NCBI C++ ToolKit
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CReadBlastApp Class Reference

Search Toolkit Book for CReadBlastApp

#include "read_blast_result.hpp"
(Private to src/app/read_blast_result.)

+ Inheritance diagram for CReadBlastApp:
+ Collaboration diagram for CReadBlastApp:

Static Public Member Functions

static string getLocusTag (const CBioseq &seq)
 
static const CSeq_locgetGenomicLocation (const CBioseq &seq)
 
static bool less_pair (const pair< int, int > &first, const pair< int, int > &second)
 
static bool less_seq (const CRef< CSeq_entry > &first, const CRef< CSeq_entry > &second)
 
static bool less_simple_seq (const TSimpleSeq &first, const TSimpleSeq &second)
 
static void getFromTo (const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)
 
static void getFromTo (const CSeq_loc_mix &mix, TSeqPos &from, TSeqPos &to, ENa_strand &strand)
 
static void getFromTo (const CPacked_seqint &mix, TSeqPos &from, TSeqPos &to, ENa_strand &strand)
 
static void getFromTo (const CSeq_interval &inter, TSeqPos &from, TSeqPos &to, ENa_strand &strand)
 
static int get_neighboring_sequences (const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs::iterator &first_user_in_range, TSimpleSeqs::iterator &first_user_non_in_range, TSimpleSeqs &seqs, const int max_distance)
 
static int sequence_proximity (const int target_from, const int target_to, const int from, const int to, const int key)
 
static int sequence_proximity (const int target_from, const int target_to, const int from, const int to, const int key, const int max_distance)
 
static void addSimpleTab (CNcbiStrstream &buffer, const string tag, const TSimpleSeqs::iterator &ext_rna, const int max_distance)
 
static bool PrintDetails (int current_verbosity=m_current_verbosity)
 
static void IncreaseVerbosity (void)
 
static void DecreaseVerbosity (void)
 
- Static Public Member Functions inherited from CNcbiApplication
static CNcbiApplicationInstance (void)
 Singleton method. More...
 
- Static Public Member Functions inherited from CNcbiApplicationAPI
static CNcbiApplicationAPIInstance (void)
 Singleton method. More...
 
static CNcbiApplicationGuard InstanceGuard (void)
 Singleton method. More...
 
static SSystemMutex & GetInstanceMutex (void)
 Mutex for application singleton object. More...
 
static string GetAppName (EAppNameType name_type=eBaseName, int argc=0, const char *const *argv=NULL)
 

Private Member Functions

virtual void Init (void)
 Initialize the application. More...
 
virtual int Run (void)
 Run the application. More...
 
int ReadBlast (const char *file, map< string, blastStr > &blastMap)
 
int ReadTRNA2 (const string &file)
 
int ReadRRNA2 (const string &file)
 
int StoreBlast (map< string, blastStr > &blastMap)
 
int ReadParents (CNcbiIstream &in, const list< long > &nacc)
 
bool ReadPreviousAcc (const string &file, list< long > &input_acc)
 
int ProcessCDD (map< string, blastStr > &blastMap)
 
int ReadTagMap (const char *file)
 
int SortSeqs (void)
 
int CollectSimpleSeqs (TSimpleSeqs &seqs)
 
int SortSeqs (CBioseq_set::TSeq_set &seqs)
 
int AnalyzeSeqs (void)
 
int AnalyzeSeqs (CBioseq_set::TSeq_set &seqs)
 
int SetParents (CSeq_entry *parent, CBioseq_set::TSeq_set &where)
 
int AnalyzeSeqsViaBioseqs (bool in_pool_prot, bool against_prot)
 
int AnalyzeSeqsViaBioseqs (CBioseq_set::TSeq_set &in_pool_seqs, CBioseq_set::TSeq_set &against_seqs, bool in_pool_prot, bool against_prot)
 
int AnalyzeSeqsViaBioseqs (CBioseq &left, CBioseq_set::TSeq_set &against_seqs, bool against_prot)
 
int AnalyzeSeqsViaBioseqs (CBioseq &left, CBioseq &right)
 
int AnalyzeSeqsViaBioseqs1 (CBioseq &left)
 
int simple_overlaps (void)
 
int short_proteins (void)
 
void ugly_simple_overlaps_call (int &n_user_neighbors, int &n_ext_neighbors, TSimpleSeqs::iterator &ext_rna, TSimpleSeqs::iterator &first_user_in_range, TSimpleSeqs::iterator &first_user_non_in_range, TSimpleSeqs &seqs, int max_distance, TSimpleSeqs::iterator &first_ext_in_range, TSimpleSeqs::iterator &first_ext_non_in_range, string &bufferstr)
 
void addLoctoSimpleSeq (TSimpleSeq &seq, const CSeq_loc &loc)
 
int CollectFrameshiftedSeqs (map< string, string > &problem_names)
 
int CollectRNAFeatures (TProblem_locs &problem_locs)
 
int RemoveProblems (map< string, string > &problem_seqs, LocMap &loc_map)
 
int FixStrands (void)
 
int RemoveProblems (CSeq_entry &entry, map< string, string > &problem_seqs, LocMap &loc_map)
 
int RemoveProblems (CBioseq_set &setseq, map< string, string > &problem_seqs, LocMap &loc_map)
 
int RemoveProblems (CBioseq &seq, map< string, string > &problem_seqs, LocMap &loc_map)
 
int RemoveProblems (CBioseq_set::TSeq_set &seqs, map< string, string > &problem_seqs, LocMap &loc_map)
 
int RemoveProblems (CBioseq::TAnnot &annots, map< string, string > &problem_seqs, LocMap &loc_map)
 
int RemoveProblems (CSeq_annot::C_Data::TFtable &table, map< string, string > &problem_seqs, LocMap &loc_map)
 
void NormalizeSeqentry (CSeq_entry &entry)
 
int RemoveInterim (void)
 
int RemoveInterim (CBioseq::TAnnot &annots)
 
int RemoveInterim2 (CBioseq::TAnnot &annots)
 
void processFeature (CSeq_annot::C_Data::TFtable::iterator &feat, TranStrMap3 &tranStrMap)
 
template<typename t >
void processAnnot (CBioseq::TAnnot::iterator &annot, t &tranStrMap)
 
void addLocation (string &prot_id, CBioseq &seq, CRef< CSeq_loc > &loc, const string &locus_tag)
 
int CopyInfoFromGenesToProteins (void)
 =========================================================================== More...
 
void dump_fasta_for_pretty_blast (diagMap &diag)
 
void append_misc_feature (CBioseq_set::TSeq_set &seqs, const string &name, EProblem problem_type)
 
const CBioseqget_nucleotide_seq (const CBioseq &seq)
 
CBeginInfo Begin (void)
 
