CShowBlastDefline Class Reference

Search Toolkit Book for CShowBlastDefline

#include <showdefline.hpp>

Inheritance diagram for CShowBlastDefline:

[legend]Collaboration diagram for CShowBlastDefline:

[legend]List of all members.

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Detailed Description

This class displays the defline for BLAST result.

Example:

 int defline_option = 0;
 defline_option += CShowBlastDefline::eShowGi;
 defline_option += CShowBlastDefline::eHtml;
 .......
 CShowBlastDefline sbd(aln_set, scope);   
 sbd.SetRid(rid);

 sbd.SetOption(defline_option);
 sbd.DisplayBlastDefline(out);

Definition at line 65 of file showdefline.hpp.

Public Types
typedef map< string, PsiblastSeqStatus >	TIdString2SeqStatus
	Map of sequence IDs to PSI-BLAST sequence status.
enum	DisplayOption {   eHtml = (1 << 0), eLinkout = (1 << 1), eShowGi = (1 << 2), eCheckbox = (1 << 3),   eShowSumN = (1 << 4), eCheckboxChecked = (1 << 5), eNoShowHeader = (1 << 6), eNewTargetWindow = (1 << 7),   eShowNewSeqGif = (1 << 8), eShowPercentIdent = (1 << 9) }
	Display options. More...
enum	PsiblastSeqStatus { eUnknown = (0 << 0), eGoodSeq = (1 << 0), eCheckedSeq = (1 << 1), eRepeatSeq = (1 << 2) }
	PSI-BLAST sequence status (applicable in HTML only). More...
enum	PsiblastStatus { eFirstPass = 0, eRepeatPass, eNewPass }
	PSI-BLAST defline groupings. More...
Public Member Functions
	CShowBlastDefline (const objects::CSeq_align_set &seqalign, objects::CScope &scope, size_t line_length=65, size_t deflines_to_show=kDfltArgNumDescriptions, bool translated_nuc_alignment=false, CRange< TSeqPos > *master_range=NULL)
	Constructors.
	~CShowBlastDefline ()
void	SetOption (int option)
	options per DisplayOption
void	SetupPsiblast (TIdString2SeqStatus *seq_status=NULL, PsiblastStatus status=eFirstPass)
	Set psiblast specific options.
void	SetImagePath (string path)
	Set path to html images.
void	SetQueryNumber (int number)
	Set this for linking to mapviewer.
void	SetNumAlignToShow (int num)
	Display top num seqalign.
void	SetEntrezTerm (string term)
	Set this for constructing structure linkout.
void	SetRid (string rid)
	Set blast request id.
void	SetCddRid (string cdd_rid)
	Set this for constructing structure linkout.
void	SetDbType (bool is_na)
	Set this for constructing seqid url.
void	SetDbName (string database)
	Set this for constructing seqid url.
void	SetBlastType (string type)
	Set this for proper construction of seqid url.
void	SetCgiContext (CCgiContext &ctx)
void	DisplayBlastDefline (CNcbiOstream &out)
	Display defline.
void	DisplayBlastDeflineTable (CNcbiOstream &out)
void	Init (void)
	Initialize defline params.
void	Display (CNcbiOstream &out)
	Display defline.
bool	HasStructureLinkout (void)
	Indicates if 'Related structures' link should show.
vector< CShowBlastDefline::SDeflineInfo * >	GetDeflineInfo (vector< CConstRef< objects::CSeq_id > > &seqIds)
	Get defline info for the set of seqIds.
Static Public Member Functions
static string	GetSeqIdListString (const list< CRef< objects::CSeq_id > > &id, bool show_gi)
	Creates a '|' delimited string, corresponding to a list of Seq-ids.
