

Utility function for sorting alignments whern all alignments are in-core.

deque< TAlignment > TAlignments

CRef< CAlignFilter > m_Filter

void SortAlignments(const vector< CRef< objects::CSeq_align > > &aligns, vector< CRef< objects::CSeq_align > > &sorted)

pair< SSortKey, CRef< CSeq_align > > TAlignment

size_t NumProcessed() const

pair< TAlignment, size_t > SKeyAndFile

SSortKey_Less m_Predicate

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void Start(void)

Start the timer.

#define NCBI_XALGOALIGN_EXPORT

Defines: CTimeFormat - storage class for time format.

SPQSort(const SSortKey_Less &sk)

vector< ESortDir > sort_dirs

pair< string, double > TItem

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