CConstBeginInfo ConstBegin (void)
 
bool IsSubmit ()
 
bool IsEntry ()
 
bool IsTbl ()
 
void printGeneralInfo (ostream &out=NcbiCerr)
 
void reportProblems (const bool report_and_forget, diagMap &diag, ostream &out, const CBioseq::TAnnot &annots, const EProblem type)
 
void reportProblems (const bool report_and_forget, diagMap &diag, ostream &out, const CSeq_annot::C_Data::TFtable &feats, const EProblem type)
 
void reportProblems (const string &qname, diagMap &diag, ostream &out, const EProblem type)
 
void reportProblems (const bool report_and_forget, diagMap &diag, ostream &out=NcbiCout, const EProblem type=eAllProblems)
 
void reportProblemMessage (const string &message, ostream &out=NcbiCout)
 
void reportProblemType (const EProblem type, ostream &out=NcbiCout)
 
void reportProblemSequenceName (const string &name, ostream &out=NcbiCout)
 
void erase_problems (const string &qname, diagMap &diag, const EProblem type)
 
void GetGenomeLen ()
 
void CheckUniqLocusTag ()
 
void GetRNAfeats (const LocMap &loc_map, CSeq_annot::C_Data::TFtable &rna_feats, const CSeq_annot::C_Data::TFtable &feats)
 
void GetLocMap (LocMap &loc_map, const CSeq_annot::C_Data::TFtable &feats)
 
bool CheckMissingRibosomalRNA (const CBioseq::TAnnot &annots)
 
bool CheckMissingRibosomalRNA (const CSeq_annot::C_Data::TFtable &feats)
 
int find_overlap (TSimpleSeqs::iterator &seq, const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs &seqs, int &overlap)
 
int find_overlap (TSimpleSeqs::iterator &seq, const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs &seqs, TSimpleSeqs &best_seq)
 
bool overlaps_na (const CBioseq::TAnnot &annots)
 
bool overlaps_na (const CSeq_annot::C_Data::TFtable &feats)
 
bool overlaps_na (const CSeq_feat &f1, const CSeq_feat &f2, int &overlap)
 
bool overlaps_prot_na (CBioseq &seq, const CBioseq::TAnnot &annots)
 
bool overlaps_prot_na (CBioseq &seq, const CSeq_annot::C_Data::TFtable &feats)
 
bool overlaps_prot_na (const string &n1, const CSeq_interval &i1, const CSeq_feat &f2, int &overlap)
 
bool match_na (const CSeq_feat &f1, const string &type1)
 
int match_na (const CSeq_feat &f1, const TSimpleSeq &ext_rna, int &left, int &right, bool &strand_match, int &abs_left)
 
int overlaps (const TSimpleSeqs::iterator &seq1, const TSimpleSeqs::iterator &seq2, int &overlap)
 
template<typename t1 , typename t2 >
bool overlaps (const t1 &l1, const t2 &l2, int &overlap)
 
bool overlaps (const CSeq_loc &l1, int from, int to, int &overlap)
 
bool complete_overlap (const CSeq_loc &l1, const CSeq_loc &l2)
 
bool overlaps (const CBioseq &left, const CBioseq &right)
 
bool fit_blast (const CBioseq &left, const CBioseq &right, string &common_subject)
 

Static Private Member Functions

static char * next_w (char *w)
 
static char * skip_space (char *w)
 
static bool is_prot_entry (const CBioseq &seq)
 
static bool has_blast_hits (const CBioseq &seq)
 
static bool skip_to_valid_seq_cand (CBioseq_set::TSeq_set::const_iterator &seq, const CBioseq_set::TSeq_set &seqs)
 
static bool skip_to_valid_seq_cand (CBioseq_set::TSeq_set::iterator &seq, CBioseq_set::TSeq_set &seqs)
 
static int skip_toprot (CTypeIterator< CBioseq > &seq)
 
static int skip_toprot (CTypeConstIterator< CBioseq > &seq)
 
static bool skip_toprot (CBioseq_set::TSeq_set::const_iterator &seq, const CBioseq_set::TSeq_set &seqs)
 
static bool skip_toprot (CBioseq_set::TSeq_set::iterator &seq, CBioseq_set::TSeq_set &seqs)
 
static bool hasGenomicLocation (const CBioseq &seq)
 
static const CSeq_intervalgetGenomicInterval (const CBioseq &seq)
 
static bool hasGenomicInterval (const CBioseq &seq)
 
static string GetProtName (const CBioseq &seq)
 
static string getAnnotName (CBioseq::TAnnot::const_iterator &annot)
 
static string getAnnotComment (CBioseq::TAnnot::const_iterator &annot)
 
static int getQueryLen (const CBioseq &seq)
 
static vector< long > getGIs (CBioseq::TAnnot::const_iterator &annot)
 
static int getLenScore (CBioseq::TAnnot::const_iterator &annot)
 
static void getBounds (CBioseq::TAnnot::const_iterator &annot, int *qFrom, int *qTo, int *sFrom, int *sTo)
 
static bool giMatch (const vector< long > &left, const vector< long > &right)
 
static int collectPerfectHits (vector< perfectHitStr > &perfect, const CBioseq &seq)
 
static void check_alignment (CBioseq::TAnnot::const_iterator &annot, const CBioseq &seq, vector< perfectHitStr > &results)
 
static ECoreDataType getCoreDataType (istream &in)
 
static void printReport (distanceReportStr *report, ostream &out=NcbiCout)
 
static void printOverlapReport (distanceReportStr *report, ostream &out=NcbiCout)
 
static void printPerfectHit (const perfectHitStr &hit, ostream &out=NcbiCout)
 
static void dumpAlignment (const string &alignment, const string &file)
 
static bool hasProblems (const CBioseq &seq, diagMap &diag, const EProblem type)
 
static bool hasProblems (const string &qname, diagMap &diag, const EProblem type)
 
static string ProblemType (const EProblem type)
 
static void PushVerbosity (void)
 
static void PopVerbosity (void)
 
static bool fit_blast (const CBioseq &left, const CBioseq &right, CBioseq::TAnnot::const_iterator &left_annot, CBioseq::TAnnot::const_iterator &right_annot, int left_qLen, int right_qLen, int space, distanceReportStr *report)
 

Private Attributes

CSeq_submit m_Submit
 
CSeq_entry m_Entry
 
int m_length
 
Ctbl m_tbl
 
ECoreDataType m_coreDataType
 
map< string, stringm_tagmap
 
bool m_usemap
 
string m_align_dir
 
diagMap m_diag
 
parent_map m_parent
 
list< long > m_previous_genome
 
TSimpleSeqs m_extRNAtable2
 
TSimpleSeqs m_simple_seqs
 

Static Private Attributes

static double m_small_tails_threshold
 
static int m_n_best_hit
 
static double m_eThreshold
 
static double m_entireThreshold
 
static double m_partThreshold
 
static int m_rna_overlapThreshold
 
static int m_cds_overlapThreshold
 
static double m_trnascan_scoreThreshold
 
static int m_shortProteinThreshold
 
static int m_verbosity_threshold
 
static int m_current_verbosity
 
static stack< intm_saved_verbosity
 

Additional Inherited Members

- Public Types inherited from CNcbiApplicationAPI
enum  EAppNameType { eBaseName , eFullName , eRealName }
 
- Public Member Functions inherited from CNcbiApplication
virtual ~CNcbiApplication (void)
 Destructor. More...
 