static void	GetSeqIdList (const objects::CBioseq_Handle &bh, list< CRef< objects::CSeq_id > > &ids)
	Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references, substituting an artificial gnl|BL_ORD_ID identifier by a corresponding first token of the title.
static void	GetBioseqHandleDeflineAndId (const objects::CBioseq_Handle &handle, list< int > &use_this_gi, string &seqid, string &defline, bool show_gi=true, int this_gi_first=-1)
	Returns sequence id and a BLAST defline as strings, given a Bioseq handle and a list of gis.
Protected Member Functions
SScoreInfo *	x_GetScoreInfo (const objects::CSeq_align &aln, int blast_rank)
	Internal function to return score info.
SScoreInfo *	x_GetScoreInfoForTable (const objects::CSeq_align_set &aln, int blast_rank)
	Internal function to return score info.
SDeflineInfo *	x_GetDeflineInfo (CConstRef< objects::CSeq_id > id, list< int > &use_this_gi, int blast_rank)
	Internal function to return defline info.
SDeflineInfo *	x_GetHitDeflineInfo (const objects::CSeq_align_set &aln)
	Internal function to return defline info.
bool	x_CheckForStructureLink ()
	Checks the first X deflines (currently X is 200) for a structure link.
void	x_FillDeflineAndId (const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< int > &use_this_gi, SDeflineInfo *sdl, int blast_rank)
	Internal function to fill defline info.
void	x_InitDefline (void)
	Initialize defline params for regular output.
void	x_InitDeflineTable (void)
	Initialize defline params for table output.
void	x_DisplayDefline (CNcbiOstream &out)
	Display defline for regular output.
void	x_DisplayDeflineTable (CNcbiOstream &out)
	Display defline for table output.
Protected Attributes
CConstRef< objects::CSeq_align_set >	m_AlnSetRef
	Seqalign.
string	m_Database
	Database name.
CRef< objects::CScope >	m_ScopeRef
	Scope to fetch sequence.
size_t	m_LineLen
	Line length.
size_t	m_NumToShow
	Number of seqalign hits to show.
int	m_Option
	Display options.
list< SScoreInfo * >	m_ScoreList
	List containing score info for all seqalign.
string	m_BlastType
	Blast type.
string	m_ImagePath
	Gif images path.
auto_ptr< CNcbiIfstream >	m_ConfigFile
	Internal configure file, i.e. .ncbirc.
auto_ptr< CNcbiRegistry >	m_Reg
int	m_QueryNumber
	query number
string	m_EntrezTerm
	entrez term
string	m_Rid
	blast request id
string	m_CddRid
	cdd blast request id
bool	m_IsDbNa
PsiblastStatus	m_PsiblastStatus
TIdString2SeqStatus *	m_SeqStatus
	hash table to track psiblast status for each sequence
bool	m_TranslatedNucAlignment
	used to calculate the alignment length
size_t	m_MaxScoreLen
	Score header size.
size_t	m_MaxEvalueLen
	Eval header size.
size_t	m_MaxSumNLen
size_t	m_MaxTotalScoreLen
	Total score header size.
size_t	m_MaxPercentIdentityLen
size_t	m_MaxQueryCoverLen
int	m_QueryLength
bool	m_StructureLinkout
	Indicates if 'Related structures' link should show.
CRange< TSeqPos > *	m_MasterRange
	blast sub-sequnce query
CCgiContext *	m_Ctx
Friends
struct	::CShowBlastDeflineTest
Classes
struct	SDeflineInfo
	Data Representing each defline. More...
struct	SScoreInfo
	Internal data with score information for each defline. More...

