fta_qscore.cpp File Reference

#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objects/seqres/Seq_graph.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqres/Byte_graph.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Annot_descr.hpp>
#include "index.h"
#include <objtools/flatfile/flatdefn.h>
#include <algorithm>
#include "ftaerr.hpp"
#include "utilfun.h"

Include dependency graph for fta_qscore.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Macros
#define	THIS_FILE   "fta_qscore.cpp"
#define	IS_DIGIT_OR_NA(c)   ((c) == 'N' || (c) == 'A' || ('0' <= (c) && (c) <= '9'))
#define	QSBUF_MAXLINE
#define	QSBUF_MAXACC
#define	QSBUF_MAXTITLE
#define	QSBUF_MAXSCORES
#define	QS_MIN_VALID_SCORE   0 /* Minimum valid quality score value */
#define	QS_MAX_VALID_SCORE   100 /* Maximum valid quality score value */

Functions
	USING_SCOPE (objects)
static bool	QSbuf_ReadLine (const char *qs_buf, char *dest_buf, Int2 max_len, int *line)
static int	QSbuf_ParseDefline (char *qs_defline, char *def_acc, char *def_ver, char *def_title, unsigned int *def_len, unsigned char *def_max, unsigned char *def_min)
static Int4	QSbuf_ParseScores (char *score_buf, unsigned char *scores, Int4 max_toks, unsigned char *max_score, unsigned char *min_score, bool allow_na)
static void	Split_Qscore_SeqGraph_By_DeltaSeq (CSeq_annot::C_Data::TGraph &graphs, CBioseq &bioseq)
static void	QSbuf_To_Single_Qscore_SeqGraph (const char *qs_buf, CBioseq &bioseq, char *def_acc, char *def_ver, bool check_minmax, bool allow_na, CSeq_annot::C_Data::TGraph &graphs)
bool	QscoreToSeqAnnot (const string &qscore, CBioseq &bioseq, char *acc, Int2 ver, bool check_minmax, bool allow_na)

Macro Definition Documentation

IS_DIGIT_OR_NA

#define IS_DIGIT_OR_NA

(

c

)

((c) == 'N' || (c) == 'A' || ('0' <= (c) && (c) <= '9'))

Definition at line 72 of file fta_qscore.cpp.

QS_MAX_VALID_SCORE

#define QS_MAX_VALID_SCORE   100 /* Maximum valid quality score value */

Definition at line 79 of file fta_qscore.cpp.

QS_MIN_VALID_SCORE

#define QS_MIN_VALID_SCORE   0 /* Minimum valid quality score value */

Definition at line 78 of file fta_qscore.cpp.

QSBUF_MAXACC

#define QSBUF_MAXACC

Value:

                                  51  /* Maximum length for an accession    \
                                  read from the 'defline' at the     \
                                  start of a buffer of quality-score \
                                  data, plus one for \0 */

Definition at line 75 of file fta_qscore.cpp.

QSBUF_MAXLINE

#define QSBUF_MAXLINE

Value:

                                  256 /* Maximum length for a line of data   \
                                  read from a buffer of quality-score \
                                  data, plus one for the terminal     \
                                  newline character. */

Definition at line 74 of file fta_qscore.cpp.

QSBUF_MAXSCORES

#define QSBUF_MAXSCORES

Value:

                                  100 /* Maximum number of scores expected \
                                  in a line of score data read from \
                                  from a quality-score buffer */

Definition at line 77 of file fta_qscore.cpp.

QSBUF_MAXTITLE

#define QSBUF_MAXTITLE

Value:

                                  101 /* Maximum length for the title read  \
                                  from the 'defline' at the start of \
                                  a buffer of quality-score data,    \
                                  plus one for \0 */

Definition at line 76 of file fta_qscore.cpp.

THIS_FILE

#define THIS_FILE   "fta_qscore.cpp"

Definition at line 64 of file fta_qscore.cpp.

Function Documentation

QSbuf_ParseDefline()

static int QSbuf_ParseDefline ( char *  qs_defline, char *  def_acc, char *  def_ver, char *  def_title, unsigned int *  def_len, unsigned char *  def_max, unsigned char *  def_min  )

static

Definition at line 183 of file fta_qscore.cpp.

References NStr::CompareNocase(), ERR_QSCORE_BadTitle, ErrPostEx, isalnum(), isdigit(), isspace(), QS_MAX_VALID_SCORE, QS_MIN_VALID_SCORE, r(), SEV_ERROR, StringChr, StringCpy(), StringEquNI(), and StringHasNoText().