 CNcbiApplication (const SBuildInfo &build_info=NCBI_SBUILDINFO_DEFAULT())
 Constructor. More...
 
- Public Member Functions inherited from CNcbiApplicationAPI
 CNcbiApplicationAPI (const SBuildInfo &build_info)
 Constructor. More...
 
virtual ~CNcbiApplicationAPI (void)
 Destructor. More...
 
int AppMain (int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)
 Main function (entry point) for the NCBI application. More...
 
virtual int DryRun (void)
 Test run the application. More...
 
virtual void Exit (void)
 Cleanup on application exit. More...
 
const CNcbiArgumentsGetArguments (void) const
 Get the application's cached unprocessed command-line arguments. More...
 
virtual const CArgsGetArgs (void) const
 Get parsed command line arguments. More...
 
const CNcbiEnvironmentGetEnvironment (void) const
 Get the application's cached environment. More...
 
CNcbiEnvironmentSetEnvironment (void)
 Get a non-const copy of the application's cached environment. More...
 
void SetEnvironment (const string &name, const string &value)
 Set a specified environment variable by name. More...
 
bool HasLoadedConfig (void) const
 Check if the config file has been loaded. More...
 
bool FinishedLoadingConfig (void) const
 Check if the application has finished loading config file (successfully or not). More...
 
const CNcbiRegistryGetConfig (void) const
 Get the application's cached configuration parameters (read-only). More...
 
CNcbiRegistryGetConfig (void)
 
const stringGetConfigPath (void) const
 Get the full path to the configuration file (if any) we ended up using. More...
 
bool ReloadConfig (CMetaRegistry::TFlags flags=CMetaRegistry::fReloadIfChanged, IRegistry::TFlags reg_flags=IRegistry::fWithNcbirc)
 Reload the configuration file. More...
 
SIZE_TYPE FlushDiag (CNcbiOstream *os, bool close_diag=false)
 Flush the in-memory diagnostic stream (for "eDS_ToMemory" case only). More...
 
const stringGetProgramDisplayName (void) const
 Get the application's "display" name. More...
 
const stringGetProgramExecutablePath (EFollowLinks follow_links=eIgnoreLinks) const
 Get the application's executable path. More...
 
CVersionInfo GetVersion (void) const
 Get the program version information. More...
 
const CVersionAPIGetFullVersion (void) const
 Get the program version information. More...
 
bool IsDryRun (void) const
 Check if it is a test run. More...
 
virtual bool SetupDiag_AppSpecific (void)
 Setup application specific diagnostic stream. More...
 
template<class TFunc >
void AddOnExitAction (TFunc func)
 Add callback to be executed from CNcbiApplicationAPI destructor. More...
 
- Protected Types inherited from CNcbiApplicationAPI
enum  EPreparseArgs { ePreparse_Continue , ePreparse_Exit }
 Result of PreparseArgs() More...
 
enum  EDisableArgDesc { fDisableStdArgs = 0x01 }
 Disable argument descriptions. More...
 
enum  EHideStdArgs {
  fHideLogfile = CArgDescriptions::fHideLogfile , fHideConffile = CArgDescriptions::fHideConffile , fHideVersion = CArgDescriptions::fHideVersion , fHideFullVersion = CArgDescriptions::fHideFullVersion ,
  fHideDryRun = CArgDescriptions::fHideDryRun , fHideHelp = CArgDescriptions::fHideHelp , fHideFullHelp = CArgDescriptions::fHideFullHelp , fHideXmlHelp = CArgDescriptions::fHideXmlHelp ,
  fHideAll = CArgDescriptions::fHideAll
}
 Which standard flag's descriptions should not be displayed in the usage message. More...
 
enum  EStdioSetup {
  fNoSyncWithStdio = 0x01 , fDefault_CinBufferSize = 0x02 , fBinaryCin = 0x04 , fBinaryCout = 0x08 ,
  fDefault_SyncWithStdio = 0x00
}
 Flags to adjust standard I/O streams' behaviour. More...
 
enum  EExitMode { eNoExits , eExceptionalExits , eAllExits }
 When to return a user-set exit code. More...
 
enum  EAppFlags { fSkipSafeStaticDestroy = 1 << 0 }
 
typedef int TDisableArgDesc
 Binary OR of "EDisableArgDesc". More...
 
typedef int THideStdArgs
 Binary OR of "EHideStdArgs". More...
 
typedef int TStdioSetupFlags
 Binary OR of "EStdioSetup". More...
 
typedef int TAppFlags
 
- Protected Member Functions inherited from CNcbiApplicationAPI
virtual EPreparseArgs PreparseArgs (int argc, const char *const *argv)
 Check the command line arguments before parsing them. More...
 
void DisableArgDescriptions (TDisableArgDesc disable=fDisableStdArgs)
 
void HideStdArgs (THideStdArgs hide_mask)
 Set the hide mask for the Hide Std Flags. More...
 
void SetStdioFlags (TStdioSetupFlags stdio_flags)
 Adjust the behavior of standard I/O streams. More...
 
void SetVersion (const CVersionInfo &version)
 Set the version number for the program. More...
 
void SetVersion (const CVersionInfo &version, const SBuildInfo &build_info)
 
void SetVersionByBuild (int major)
 
void SetFullVersion (CRef< CVersionAPI > version)
 Set version data for the program. More...
 
virtual void SetupArgDescriptions (CArgDescriptions *arg_desc)
 Setup the command line argument descriptions. More...
 
const CArgDescriptionsGetArgDescriptions (void) const
 Get argument descriptions (set by SetupArgDescriptions) More...
 
bool SetupDiag (EAppDiagStream diag)
 Setup the application diagnostic stream. More...
 
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf, CNcbiRegistry::TFlags reg_flags)
 Load settings from the configuration file to the registry. More...
 
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf)
 Load settings from the configuration file to the registry. More...
 
CNcbiRegistryGetRWConfig (void)
 Get the application's cached configuration parameters, accessible for read-write for an application's internal use only. More...
 
void SetProgramDisplayName (const string &app_name)
 Set program's display name. More...
 
virtual void AppStart (void)
 Method to be called before application start. More...
 
virtual void AppStop (int exit_code)
 Method to be called before application exit. More...
 
void SetExitCode (int exit_code, EExitMode when=eExceptionalExits)
 Force the program to return a specific exit code later, either when it exits due to an exception or unconditionally. More...
 
void SetAppFlags (TAppFlags flags)
 
void ExecuteOnExitActions ()
 Should only be called from the destructors of classes derived from CNcbiApplicationAPI - if it is necessary to access their data members and virtual methods; or to dynamic_cast<> from the base app class. More...
 
void SetPhoneHomePolicy (IPhoneHomePolicy *policy, ENcbiOwnership ownership=eNoOwnership)
 Set Phone Home Policy. More...
 