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Member Typedef Documentation

typedef map<string, PsiblastSeqStatus> CShowBlastDefline::TIdString2SeqStatus

Map of sequence IDs to PSI-BLAST sequence status. Definition at line 134 of file showdefline.hpp.

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Member Enumeration Documentation

enum CShowBlastDefline::DisplayOption

Display options. Enumerator: eHtml  eLinkout  eShowGi  eCheckbox  eShowSumN  eCheckboxChecked  eNoShowHeader  eNewTargetWindow  eShowNewSeqGif  eShowPercentIdent  Definition at line 85 of file showdefline.hpp.

enum CShowBlastDefline::PsiblastSeqStatus

PSI-BLAST sequence status (applicable in HTML only). Enumerator: eUnknown  Uninitialized. eGoodSeq  above the threshold evalue eCheckedSeq  user checked eRepeatSeq  previously already found Definition at line 119 of file showdefline.hpp.

enum CShowBlastDefline::PsiblastStatus

PSI-BLAST defline groupings. Enumerator: eFirstPass  First pass. Default. eRepeatPass  Sequences were found in previous pass. eNewPass  Sequences are newly found in current pass. Definition at line 127 of file showdefline.hpp.

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Constructor & Destructor Documentation

CShowBlastDefline::CShowBlastDefline (  const objects::CSeq_align_set &  seqalign, objects::CScope &  scope, size_t  line_length = 65, size_t  deflines_to_show = kDfltArgNumDescriptions, bool  translated_nuc_alignment = false, CRange< TSeqPos > *  master_range = NULL )

Constructors. Parameters: seqalign,:  input seqalign scope,:  scope to fetch sequences line_length,:  length of defline desired deflines_to_show,:  number of seqalign hits to show

CShowBlastDefline::~CShowBlastDefline (   )

Definition at line 563 of file showdefline.cpp. References ITERATE, and m_ScoreList.

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Member Function Documentation

void CShowBlastDefline::Display (  CNcbiOstream &  out  )

Display defline. Parameters: out,:  stream to output Definition at line 585 of file showdefline.cpp. References CCgiContext::GetRequestValue(), CCgiEntry::GetValue(), kEmptyStr, m_Ctx, NStr::ToLower(), x_DisplayDefline(), and x_DisplayDeflineTable().

void CShowBlastDefline::DisplayBlastDefline (  CNcbiOstream &  out  )

Display defline. Parameters: out,:  stream to output Definition at line 869 of file showdefline.cpp. References buf, kStructure_Overview, m_CddRid, m_EntrezTerm, m_Rid, m_StructureLinkout, NcbiEmptyString, x_DisplayDefline(), and x_InitDefline(). Referenced by CBlastFormat::x_DisplayDeflines().

void CShowBlastDefline::DisplayBlastDeflineTable (  CNcbiOstream &  out  )

Definition at line 1377 of file showdefline.cpp. References buf, kStructure_Overview, m_CddRid, m_EntrezTerm, m_Rid, m_StructureLinkout, NcbiEmptyString, x_DisplayDeflineTable(), and x_InitDeflineTable().

static void CShowBlastDefline::GetBioseqHandleDeflineAndId (  const objects::CBioseq_Handle &  handle, list< int > &  use_this_gi, string &  seqid, string &  defline, bool  show_gi = true, int  this_gi_first = -1 )  [static]

Returns sequence id and a BLAST defline as strings, given a Bioseq handle and a list of gis. to use. Does not need an object. Parameters: handle  Bioseq handle to retrieve data from [in] use_this_gi  List of gis to use in the defline. All will be used if the list is empty. [in] seqid  Seq-id string, combining all Seq-ids from the first defline. defline  Defline string, combining all deflines in case of redundant sequences. show_gi  Should gi Seq-ids be included? [in] this_gi_first,:  if not -1, sort the return value if necessary so that the first element in the list is the requested gi Referenced by s_SeqAlignToXMLHit().

vector<CShowBlastDefline::SDeflineInfo*> CShowBlastDefline::GetDeflineInfo (  vector< CConstRef< objects::CSeq_id > > &  seqIds  )

Get defline info for the set of seqIds. Parameters: seqIds,:  vector of CConstRef<objects::CSeq_id> Returns: : vector of SDeflineInfo

void CShowBlastDefline::GetSeqIdList (  const objects::CBioseq_Handle &  bh, list< CRef< objects::CSeq_id > > &  ids )  [static]

Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references, substituting an artificial gnl|BL_ORD_ID identifier by a corresponding first token of the title. Parameters: bh  Bioseq handle [in] ids  list of Seq-ids from this Bioseq handle. [out] Definition at line 245 of file showdefline.cpp. References GetTitle(), ITERATE, NcbiEmptyString, and NStr::Tokenize().

string CShowBlastDefline::GetSeqIdListString (  const list< CRef< objects::CSeq_id > > &  id, bool  show_gi )  [static]

Creates a '|' delimited string, corresponding to a list of Seq-ids. Parameters: id  List of Seq-ids [in] show_gi  Should gi ids be shown or skipped? Returns: Corresponding string. Definition at line 223 of file showdefline.cpp. References CSeq_id::eContent, ITERATE, and NcbiEmptyString. Referenced by s_GetSeqIdListString().

bool CShowBlastDefline::HasStructureLinkout (  void   )  [inline]

