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

CVecscreenRunm_Screener
 the vecscreen run instance More...
 
CScopem_Scope
 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.

Enumerator
eShowAlignments 

Show the alignments.

eShowIntervalsOnly 

Only show the contaminated intervals.

eBlastTab 

switch to a blast-tab-like fmt

eJson 

blast-tab values, but json formatted

eAsnText 

entire seq-aligns in asn text

eAsnTextNoProcess 

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

eEndValue 

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 
)
inline

Definition at line 121 of file vecscreen_run.hpp.

◆ CFormatter() [2/2]

CVecscreenRun::CFormatter::CFormatter ( const CFormatter )
private

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 )
private

Prohibit assignment operator.

◆ x_GetIdsAndTitlesForSeqAlign()

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

Member Data Documentation

◆ m_HtmlOutput

bool CVecscreenRun::CFormatter::m_HtmlOutput
private

Whether HTML output is requested or not.

Definition at line 138 of file vecscreen_run.hpp.

◆ m_Outfmt

TOutputFormat CVecscreenRun::CFormatter::m_Outfmt
private

the requested output format

Definition at line 137 of file vecscreen_run.hpp.

◆ m_Scope

CScope& CVecscreenRun::CFormatter::m_Scope
private

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
private

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 modify_doxy.py rev. 669887