IPhoneHomePolicyGetPhoneHomePolicy () const
 Return pointer to current Phone Home Policy or NULL. More...
 
- Static Protected Member Functions inherited from CNcbiApplicationAPI
static CRWLockGetInstanceLock (void)
 
static string FindProgramExecutablePath (int argc, const char *const *argv, string *real_path=0)
 Find the application's executable file. More...
 

Detailed Description

Definition at line 276 of file read_blast_result.hpp.

Member Function Documentation

◆ addLocation()

void CReadBlastApp::addLocation ( string prot_id,
CBioseq seq,
CRef< CSeq_loc > &  loc,
const string locus_tag 
)
private

◆ addLoctoSimpleSeq()

void CReadBlastApp::addLoctoSimpleSeq ( TSimpleSeq seq,
const CSeq_loc loc 
)
private

◆ addSimpleTab()

void CReadBlastApp::addSimpleTab ( CNcbiStrstream buffer,
const string  tag,
const TSimpleSeqs::iterator &  ext_rna,
const int  max_distance 
)
static

Definition at line 376 of file missing.cpp.

References buffer, eNa_strand_minus, ITERATE, NcbiEndl, and tag.

Referenced by ugly_simple_overlaps_call().

◆ AnalyzeSeqs() [1/2]

int CReadBlastApp::AnalyzeSeqs ( CBioseq_set::TSeq_set seqs)
private

◆ AnalyzeSeqs() [2/2]

int CReadBlastApp::AnalyzeSeqs ( void  )
private

◆ AnalyzeSeqsViaBioseqs() [1/4]

int CReadBlastApp::AnalyzeSeqsViaBioseqs ( bool  in_pool_prot,
bool  against_prot 
)
private

◆ AnalyzeSeqsViaBioseqs() [2/4]

int CReadBlastApp::AnalyzeSeqsViaBioseqs ( CBioseq left,
CBioseq right 
)
private

Definition at line 128 of file analyze.cpp.

References CBioseq_Base::GetAnnot(), is_prot_entry(), and overlaps_prot_na().

◆ AnalyzeSeqsViaBioseqs() [3/4]

int CReadBlastApp::AnalyzeSeqsViaBioseqs ( CBioseq left,
CBioseq_set::TSeq_set against_seqs,
bool  against_prot 
)
private

◆ AnalyzeSeqsViaBioseqs() [4/4]

int CReadBlastApp::AnalyzeSeqsViaBioseqs ( CBioseq_set::TSeq_set in_pool_seqs,
CBioseq_set::TSeq_set against_seqs,
bool  in_pool_prot,
bool  against_prot 
)
private

◆ AnalyzeSeqsViaBioseqs1()

int CReadBlastApp::AnalyzeSeqsViaBioseqs1 ( CBioseq left)
private

Definition at line 143 of file analyze.cpp.

Referenced by AnalyzeSeqsViaBioseqs().

◆ append_misc_feature()

void CReadBlastApp::append_misc_feature ( CBioseq_set::TSeq_set seqs,
const string name,
EProblem  problem_type 
)
private

◆ Begin()

CBeginInfo CReadBlastApp::Begin ( void  )
private

◆ check_alignment()

void CReadBlastApp::check_alignment ( CBioseq::TAnnot::const_iterator &  annot,
const CBioseq seq,
vector< perfectHitStr > &  results 
)
staticprivate

◆ CheckMissingRibosomalRNA() [1/2]

bool CReadBlastApp::CheckMissingRibosomalRNA ( const CBioseq::TAnnot annots)
private

◆ CheckMissingRibosomalRNA() [2/2]

bool CReadBlastApp::CheckMissingRibosomalRNA ( const CSeq_annot::C_Data::TFtable feats)
private

◆ CheckUniqLocusTag()

void CReadBlastApp::CheckUniqLocusTag ( )
private

Definition at line 47 of file shortcuts.cpp.

References Begin(), f(), ITERATE, NcbiCerr, and NcbiEndl.

Referenced by Run().

◆ CollectFrameshiftedSeqs()

int CReadBlastApp::CollectFrameshiftedSeqs ( map< string, string > &  problem_names)
private

◆ collectPerfectHits()

int CReadBlastApp::collectPerfectHits ( vector< perfectHitStr > &  perfect,
const CBioseq seq 
)
staticprivate

Definition at line 446 of file read_blast_result_lib.cpp.

References check_alignment(), CBioseq_Base::GetAnnot(), and ITERATE.

Referenced by fit_blast().

◆ CollectRNAFeatures()

int CReadBlastApp::CollectRNAFeatures ( TProblem_locs problem_locs)
private

◆ CollectSimpleSeqs()

int CReadBlastApp::CollectSimpleSeqs ( TSimpleSeqs seqs)
private

◆ complete_overlap()

bool CReadBlastApp::complete_overlap ( const CSeq_loc l1,
const CSeq_loc l2 
)
private

Definition at line 536 of file overlaps.cpp.

References ConstBegin(), max(), min(), NcbiCerr, NcbiEndl, and result.

◆ ConstBegin()

CConstBeginInfo CReadBlastApp::ConstBegin ( void  )
private

◆ CopyInfoFromGenesToProteins()

int CReadBlastApp::CopyInfoFromGenesToProteins ( void  )
private

===========================================================================

PUBLIC DOMAIN NOTICE National Center for Biotechnology Information

This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.

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===========================================================================

Author: Azat Badretdin

File Description:

===========================================================================

Definition at line 33 of file copy_loc.cpp.

References addLocation(), Begin(), CollectSimpleSeqs(), DecreaseVerbosity(), CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, map_checker< Container >::end(), map_checker< Container >::find(), GetStringDescr(), IncreaseVerbosity(), ITERATE, m_simple_seqs, NcbiCerr, NcbiEndl, NON_CONST_ITERATE, PrintDetails(), and processAnnot().

Referenced by Run().

◆ DecreaseVerbosity()

static void CReadBlastApp::DecreaseVerbosity ( void  )
inlinestatic

◆ dump_fasta_for_pretty_blast()

void CReadBlastApp::dump_fasta_for_pretty_blast ( diagMap diag)
private

◆ dumpAlignment()

void CReadBlastApp::dumpAlignment ( const string alignment,
const string file 
)
staticprivate

Definition at line 108 of file read_blast_result_lib.cpp.

References file, and out().

◆ erase_problems()

void CReadBlastApp::erase_problems ( const string qname,
diagMap diag,
const EProblem  type 
)
private

◆ find_overlap() [1/2]

int CReadBlastApp::find_overlap ( TSimpleSeqs::iterator &  seq,
const TSimpleSeqs::iterator &  ext_rna,
TSimpleSeqs seqs,
int overlap 
)
private

Definition at line 92 of file overlaps.cpp.

References NcbiCerr, NcbiEndl, overlaps(), and PrintDetails().

Referenced by simple_overlaps().

◆ find_overlap() [2/2]

int CReadBlastApp::find_overlap ( TSimpleSeqs::iterator &  seq,
const TSimpleSeqs::iterator &  ext_rna,
TSimpleSeqs seqs,
TSimpleSeqs best_seq 
)
private

Definition at line 39 of file overlaps.cpp.