Referenced by QSbuf_To_Single_Qscore_SeqGraph().

QSbuf_ParseScores()

static Int4 QSbuf_ParseScores ( char *  score_buf, unsigned char *  scores, Int4  max_toks, unsigned char *  max_score, unsigned char *  min_score, bool  allow_na  )

static

Definition at line 465 of file fta_qscore.cpp.

References IS_DIGIT_OR_NA, isspace(), max(), min(), QS_MAX_VALID_SCORE, QS_MIN_VALID_SCORE, StringEqu(), and val.

Referenced by QSbuf_To_Single_Qscore_SeqGraph().

QSbuf_ReadLine()

static bool QSbuf_ReadLine ( const char *  qs_buf, char *  dest_buf, Int2  max_len, int *  line  )

static

Definition at line 97 of file fta_qscore.cpp.

References i.

Referenced by QSbuf_To_Single_Qscore_SeqGraph().

QSbuf_To_Single_Qscore_SeqGraph()

static void QSbuf_To_Single_Qscore_SeqGraph ( const char *  qs_buf, CBioseq &  bioseq, char *  def_acc, char *  def_ver, bool  check_minmax, bool  allow_na, CSeq_annot::C_Data::TGraph &  graphs  )

static

Definition at line 855 of file fta_qscore.cpp.

References copy(), CRef< C, Locker >::Empty(), ERR_QSCORE_BadBioseqId, ERR_QSCORE_BadBioseqLen, ERR_QSCORE_BadDefline, ERR_QSCORE_BadLength, ERR_QSCORE_BadMax, ERR_QSCORE_BadMin, ERR_QSCORE_BadMinMax, ERR_QSCORE_BadQscoreRead, ERR_QSCORE_BadScoreLine, ERR_QSCORE_InvalidArgs, ERR_QSCORE_MemAlloc, ERR_QSCORE_NoAccession, ERR_QSCORE_NoSeqVer, ERR_QSCORE_NoTitle, ERR_QSCORE_ScoresVsBspLen, ERR_QSCORE_ScoresVsLen, ErrPostEx, CBioseq::GetLength(), CBioseq_Base::IsSetId(), QS_MAX_VALID_SCORE, QS_MIN_VALID_SCORE, QSBUF_MAXLINE, QSBUF_MAXSCORES, QSBUF_MAXTITLE, QSbuf_ParseDefline(), QSbuf_ParseScores(), QSbuf_ReadLine(), CRef< C, Locker >::Reset(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetLoc(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::SetTitle(), SEV_ERROR, StringEqu(), and StringLen().

QscoreToSeqAnnot()

bool QscoreToSeqAnnot	(	const string &	qscore,
		CBioseq &	bioseq,
		char *	acc,
		Int2	ver,
		bool	check_minmax,
		bool	allow_na
	)

Definition at line 1082 of file fta_qscore.cpp.

Referenced by EmblAscii(), GenBankAsciiOrig(), and XMLAscii().

Split_Qscore_SeqGraph_By_DeltaSeq()

static void Split_Qscore_SeqGraph_By_DeltaSeq ( CSeq_annot::C_Data::TGraph &  graphs, CBioseq &  bioseq  )

static

Definition at line 613 of file fta_qscore.cpp.

References byte(), delta(), CSeq_inst_Base::eRepr_delta, ERR_QSCORE_MissingByteStore, ERR_QSCORE_NonByteGraph, ERR_QSCORE_NonLiteralDelta, ERR_QSCORE_NonZeroInGap, ERR_QSCORE_OutOfScores, ERR_QSCORE_UnknownDelta, ERR_QSCORE_ZeroLengthLiteral, ErrPostEx, CDelta_ext_Base::Get(), CSeq_graph_Base::C_Graph::GetByte(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CSeq_graph_Base::GetGraph(), CBioseq_Base::GetInst(), CBioseq::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_graph_Base::GetTitle(), CByte_graph_Base::GetValues(), i, CSeq_graph_Base::C_Graph::IsByte(), CSeq_inst_Base::IsSetExt(), CSeq_graph_Base::IsSetTitle(), literal(), QS_MAX_VALID_SCORE, QS_MIN_VALID_SCORE, CSeq_interval_Base::SetFrom(), CSeq_graph_Base::SetGraph(), CSeq_interval_Base::SetId(), CBioseq_Base::SetId(), CSeq_graph_Base::SetLoc(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::SetTitle(), CSeq_interval_Base::SetTo(), SEV_ERROR, and SEV_WARNING.

USING_SCOPE()

USING_SCOPE

(

objects

)