Indicates if 'Related structures' link should show. Returns: : true if show Definition at line 262 of file showdefline.hpp.

void CShowBlastDefline::Init (  void   )

Initialize defline params. Definition at line 571 of file showdefline.cpp. References CCgiContext::GetRequestValue(), CCgiEntry::GetValue(), kEmptyStr, m_Ctx, NStr::ToLower(), x_InitDefline(), and x_InitDeflineTable().

void CShowBlastDefline::SetBlastType (  string  type  )  [inline]

Set this for proper construction of seqid url. Parameters: type,:  refer to blobj->adm->trace->created_by Definition at line 204 of file showdefline.hpp.

void CShowBlastDefline::SetCddRid (  string  cdd_rid  )  [inline]

Set this for constructing structure linkout. Parameters: cdd_rid,:  cdd request id Definition at line 183 of file showdefline.hpp.

void CShowBlastDefline::SetCgiContext (  CCgiContext &  ctx  )  [inline]

Definition at line 208 of file showdefline.hpp.

void CShowBlastDefline::SetDbName (  string  database  )  [inline]

Set this for constructing seqid url. Parameters: database,:  name of the database Definition at line 197 of file showdefline.hpp.

void CShowBlastDefline::SetDbType (  bool  is_na  )  [inline]

Set this for constructing seqid url. Parameters: is_na,:  nucleotide or protein database? Definition at line 190 of file showdefline.hpp.

void CShowBlastDefline::SetEntrezTerm (  string  term  )  [inline]

Set this for constructing structure linkout. Parameters: term,:  entrez query term Definition at line 169 of file showdefline.hpp.

void CShowBlastDefline::SetImagePath (  string  path  )  [inline]

Set path to html images. Parameters: path,:  i.e. "mypath/". internal defaul current dir if this function is not called Definition at line 150 of file showdefline.hpp.

void CShowBlastDefline::SetNumAlignToShow (  int  num  )  [inline]

Display top num seqalign. Parameters: num,:  number desired Definition at line 162 of file showdefline.hpp.

void CShowBlastDefline::SetOption (  int  option  )  [inline]

options per DisplayOption Parameters: option,:  input option using bit numbers defined in DisplayOption Definition at line 114 of file showdefline.hpp. Referenced by CShowBlastDeflineTest::GetDeflineInfo().

void CShowBlastDefline::SetQueryNumber (  int  number  )  [inline]

Set this for linking to mapviewer. Parameters: number,:  the query number Definition at line 156 of file showdefline.hpp.

void CShowBlastDefline::SetRid (  string  rid  )  [inline]

Set blast request id. Parameters: rid,:  blast request id Definition at line 176 of file showdefline.hpp.

void CShowBlastDefline::SetupPsiblast (  TIdString2SeqStatus *  seq_status = NULL, PsiblastStatus  status = eFirstPass )  [inline]

Set psiblast specific options. Parameters: seq_status,:  the hash table containing status for each sequence. The key contains id only (no type tag) status,:  status for this round of search Definition at line 140 of file showdefline.hpp. Referenced by CBlastFormat::x_DisplayDeflines().

bool CShowBlastDefline::x_CheckForStructureLink (   )  [protected]

Checks the first X deflines (currently X is 200) for a structure link. If one is not found there it is assumed one is not in the results. If one is found we exit right away. We do this so we can fetch most of the Bioseqs for large results as we format. Returns: true if structure link present, false if not. Definition at line 598 of file showdefline.cpp. References eStructure, CAlignFormatUtil::GetBlastDefline(), ITERATE, m_ScopeRef, and m_ScoreList.

void CShowBlastDefline::x_DisplayDefline (  CNcbiOstream &  out  )  [protected]