References m_length, NcbiCerr, NcbiEndl, overlaps(), PrintDetails(), and printed_range().

◆ fit_blast() [1/2]

bool CReadBlastApp::fit_blast ( const CBioseq left,
const CBioseq right,
CBioseq::TAnnot::const_iterator &  left_annot,
CBioseq::TAnnot::const_iterator &  right_annot,
int  left_qLen,
int  right_qLen,
int  space,
distanceReportStr report 
)
staticprivate

◆ fit_blast() [2/2]

bool CReadBlastApp::fit_blast ( const CBioseq left,
const CBioseq right,
string common_subject 
)
private

◆ FixStrands()

int CReadBlastApp::FixStrands ( void  )
private

◆ get_neighboring_sequences()

int CReadBlastApp::get_neighboring_sequences ( const TSimpleSeqs::iterator &  ext_rna,
TSimpleSeqs::iterator &  first_user_in_range,
TSimpleSeqs::iterator &  first_user_non_in_range,
TSimpleSeqs seqs,
const int  max_distance 
)
static

◆ get_nucleotide_seq()

const CBioseq & CReadBlastApp::get_nucleotide_seq ( const CBioseq seq)
private

◆ getAnnotComment()

string CReadBlastApp::getAnnotComment ( CBioseq::TAnnot::const_iterator &  annot)
staticprivate

Definition at line 471 of file shortcuts.cpp.

References ITERATE.

Referenced by fit_blast().

◆ getAnnotName()

string CReadBlastApp::getAnnotName ( CBioseq::TAnnot::const_iterator &  annot)
staticprivate

Definition at line 459 of file shortcuts.cpp.

References ITERATE.

Referenced by check_alignment(), and fit_blast().

◆ getBounds()

void CReadBlastApp::getBounds ( CBioseq::TAnnot::const_iterator &  annot,
int qFrom,
int qTo,
int sFrom,
int sTo 
)
staticprivate

Definition at line 434 of file shortcuts.cpp.

References bounds, i, and ITERATE.

Referenced by check_alignment(), and fit_blast().

◆ getCoreDataType()

ECoreDataType CReadBlastApp::getCoreDataType ( istream &  in)
staticprivate

Definition at line 628 of file read_blast_result_lib.cpp.

References buffer, eEntry, eSubmit, eTbl, eUndefined, in(), result, and NStr::StartsWith().

Referenced by Run().

◆ getFromTo() [1/4]

void CReadBlastApp::getFromTo ( const CPacked_seqint mix,
TSeqPos from,
TSeqPos to,
ENa_strand strand 
)
static

Definition at line 75 of file locations.cpp.

References CPacked_seqint_Base::Get(), getFromTo(), and ITERATE.

◆ getFromTo() [2/4]

void CReadBlastApp::getFromTo ( const CSeq_interval inter,
TSeqPos from,
TSeqPos to,
ENa_strand strand 
)
static

◆ getFromTo() [3/4]

void CReadBlastApp::getFromTo ( const CSeq_loc loc,
TSeqPos from,
TSeqPos to,
ENa_strand strand 
)
static

◆ getFromTo() [4/4]

void CReadBlastApp::getFromTo ( const CSeq_loc_mix mix,
TSeqPos from,
TSeqPos to,
ENa_strand strand 
)
static

Definition at line 61 of file locations.cpp.

References CSeq_loc_mix_Base::Get(), getFromTo(), and ITERATE.

◆ GetGenomeLen()

void CReadBlastApp::GetGenomeLen ( )
private

Definition at line 36 of file shortcuts.cpp.

References Begin(), CSeq_inst_Base::eMol_dna, m_length, NcbiCerr, NcbiEndl, and PrintDetails().

Referenced by Run().

◆ getGenomicInterval()

const CSeq_interval & CReadBlastApp::getGenomicInterval ( const CBioseq seq)
staticprivate

◆ getGenomicLocation()

const CSeq_loc & CReadBlastApp::getGenomicLocation ( const CBioseq seq)
static

◆ getGIs()

vector< long > CReadBlastApp::getGIs ( CBioseq::TAnnot::const_iterator &  annot)
staticprivate

Definition at line 68 of file read_blast_result_lib.cpp.

References ITERATE, and result.

Referenced by fit_blast().

◆ getLenScore()

int CReadBlastApp::getLenScore ( CBioseq::TAnnot::const_iterator &  annot)
staticprivate

Definition at line 420 of file shortcuts.cpp.

References ITERATE, and len.

Referenced by check_alignment(), and fit_blast().

◆ GetLocMap()

void CReadBlastApp::GetLocMap ( LocMap loc_map,
const CSeq_annot::C_Data::TFtable feats 
)
private

◆ getLocusTag()

string CReadBlastApp::getLocusTag ( const CBioseq seq)
static

Definition at line 141 of file locations.cpp.

References CBioseq_Base::GetAnnot(), ITERATE, and tag.

Referenced by GetStringDescr().

◆ GetProtName()

string CReadBlastApp::GetProtName ( const CBioseq seq)
staticprivate

Definition at line 82 of file shortcuts.cpp.

References CBioseq_Base::GetAnnot(), and ITERATE.

Referenced by check_alignment(), CollectSimpleSeqs(), fit_blast(), and overlaps_prot_na().

◆ getQueryLen()

int CReadBlastApp::getQueryLen ( const CBioseq seq)
staticprivate

Definition at line 96 of file shortcuts.cpp.

References CBioseq_Base::GetInst(), and CSeq_inst_Base::GetLength().

Referenced by check_alignment(), and fit_blast().

◆ GetRNAfeats()

void CReadBlastApp::GetRNAfeats ( const LocMap loc_map,
CSeq_annot::C_Data::TFtable rna_feats,
const CSeq_annot::C_Data::TFtable feats 
)
private

◆ giMatch()

bool CReadBlastApp::giMatch ( const vector< long > &  left,
const vector< long > &  right 
)
staticprivate

◆ has_blast_hits()

bool CReadBlastApp::has_blast_hits ( const CBioseq seq)
staticprivate

Definition at line 369 of file fit_blast.cpp.

References CBioseq_Base::GetAnnot(), NcbiCerr, NcbiEndl, PrintDetails(), and result.

Referenced by AnalyzeSeqs(), and skip_to_valid_seq_cand().

◆ hasGenomicInterval()

bool CReadBlastApp::hasGenomicInterval ( const CBioseq seq)
staticprivate

◆ hasGenomicLocation()

bool CReadBlastApp::hasGenomicLocation ( const CBioseq seq)
staticprivate

◆ hasProblems() [1/2]

bool CReadBlastApp::hasProblems ( const CBioseq seq,
diagMap diag,
const EProblem  type 
)
staticprivate

◆ hasProblems() [2/2]

bool CReadBlastApp::hasProblems ( const string qname,
diagMap diag,
const EProblem  type 
)
staticprivate

◆ IncreaseVerbosity()

static void CReadBlastApp::IncreaseVerbosity ( void  )
inlinestatic

◆ Init()

void CReadBlastApp::Init ( void  )
privatevirtual

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplicationAPI.

