Importer.cxx File Reference

#include "tools.h"
#include "DBwriter.h"
#include <arbdb.h>
#include <arb_stdstr.h>

Include dependency graph for Importer.cxx:

Go to the source code of this file.

Functions
static bool	is_escaped (const string &str, size_t pos)
static bool	splitGenebankTag (const string &line, string &tag, string &content)
static long	scanSeqlenFromLOCUS (const string &locusContent)
static bool	splitEmblTag (const string &line, string &tag, string &content)
static long	scanSeqlenFromID (const string &idContent)
bool	parseCounter (bool expect, BaseCounter &headerCount, StringParser &parser, Base base, const char *word)

Variables
static MetaTag	genebank_meta_description []
static MetaTag	embl_meta_description []

Function Documentation

static bool is_escaped ( const string &  str, size_t  pos  )

static

Definition at line 21 of file Importer.cxx.

Referenced by FeatureLine::FeatureLine().

static bool splitGenebankTag ( const string &  line, string &  tag, string &  content  )

static

Definition at line 366 of file Importer.cxx.

References gi_assert, and line.

static long scanSeqlenFromLOCUS ( const string &  locusContent )

static

Definition at line 401 of file Importer.cxx.

References StringParser::eatSpaces(), StringParser::expectContent(), StringParser::extractNumber(), and StringParser::extractWord().

static bool splitEmblTag ( const string &  line, string &  tag, string &  content  )

static

Definition at line 509 of file Importer.cxx.

References line.

static long scanSeqlenFromID ( const string &  idContent )

static

Definition at line 538 of file Importer.cxx.

References StringParser::eatSpaces(), and StringParser::extractWord().

bool parseCounter ( bool  expect, BaseCounter &  headerCount, StringParser &  parser, Base  base, const char *  word  )

inline

Definition at line 652 of file Importer.cxx.

References BaseCounter::addCount(), StringParser::advance(), StringParser::eatNumber(), StringParser::eatSpaces(), StringParser::expectSpaces(), GBS_global_string(), StringParser::getPosition(), StringParser::lookingAt(), StringParser::rest(), StringParser::setPosition(), and start.

Variable Documentation

MetaTag genebank_meta_description[]

static

Initial value:

= {
    { "LOCUS",     "org_locus",   MT_HEADER },

    { "REFERENCE", "",            MT_REF_START },
    { "  AUTHORS", "author",      MT_REF },
    { "  TITLE",   "title",       MT_REF },
    { "  CONSRTM", "refgrp",      MT_REF },
    { "  JOURNAL", "journal",     MT_REF },
    { "   PUBMED", "pubmed_id",   MT_REF },
    { "  MEDLINE", "medline_id",  MT_REF },
    { "  REMARK",  "refremark",   MT_REF },

    { "DEFINITION", "definition", MT_BASIC },
    { "ACCESSION",  "acc",        MT_BASIC },
    { "VERSION",    "version",    MT_BASIC },
    { "DBLINK",     "db_xref",    MT_BASIC },
    { "KEYWORDS",   "keywd",      MT_BASIC },
    { "SOURCE",     "full_name",  MT_BASIC },
    { "  ORGANISM", "tax",        MT_BASIC },
    { "COMMENT",    "comment",    MT_BASIC },
    { "PROJECT",    "projref",    MT_BASIC },

    { "FEATURES", "", MT_FEATURE_START },
    { "CONTIG",   "", MT_CONTIG },
    { "BASE",     "", MT_SEQUENCE_START }, 
    { "ORIGIN",   "", MT_SEQUENCE_START }, 
    { "//",       "", MT_END },

    { "", "", MT_IGNORE },      
}

Definition at line 281 of file Importer.cxx.

MetaTag embl_meta_description[]

static

Definition at line 312 of file Importer.cxx.