Display defline for regular output. Definition at line 694 of file showdefline.cpp. References CAlignFormatUtil::AddSpace(), buf, eCheckbox, eCheckboxChecked, eFirstPass, CConstRef< C, Locker >::Empty(), eNewPass, eNoShowHeader, eRepeatPass, eShowGi, eShowNewSeqGif, eShowSumN, CSeq_align_Base::eType_global, CShowBlastDefline::SDeflineInfo::gi, CShowBlastDefline::SDeflineInfo::id, CShowBlastDefline::SDeflineInfo::id_url, NStr::IntToString(), CShowBlastDefline::SDeflineInfo::is_new, ITERATE, kBits, kE, kEllipsis, kHeader, kN, kNewSeqHeader, kOneSpaceMargin, kPsiblastCheckbox, kPsiblastCheckboxChecked, kPsiblastCheckedBackgroundGif, kPsiblastCheckedGif, kPsiblastEvalueLink, kPsiblastNewSeqBackgroundGif, kPsiblastNewSeqGif, kRepeatHeader, kScore, kTwoSpaceMargin, kValue, m_AlnSetRef, m_LineLen, m_MaxEvalueLen, m_MaxScoreLen, m_Option, m_PsiblastStatus, m_ScoreList, NcbiEmptyString, CShowBlastDefline::SDeflineInfo::was_checked, and x_GetDeflineInfo(). Referenced by Display(), and DisplayBlastDefline().

void CShowBlastDefline::x_DisplayDeflineTable (  CNcbiOstream &  out  )  [protected]

Display defline for table output. ??? Definition at line 1025 of file showdefline.cpp. References CAlignFormatUtil::AddSpace(), buf, CAlignFormatUtil::BuildFormatQueryString(), map_checker< std::map< Key, T, Compare > >::clear(), eCheckbox, eCheckboxChecked, CSeq_id::eContent, CAlignFormatUtil::eEvalue, eFirstPass, CAlignFormatUtil::eGenomicFirst, eGenomicSeq, CAlignFormatUtil::eHighestScore, CAlignFormatUtil::eHspEvalue, CAlignFormatUtil::eHspPercentIdentity, CConstRef< C, Locker >::Empty(), CAlignFormatUtil::eNonGenomicFirst, eNoShowHeader, CAlignFormatUtil::ePercentIdentity, CAlignFormatUtil::eQueryCoverage, eRepeatPass, CAlignFormatUtil::eScore, eShowGi, eShowNewSeqGif, eShowPercentIdent, CAlignFormatUtil::eTotalScore, CCgiContext::GetRequestValue(), CShowBlastDefline::SDeflineInfo::gi, CHTMLHelper::HTMLEncode(), CShowBlastDefline::SDeflineInfo::id, CShowBlastDefline::SDeflineInfo::id_url, map_checker< std::map< Key, T, Compare > >::insert(), NStr::IntToString(), CShowBlastDefline::SDeflineInfo::is_new, CAlignFormatUtil::IsMixedDatabase(), ITERATE, kCoverage, kEvalue, kHeader, kIdentity, kMaxScore, kN, kOneSpaceMargin, kPsiblastCheckbox, kPsiblastCheckboxChecked, kPsiblastCheckedBackgroundGif, kPsiblastCheckedGif, kPsiblastEvalueLink, kPsiblastNewSeqBackgroundGif, kPsiblastNewSeqGif, kTotalScore, CShowBlastDefline::SDeflineInfo::linkout, m_AlnSetRef, m_Ctx, m_IsDbNa, m_MaxEvalueLen, m_MaxPercentIdentityLen, m_MaxQueryCoverLen, m_MaxScoreLen, m_MaxSumNLen, m_MaxTotalScoreLen, m_Option, m_PsiblastStatus, m_QueryLength, m_ScopeRef, m_ScoreList, NcbiEmptyString, s_DisplayDescrColumnHeader(), size, NStr::StringToInt(), CShowBlastDefline::SDeflineInfo::was_checked, and x_GetDeflineInfo(). Referenced by Display(), and DisplayBlastDeflineTable().

void CShowBlastDefline::x_FillDeflineAndId (  const objects::CBioseq_Handle &  handle, const objects::CSeq_id &  aln_id, list< int > &  use_this_gi, SDeflineInfo *  sdl, int  blast_rank )  [protected]

Internal function to fill defline info. Parameters: handle,:  sequence handle for current seqalign aln_id,:  seqid from current seqalign use_this_gi,:  gi from use_this_gi in seqalign sdl,:  this is where is info is filled to

SDeflineInfo* CShowBlastDefline::x_GetDeflineInfo (  CConstRef< objects::CSeq_id >  id, list< int > &  use_this_gi, int  blast_rank )  [protected]

Internal function to return defline info. Parameters: id,:  seq-id we are working with [in] use_this_gi,:  list of GI's to limit formatting by [in] Returns: defline info Referenced by CShowBlastDeflineTest::GetDeflineInfo(), x_DisplayDefline(), and x_DisplayDeflineTable().