Definition at line 39 of file read_blast_result.cpp.

References map_checker< Container >::clear(), CArgDescriptions::eDouble, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, CArgDescriptions::eString, eUndefined, CArgDescriptions::fPreOpen, CNcbiApplicationAPI::GetArguments(), m_coreDataType, m_current_verbosity, m_saved_verbosity, m_tagmap, m_usemap, and CNcbiApplicationAPI::SetupArgDescriptions().

◆ is_prot_entry()

bool CReadBlastApp::is_prot_entry ( const CBioseq seq)
staticprivate

◆ IsEntry()

bool CReadBlastApp::IsEntry ( void  )
private

Definition at line 654 of file read_blast_result_lib.cpp.

References eEntry, and m_coreDataType.

Referenced by Run().

◆ IsSubmit()

bool CReadBlastApp::IsSubmit ( void  )
private

◆ IsTbl()

bool CReadBlastApp::IsTbl ( )
private

Definition at line 659 of file read_blast_result_lib.cpp.

References eTbl, and m_coreDataType.

Referenced by Run().

◆ less_pair()

bool CReadBlastApp::less_pair ( const pair< int, int > &  first,
const pair< int, int > &  second 
)
static

Definition at line 561 of file read_blast_result_lib.cpp.

References first().

Referenced by printed_ranges().

◆ less_seq()

bool CReadBlastApp::less_seq ( const CRef< CSeq_entry > &  first,
const CRef< CSeq_entry > &  second 
)
static

◆ less_simple_seq()

bool CReadBlastApp::less_simple_seq ( const TSimpleSeq first,
const TSimpleSeq second 
)
static

Definition at line 555 of file read_blast_result_lib.cpp.

References first(), and TSimpleSeq::key.

Referenced by CollectSimpleSeqs(), and Run().

◆ match_na() [1/2]

bool CReadBlastApp::match_na ( const CSeq_feat f1,
const string type1 
)
private

◆ match_na() [2/2]

int CReadBlastApp::match_na ( const CSeq_feat f1,
const TSimpleSeq ext_rna,
int left,
int right,
bool strand_match,
int abs_left 
)
private

◆ next_w()

char * CReadBlastApp::next_w ( char *  w)
staticprivate

Definition at line 682 of file read_blast_result_lib.cpp.

References isspace().

Referenced by ReadBlast().

◆ NormalizeSeqentry()

void CReadBlastApp::NormalizeSeqentry ( CSeq_entry entry)
private

◆ overlaps() [1/4]

bool CReadBlastApp::overlaps ( const CBioseq left,
const CBioseq right 
)
private

◆ overlaps() [2/4]

bool CReadBlastApp::overlaps ( const CSeq_loc l1,
int  from,
int  to,
int overlap 
)
private

Definition at line 506 of file overlaps.cpp.

References ConstBegin(), getFromTo(), max(), min(), and result.

◆ overlaps() [3/4]

template<typename t1 , typename t2 >
bool CReadBlastApp::overlaps ( const t1 &  l1,
const t2 &  l2,
int overlap 
)
private

Definition at line 467 of file overlaps.cpp.

References ConstBegin(), getFromTo(), max(), min(), and result.

◆ overlaps() [4/4]

int CReadBlastApp::overlaps ( const TSimpleSeqs::iterator &  seq1,
const TSimpleSeqs::iterator &  seq2,
int overlap 
)
private

Definition at line 146 of file overlaps.cpp.

References max(), and min().

Referenced by AnalyzeSeqs(), find_overlap(), match_na(), overlaps_na(), overlaps_prot_na(), and simple_overlaps().

◆ overlaps_na() [1/3]

bool CReadBlastApp::overlaps_na ( const CBioseq::TAnnot annots)
private

Definition at line 181 of file overlaps.cpp.

References DecreaseVerbosity(), IncreaseVerbosity(), ITERATE, NcbiCerr, NcbiEndl, PrintDetails(), and result.

Referenced by AnalyzeSeqs().

◆ overlaps_na() [2/3]

bool CReadBlastApp::overlaps_na ( const CSeq_annot::C_Data::TFtable feats)
private

◆ overlaps_na() [3/3]

bool CReadBlastApp::overlaps_na ( const CSeq_feat f1,
const CSeq_feat f2,
int overlap 
)
private

◆ overlaps_prot_na() [1/3]

bool CReadBlastApp::overlaps_prot_na ( CBioseq seq,
const CBioseq::TAnnot annots 
)
private

◆ overlaps_prot_na() [2/3]

bool CReadBlastApp::overlaps_prot_na ( CBioseq seq,
const CSeq_annot::C_Data::TFtable feats 
)
private

◆ overlaps_prot_na() [3/3]

bool CReadBlastApp::overlaps_prot_na ( const string n1,
const CSeq_interval i1,
const CSeq_feat f2,
int overlap 
)
private

◆ PopVerbosity()

static void CReadBlastApp::PopVerbosity ( void  )
inlinestaticprivate

◆ PrintDetails()

static bool CReadBlastApp::PrintDetails ( int  current_verbosity = m_current_verbosity)
inlinestatic

◆ printGeneralInfo()

void CReadBlastApp::printGeneralInfo ( ostream &  out = NcbiCerr)
private

◆ printOverlapReport()

void CReadBlastApp::printOverlapReport ( distanceReportStr report,
ostream &  out = NcbiCout 
)
staticprivate

◆ printPerfectHit()

void CReadBlastApp::printPerfectHit ( const perfectHitStr hit,
ostream &  out = NcbiCout 
)
staticprivate

Definition at line 177 of file read_blast_result_lib.cpp.

References NcbiEndl, out(), and perfectHitStr::s_name.

Referenced by fit_blast().

◆ printReport()

void CReadBlastApp::printReport ( distanceReportStr report,
ostream &  out = NcbiCout 
)
staticprivate

◆ ProblemType()

string CReadBlastApp::ProblemType ( const EProblem  type)
staticprivate

◆ processAnnot()

template<typename t >
void CReadBlastApp::processAnnot ( CBioseq::TAnnot::iterator &  annot,
t tranStrMap 
)
private

◆ ProcessCDD()

int CReadBlastApp::ProcessCDD ( map< string, blastStr > &  blastMap)
private

◆ processFeature()

void CReadBlastApp::processFeature ( CSeq_annot::C_Data::TFtable::iterator &  feat,
TranStrMap3 tranStrMap 
)
private

◆ PushVerbosity()

static void CReadBlastApp::PushVerbosity ( void  )
inlinestaticprivate

◆ ReadBlast()

int CReadBlastApp::ReadBlast ( const char *  file,
map< string, blastStr > &  blastMap 
)
private

◆ ReadParents()

int CReadBlastApp::ReadParents ( CNcbiIstream in,
const list< long > &  nacc 
)
private

Definition at line 35 of file read_parents.cpp.

