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NCBI C++ ToolKit: src/algo/blast/format/sam.cpp Source File

& custom_spec,

sorted.

() = aln.

();

dense_seg->

().swap(scores);

d_aln.

().push_back(dense_seg);

vector<string> format_tokens;

(vector<string>, iter, format_tokens) {

void x_ProcessCustomSpec(const string &custom_spec, const CSAM_Formatter::SProgramInfo &info)

void Print(const CSeq_align_set &aln)

CBlast_SAM_Formatter(CNcbiOstream &out, CScope &scope, const string &custom_spec, const CSAM_Formatter::SProgramInfo &info)

void x_Print(const CSeq_align_set &aln)

std::ofstream out("events_result.xml")

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void SetGroupOrder(EGroupOrder go, const string &go_value=kEmptyStr)

Set GO tag value.

SProgramInfo & SetProgram(void)

void SetFlag(EFlags flag)

CSAM_Formatter & Print(const CSeq_align &aln, const CSeq_id &query_id)

void SetSortOrder(ESortOrder so, const string &so_value=kEmptyStr)

Set SO tag value.

@ eSO_Coordinate

SO:coordinate.

@ eGO_Reference

GO:reference.

@ fSAM_SeqData

Print sequence data.

@ fSAM_PlainSeqIds

Drop type prefix in seq-ids.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

Tdata & Set(void)

Assign a value to data member.

TScore & SetScore(void)

Assign a value to Score data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< CRef< CScore > > TScores

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

static CRef< CSeq_align > CreateDensegFromDendiag(CSeq_align const &aln)

static bool SortHspByMasterStartAscending(const SHspInfo *info1, const SHspInfo *info2)

Formatting of pairwise sequence alignments in SAM form.

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