SDeflineInfo* CShowBlastDefline::x_GetHitDeflineInfo (  const objects::CSeq_align_set &  aln  )  [protected]

Internal function to return defline info. Parameters: aln,:  seqalign we are working on Returns: defline info

SScoreInfo* CShowBlastDefline::x_GetScoreInfo (  const objects::CSeq_align &  aln, int  blast_rank )  [protected]

Internal function to return score info. Parameters: aln  seq-align we are working with [in] blast_rank  ordinal nubmer of defline [in] Returns: score info Referenced by CShowBlastDeflineTest::GetDeflineInfo(), and x_InitDefline().

SScoreInfo* CShowBlastDefline::x_GetScoreInfoForTable (  const objects::CSeq_align_set &  aln, int  blast_rank )  [protected]

Internal function to return score info. Parameters: aln  seq-align-set we are working with [in] blast_rank  ordinal nubmer of defline [in] Returns: score info Referenced by x_InitDeflineTable().

void CShowBlastDefline::x_InitDefline (  void   )  [protected]

Initialize defline params for regular output. Definition at line 633 of file showdefline.cpp. References _ASSERT, CShowBlastDefline::SScoreInfo::evalue_string, CBioseq_Handle::GetBioseqCore(), NStr::IntToString(), kBits, kValue, m_AlnSetRef, m_ConfigFile, m_MaxEvalueLen, m_MaxScoreLen, m_MaxSumNLen, m_NumToShow, m_Option, m_Reg, m_ScopeRef, m_ScoreList, auto_ptr< X >::reset(), and x_GetScoreInfo(). Referenced by DisplayBlastDefline(), and Init().

void CShowBlastDefline::x_InitDeflineTable (  void   )  [protected]

Initialize defline params for table output. Definition at line 920 of file showdefline.cpp. References COpenRange< Position >::GetLength(), NStr::IntToString(), kCoverage, kIdentity, kMaxScore, kTotal, kValue, m_AlnSetRef, m_ConfigFile, m_MasterRange, m_MaxEvalueLen, m_MaxPercentIdentityLen, m_MaxQueryCoverLen, m_MaxScoreLen, m_MaxSumNLen, m_MaxTotalScoreLen, m_NumToShow, m_Option, m_QueryLength, m_Reg, m_ScopeRef, m_ScoreList, auto_ptr< X >::reset(), size, CShowBlastDefline::SScoreInfo::total_bit_string, and x_GetScoreInfoForTable(). Referenced by DisplayBlastDeflineTable(), and Init().

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Friends And Related Function Documentation

friend struct ::CShowBlastDeflineTest [friend]

Definition at line 416 of file showdefline.hpp.

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Member Data Documentation

CConstRef<objects::CSeq_align_set> CShowBlastDefline::m_AlnSetRef [protected]

Seqalign. Definition at line 287 of file showdefline.hpp. Referenced by x_DisplayDefline(), x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

string CShowBlastDefline::m_BlastType [protected]

Blast type. Definition at line 308 of file showdefline.hpp.

string CShowBlastDefline::m_CddRid [protected]

cdd blast request id Definition at line 327 of file showdefline.hpp. Referenced by DisplayBlastDefline(), and DisplayBlastDeflineTable().

auto_ptr<CNcbiIfstream> CShowBlastDefline::m_ConfigFile [protected]

Internal configure file, i.e. .ncbirc. Definition at line 314 of file showdefline.hpp. Referenced by x_InitDefline(), and x_InitDeflineTable().