References in(), m_parent, n, NcbiCerr, NcbiEndl, and PrintDetails().

Referenced by Run().

◆ ReadPreviousAcc()

bool CReadBlastApp::ReadPreviousAcc ( const string file,
list< long > &  input_acc 
)
private

Definition at line 811 of file read_blast_result_lib.cpp.

References buffer, file, in(), and test.

Referenced by Run().

◆ ReadRRNA2()

int CReadBlastApp::ReadRRNA2 ( const string file)
private

◆ ReadTagMap()

int CReadBlastApp::ReadTagMap ( const char *  file)
private

◆ ReadTRNA2()

int CReadBlastApp::ReadTRNA2 ( const string file)
private

◆ RemoveInterim() [1/2]

int CReadBlastApp::RemoveInterim ( CBioseq::TAnnot annots)
private

Definition at line 731 of file problems.cpp.

References NcbiCerr, NcbiEndl, PrintDetails(), table, and test.

◆ RemoveInterim() [2/2]

int CReadBlastApp::RemoveInterim ( void  )
private

Definition at line 713 of file problems.cpp.

References Begin(), NcbiCerr, NcbiEndl, PopVerbosity(), PrintDetails(), PushVerbosity(), and RemoveInterim2().

Referenced by Run().

◆ RemoveInterim2()

int CReadBlastApp::RemoveInterim2 ( CBioseq::TAnnot annots)
private

◆ RemoveProblems() [1/7]

int CReadBlastApp::RemoveProblems ( CBioseq seq,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ RemoveProblems() [2/7]

int CReadBlastApp::RemoveProblems ( CBioseq::TAnnot annots,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

Definition at line 537 of file problems.cpp.

References NcbiCerr, NcbiEndl, PrintDetails(), remove(), and RemoveProblems().

◆ RemoveProblems() [3/7]

int CReadBlastApp::RemoveProblems ( CBioseq_set setseq,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ RemoveProblems() [4/7]

int CReadBlastApp::RemoveProblems ( CBioseq_set::TSeq_set seqs,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ RemoveProblems() [5/7]

int CReadBlastApp::RemoveProblems ( CSeq_annot::C_Data::TFtable table,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ RemoveProblems() [6/7]

int CReadBlastApp::RemoveProblems ( CSeq_entry entry,
map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ RemoveProblems() [7/7]

int CReadBlastApp::RemoveProblems ( map< string, string > &  problem_seqs,
LocMap loc_map 
)
private

◆ reportProblemMessage()

void CReadBlastApp::reportProblemMessage ( const string message,
ostream &  out = NcbiCout 
)
private

Definition at line 172 of file problems.cpp.

References NcbiEndl, and out().

Referenced by reportProblems().

◆ reportProblems() [1/4]

void CReadBlastApp::reportProblems ( const bool  report_and_forget,
diagMap diag,
ostream &  out,
const CBioseq::TAnnot annots,
const EProblem  type 
)
private

Definition at line 36 of file problems.cpp.

References ITERATE, and out().

Referenced by reportProblems(), and Run().

◆ reportProblems() [2/4]

void CReadBlastApp::reportProblems ( const bool  report_and_forget,
diagMap diag,
ostream &  out,
const CSeq_annot::C_Data::TFtable feats,
const EProblem  type 
)
private

◆ reportProblems() [3/4]

void CReadBlastApp::reportProblems ( const bool  report_and_forget,
diagMap diag,
ostream &  out = NcbiCout,
const EProblem  type = eAllProblems 
)
private

◆ reportProblems() [4/4]

void CReadBlastApp::reportProblems ( const string qname,
diagMap diag,
ostream &  out,
const EProblem  type 
)
private

◆ reportProblemSequenceName()

void CReadBlastApp::reportProblemSequenceName ( const string name,
ostream &  out = NcbiCout 
)
private

Definition at line 238 of file problems.cpp.

References NcbiEndl, and out().

Referenced by reportProblems().

◆ reportProblemType()

void CReadBlastApp::reportProblemType ( const EProblem  type,
ostream &  out = NcbiCout 
)
private

Definition at line 217 of file problems.cpp.

References NcbiCerr, NcbiEndl, out(), and ProblemType().

Referenced by reportProblems().

◆ Run()

int CReadBlastApp::Run ( void  )
privatevirtual

Run the application.

It is defined as a pure virtual method – so you must(!) supply the Run() method to implement the application-specific logic.

Returns
Exit code.

Implements CNcbiApplicationAPI.

Definition at line 220 of file read_blast_result.cpp.

References AnalyzeSeqs(), AnalyzeSeqsViaBioseqs(), CheckUniqLocusTag(), CollectFrameshiftedSeqs(), CopyInfoFromGenesToProteins(), dump_fasta_for_pretty_blast(), eCompleteOverlap, eOverlap, ePartial, eRelFrameShift, eRemoveOverlap, eRnaOverlap, eShortProtein, eTRNAAbsent, eTRNABadStrand, eTRNAComMismatch, eTRNAMismatch, eTRNAMissing, eTRNAUndefStrand, FixStrands(), CNcbiApplicationAPI::GetArgs(), getCoreDataType(), GetGenomeLen(), in(), IsEntry(), IsSubmit(), IsTbl(), less_simple_seq(), m_cds_overlapThreshold, m_coreDataType, m_diag, m_entireThreshold, m_Entry, m_eThreshold, m_extRNAtable2, m_n_best_hit, m_partThreshold, m_previous_genome, m_rna_overlapThreshold, m_shortProteinThreshold, m_small_tails_threshold, m_Submit, m_tbl, m_trnascan_scoreThreshold, m_usemap, m_verbosity_threshold, NcbiCerr, NcbiEndl, CObjectIStream::Open(), CObjectOStream::Open(), out(), CSeq_entry::Parentize(), PopVerbosity(), CArgs::Print(), PrintDetails(), printGeneralInfo(), ProcessCDD(), PushVerbosity(), Ctbl::Read(), ReadBlast(), ReadParents(), ReadPreviousAcc(), ReadRRNA2(), ReadTagMap(), ReadTRNA2(), RemoveInterim(), RemoveProblems(), reportProblems(), s_GetFormat(), CSeq_submit_Base::SetData(), short_proteins(), simple_overlaps(), SortSeqs(), and StoreBlast().

◆ sequence_proximity() [1/2]

int CReadBlastApp::sequence_proximity ( const int  target_from,
const int  target_to,
const int  from,
const int  to,
const int  key 
)
static

◆ sequence_proximity() [2/2]

int CReadBlastApp::sequence_proximity ( const int  target_from,
const int  target_to,
const int  from,
const int  to,
const int  key,
const int  max_distance 
)
static

Definition at line 368 of file missing.cpp.

◆ SetParents()

int CReadBlastApp::SetParents ( CSeq_entry parent,
CBioseq_set::TSeq_set where 
)
private

Definition at line 534 of file read_blast_result_lib.cpp.

