NCBI C++ ToolKit
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CVecscreenRun::CFormatter Class Reference

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The Vecscreen formatter. More...

#include <algo/blast/format/vecscreen_run.hpp>

+ Collaboration diagram for CVecscreenRun::CFormatter:

Public Types

enum  EOutputFormat {
  eShowAlignments = 0 , eShowIntervalsOnly = 1 , eBlastTab = 2 , eJson = 3 ,
  eAsnText = 4 , eAsnTextNoProcess = 5 , eEndValue
 Controls the output formats supported by command line VecScreen. More...
typedef int TOutputFormat

Public Member Functions

 CFormatter (CVecscreenRun &vs, CScope &scope, TOutputFormat fmt=eShowAlignments, bool html_output=true)
void FormatResults (CNcbiOstream &out, CRef< blast::CBlastOptionsHandle > vs_opts)
 Format the VecScreen results. More...

Private Member Functions

 CFormatter (const CFormatter &)
 Prohibit copy constructor. More...
CFormatteroperator= (const CFormatter &)
 Prohibit assignment operator. More...
void x_GetIdsAndTitlesForSeqAlign (const objects::CSeq_align &align, string &qid, string &qtitle, string &sid, string &stitle)

Private Attributes

 the vecscreen run instance More...
 from which we get the sequence data More...
TOutputFormat m_Outfmt
 the requested output format More...
bool m_HtmlOutput
 Whether HTML output is requested or not. More...

Detailed Description

The Vecscreen formatter.

Definition at line 106 of file vecscreen_run.hpp.

Member Typedef Documentation

◆ TOutputFormat

Definition at line 119 of file vecscreen_run.hpp.

Member Enumeration Documentation

◆ EOutputFormat

Controls the output formats supported by command line VecScreen.


Show the alignments.


Only show the contaminated intervals.


switch to a blast-tab-like fmt


blast-tab values, but json formatted


entire seq-aligns in asn text


entire seq-aligns in asn text, the raw blast hits without post-processing


Sentinel value, not an actual output format.

Definition at line 110 of file vecscreen_run.hpp.

Constructor & Destructor Documentation

◆ CFormatter() [1/2]

CVecscreenRun::CFormatter::CFormatter ( CVecscreenRun vs,
CScope scope,
TOutputFormat  fmt = eShowAlignments,
bool  html_output = true 

Definition at line 121 of file vecscreen_run.hpp.

◆ CFormatter() [2/2]

CVecscreenRun::CFormatter::CFormatter ( const CFormatter )

Prohibit copy constructor.

Member Function Documentation

◆ FormatResults()

void CVecscreenRun::CFormatter::FormatResults ( CNcbiOstream out,
CRef< blast::CBlastOptionsHandle >  vs_opts 

◆ operator=()

CFormatter& CVecscreenRun::CFormatter::operator= ( const CFormatter )

Prohibit assignment operator.

◆ x_GetIdsAndTitlesForSeqAlign()

void CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign ( const objects::CSeq_align &  align,
string qid,
string qtitle,
string sid,
string stitle 

Member Data Documentation

◆ m_HtmlOutput

bool CVecscreenRun::CFormatter::m_HtmlOutput

Whether HTML output is requested or not.

Definition at line 138 of file vecscreen_run.hpp.

◆ m_Outfmt

TOutputFormat CVecscreenRun::CFormatter::m_Outfmt

the requested output format

Definition at line 137 of file vecscreen_run.hpp.

◆ m_Scope

CScope& CVecscreenRun::CFormatter::m_Scope

from which we get the sequence data

Definition at line 136 of file vecscreen_run.hpp.

Referenced by x_GetIdsAndTitlesForSeqAlign().

◆ m_Screener

CVecscreenRun& CVecscreenRun::CFormatter::m_Screener

the vecscreen run instance

Definition at line 135 of file vecscreen_run.hpp.

The documentation for this class was generated from the following files:
Modified on Sat May 18 11:36:03 2024 by rev. 669887