CCgiContext* CShowBlastDefline::m_Ctx [protected]

Definition at line 357 of file showdefline.hpp. Referenced by Display(), Init(), and x_DisplayDeflineTable().

string CShowBlastDefline::m_Database [protected]

Database name. Definition at line 290 of file showdefline.hpp.

string CShowBlastDefline::m_EntrezTerm [protected]

entrez term Definition at line 321 of file showdefline.hpp. Referenced by DisplayBlastDefline(), and DisplayBlastDeflineTable().

string CShowBlastDefline::m_ImagePath [protected]

Gif images path. Definition at line 311 of file showdefline.hpp.

bool CShowBlastDefline::m_IsDbNa [protected]

Definition at line 329 of file showdefline.hpp. Referenced by x_DisplayDeflineTable().

size_t CShowBlastDefline::m_LineLen [protected]

Line length. Definition at line 296 of file showdefline.hpp. Referenced by x_DisplayDefline().

CRange<TSeqPos>* CShowBlastDefline::m_MasterRange [protected]

blast sub-sequnce query Definition at line 355 of file showdefline.hpp. Referenced by x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxEvalueLen [protected]

Eval header size. Definition at line 341 of file showdefline.hpp. Referenced by x_DisplayDefline(), x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxPercentIdentityLen [protected]

Definition at line 346 of file showdefline.hpp. Referenced by x_DisplayDeflineTable(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxQueryCoverLen [protected]

Definition at line 348 of file showdefline.hpp. Referenced by x_DisplayDeflineTable(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxScoreLen [protected]

Score header size. Definition at line 339 of file showdefline.hpp. Referenced by x_DisplayDefline(), x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxSumNLen [protected]

Definition at line 342 of file showdefline.hpp. Referenced by x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_MaxTotalScoreLen [protected]

Total score header size. Definition at line 344 of file showdefline.hpp. Referenced by x_DisplayDeflineTable(), and x_InitDeflineTable().

size_t CShowBlastDefline::m_NumToShow [protected]

Number of seqalign hits to show. Definition at line 299 of file showdefline.hpp. Referenced by x_InitDefline(), and x_InitDeflineTable().

int CShowBlastDefline::m_Option [protected]

Display options. Definition at line 302 of file showdefline.hpp. Referenced by x_DisplayDefline(), x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

PsiblastStatus CShowBlastDefline::m_PsiblastStatus [protected]

Definition at line 330 of file showdefline.hpp. Referenced by x_DisplayDefline(), and x_DisplayDeflineTable().

int CShowBlastDefline::m_QueryLength [protected]

Definition at line 350 of file showdefline.hpp. Referenced by x_DisplayDeflineTable(), and x_InitDeflineTable().

int CShowBlastDefline::m_QueryNumber [protected]

query number Definition at line 318 of file showdefline.hpp.

auto_ptr<CNcbiRegistry> CShowBlastDefline::m_Reg [protected]

Definition at line 315 of file showdefline.hpp. Referenced by x_InitDefline(), and x_InitDeflineTable().

string CShowBlastDefline::m_Rid [protected]

blast request id Definition at line 324 of file showdefline.hpp. Referenced by DisplayBlastDefline(), and DisplayBlastDeflineTable().

CRef<objects::CScope> CShowBlastDefline::m_ScopeRef [protected]

Scope to fetch sequence. Definition at line 293 of file showdefline.hpp. Referenced by x_CheckForStructureLink(), x_DisplayDeflineTable(), x_InitDefline(), and x_InitDeflineTable().

list<SScoreInfo*> CShowBlastDefline::m_ScoreList [protected]

List containing score info for all seqalign. Definition at line 305 of file showdefline.hpp. Referenced by x_CheckForStructureLink(), x_DisplayDefline(), x_DisplayDeflineTable(), x_InitDefline(), x_InitDeflineTable(), and ~CShowBlastDefline().

TIdString2SeqStatus* CShowBlastDefline::m_SeqStatus [protected]

hash table to track psiblast status for each sequence Definition at line 333 of file showdefline.hpp.

bool CShowBlastDefline::m_StructureLinkout [protected]

Indicates if 'Related structures' link should show. Definition at line 352 of file showdefline.hpp. Referenced by DisplayBlastDefline(), and DisplayBlastDeflineTable().

bool CShowBlastDefline::m_TranslatedNucAlignment [protected]

used to calculate the alignment length Definition at line 336 of file showdefline.hpp.

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The documentation for this class was generated from the following files:

• include/objtools/align_format/showdefline.hpp
• src/objtools/align_format/showdefline.cpp

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