◆ short_proteins()

int CReadBlastApp::short_proteins ( void  )
private

◆ simple_overlaps()

int CReadBlastApp::simple_overlaps ( void  )
private

◆ skip_space()

char * CReadBlastApp::skip_space ( char *  w)
staticprivate

Definition at line 689 of file read_blast_result_lib.cpp.

References isspace().

Referenced by ReadBlast().

◆ skip_to_valid_seq_cand() [1/2]

bool CReadBlastApp::skip_to_valid_seq_cand ( CBioseq_set::TSeq_set::const_iterator &  seq,
const CBioseq_set::TSeq_set seqs 
)
staticprivate

◆ skip_to_valid_seq_cand() [2/2]

bool CReadBlastApp::skip_to_valid_seq_cand ( CBioseq_set::TSeq_set::iterator &  seq,
CBioseq_set::TSeq_set seqs 
)
staticprivate

◆ skip_toprot() [1/4]

bool CReadBlastApp::skip_toprot ( CBioseq_set::TSeq_set::const_iterator &  seq,
const CBioseq_set::TSeq_set seqs 
)
staticprivate

◆ skip_toprot() [2/4]

bool CReadBlastApp::skip_toprot ( CBioseq_set::TSeq_set::iterator &  seq,
CBioseq_set::TSeq_set seqs 
)
staticprivate

◆ skip_toprot() [3/4]

int CReadBlastApp::skip_toprot ( CTypeConstIterator< CBioseq > &  seq)
staticprivate

Definition at line 707 of file read_blast_result_lib.cpp.

References CSeq_inst::IsAa().

◆ skip_toprot() [4/4]

int CReadBlastApp::skip_toprot ( CTypeIterator< CBioseq > &  seq)
staticprivate

◆ SortSeqs() [1/2]

int CReadBlastApp::SortSeqs ( CBioseq_set::TSeq_set seqs)
private

◆ SortSeqs() [2/2]

int CReadBlastApp::SortSeqs ( void  )
private

◆ StoreBlast()

int CReadBlastApp::StoreBlast ( map< string, blastStr > &  blastMap)
private

◆ ugly_simple_overlaps_call()

void CReadBlastApp::ugly_simple_overlaps_call ( int n_user_neighbors,
int n_ext_neighbors,
TSimpleSeqs::iterator &  ext_rna,
TSimpleSeqs::iterator &  first_user_in_range,
TSimpleSeqs::iterator &  first_user_non_in_range,
TSimpleSeqs seqs,
int  max_distance,
TSimpleSeqs::iterator &  first_ext_in_range,
TSimpleSeqs::iterator &  first_ext_non_in_range,
string bufferstr 
)
private

Member Data Documentation

◆ m_align_dir

string CReadBlastApp::m_align_dir
private

Definition at line 550 of file read_blast_result.hpp.

◆ m_cds_overlapThreshold

int CReadBlastApp::m_cds_overlapThreshold
staticprivate

Definition at line 567 of file read_blast_result.hpp.

Referenced by Run().

◆ m_coreDataType

ECoreDataType CReadBlastApp::m_coreDataType
private

Definition at line 547 of file read_blast_result.hpp.

Referenced by Begin(), ConstBegin(), Init(), IsEntry(), IsSubmit(), IsTbl(), and Run().

◆ m_current_verbosity

int CReadBlastApp::m_current_verbosity
staticprivate

◆ m_diag

diagMap CReadBlastApp::m_diag
private

◆ m_entireThreshold

double CReadBlastApp::m_entireThreshold
staticprivate

Definition at line 564 of file read_blast_result.hpp.

Referenced by ProcessCDD(), and Run().

◆ m_Entry

CSeq_entry CReadBlastApp::m_Entry
private

◆ m_eThreshold

double CReadBlastApp::m_eThreshold
staticprivate

Definition at line 563 of file read_blast_result.hpp.

Referenced by ProcessCDD(), and Run().

◆ m_extRNAtable2

TSimpleSeqs CReadBlastApp::m_extRNAtable2
private

◆ m_length

int CReadBlastApp::m_length
private

Definition at line 545 of file read_blast_result.hpp.

Referenced by addLoctoSimpleSeq(), find_overlap(), and GetGenomeLen().

◆ m_n_best_hit

int CReadBlastApp::m_n_best_hit
staticprivate

Definition at line 562 of file read_blast_result.hpp.

Referenced by ReadBlast(), and Run().

◆ m_parent

parent_map CReadBlastApp::m_parent
private

Definition at line 552 of file read_blast_result.hpp.

Referenced by ReadParents(), and StoreBlast().

◆ m_partThreshold

double CReadBlastApp::m_partThreshold
staticprivate

Definition at line 565 of file read_blast_result.hpp.

Referenced by ProcessCDD(), and Run().

◆ m_previous_genome

list<long> CReadBlastApp::m_previous_genome
private

Definition at line 554 of file read_blast_result.hpp.

Referenced by Run(), and StoreBlast().

◆ m_rna_overlapThreshold

int CReadBlastApp::m_rna_overlapThreshold
staticprivate

Definition at line 566 of file read_blast_result.hpp.

Referenced by overlaps_prot_na(), and Run().

◆ m_saved_verbosity

stack< int > CReadBlastApp::m_saved_verbosity
staticprivate

Definition at line 575 of file read_blast_result.hpp.

Referenced by Init(), PopVerbosity(), and PushVerbosity().

◆ m_shortProteinThreshold

int CReadBlastApp::m_shortProteinThreshold
staticprivate

Definition at line 569 of file read_blast_result.hpp.

Referenced by Run(), and short_proteins().

◆ m_simple_seqs

TSimpleSeqs CReadBlastApp::m_simple_seqs
private

◆ m_small_tails_threshold

double CReadBlastApp::m_small_tails_threshold
staticprivate

Definition at line 561 of file read_blast_result.hpp.

Referenced by check_alignment(), and Run().

◆ m_Submit

CSeq_submit CReadBlastApp::m_Submit
private

◆ m_tagmap

map< string, string > CReadBlastApp::m_tagmap
private

Definition at line 548 of file read_blast_result.hpp.

Referenced by Init(), ReadBlast(), and ReadTagMap().

◆ m_tbl

Ctbl CReadBlastApp::m_tbl
private

Definition at line 546 of file read_blast_result.hpp.

Referenced by Run().

◆ m_trnascan_scoreThreshold

double CReadBlastApp::m_trnascan_scoreThreshold
staticprivate

Definition at line 568 of file read_blast_result.hpp.

Referenced by ReadTRNA2(), and Run().

◆ m_usemap

bool CReadBlastApp::m_usemap
private

Definition at line 549 of file read_blast_result.hpp.

Referenced by Init(), ReadBlast(), and Run().

◆ m_verbosity_threshold

int CReadBlastApp::m_verbosity_threshold
staticprivate

Definition at line 573 of file read_blast_result.hpp.

Referenced by PrintDetails(), Run(), and simple_overlaps().


The documentation for this class was generated from the following files:
Modified on Wed May 29 18:43:35 2024 by modify_doxy.py rev. 669887