#include "ftablock.h"

Include dependency graph for fta_xml.h:

This graph shows which files directly or indirectly include this file:

Macros
#define	INSDSEQ_START "<INSDSeq>"

#define	INSDSEQ_END "</INSDSeq>"

#define	INSDSEQ_LOCUS 1

#define	INSDSEQ_LENGTH 2

#define	INSDSEQ_STRANDEDNESS 3

#define	INSDSEQ_MOLTYPE 4

#define	INSDSEQ_TOPOLOGY 5

#define	INSDSEQ_DIVISION 6

#define	INSDSEQ_UPDATE_DATE 7

#define	INSDSEQ_CREATE_DATE 8

#define	INSDSEQ_UPDATE_RELEASE 9

#define	INSDSEQ_CREATE_RELEASE 10

#define	INSDSEQ_DEFINITION 11

#define	INSDSEQ_PRIMARY_ACCESSION 12

#define	INSDSEQ_ENTRY_VERSION 13

#define	INSDSEQ_ACCESSION_VERSION 14

#define	INSDSEQ_OTHER_SEQIDS 15

#define	INSDSEQ_SECONDARY_ACCESSIONS 16

#define	INSDSEQ_KEYWORDS 17

#define	INSDSEQ_SEGMENT 18

#define	INSDSEQ_SOURCE 19

#define	INSDSEQ_ORGANISM 20

#define	INSDSEQ_TAXONOMY 21

#define	INSDSEQ_REFERENCES 22

#define	INSDSEQ_COMMENT 23

#define	INSDSEQ_PRIMARY 24

#define	INSDSEQ_SOURCE_DB 25

#define	INSDSEQ_DATABASE_REFERENCE 26

#define	INSDSEQ_FEATURE_TABLE 27

#define	INSDSEQ_SEQUENCE 28

#define	INSDSEQ_CONTIG 29

#define	INSDSECONDARY_ACCN 30

#define	INSDKEYWORD 31

#define	INSDFEATURE 32

#define	INSDFEATURE_KEY 33

#define	INSDFEATURE_LOCATION 34

#define	INSDFEATURE_INTERVALS 35

#define	INSDFEATURE_QUALS 36

#define	INSDINTERVAL 37

#define	INSDINTERVAL_FROM 38

#define	INSDINTERVAL_TO 39

#define	INSDINTERVAL_POINT 40

#define	INSDINTERVAL_ACCESSION 41

#define	INSDQUALIFIER 42

#define	INSDQUALIFIER_NAME 43

#define	INSDQUALIFIER_VALUE 44

#define	INSDREFERENCE 45

#define	INSDREFERENCE_REFERENCE 46

#define	INSDREFERENCE_POSITION 47

#define	INSDREFERENCE_AUTHORS 48

#define	INSDREFERENCE_CONSORTIUM 49

#define	INSDREFERENCE_TITLE 50

#define	INSDREFERENCE_JOURNAL 51

#define	INSDREFERENCE_MEDLINE 52

#define	INSDREFERENCE_PUBMED 53

#define	INSDREFERENCE_REMARK 54

#define	INSDREFERENCE_XREF 55

#define	INSDXREF 56

#define	INSDXREF_DBNAME 57

#define	INSDXREF_ID 58

#define	INSDAUTHOR 59

#define	XML_FEATURES 1

Functions
char *	XMLLoadEntry (ParserPtr pp, bool err)

unique_ptr< string >	XMLGetTagValue (const char entry, const XmlIndex xip)

unique_ptr< string >	XMLFindTagValue (const char entry, const XmlIndex xip, Int4 tag)

DataBlkPtr	XMLBuildRefDataBlk (char entry, const XmlIndex xip, int type)

unique_ptr< string >	XMLConcatSubTags (const char entry, const XmlIndex xip, Int4 tag, Char sep)

void	XMLGetKeywords (const char entry, const XmlIndex xip, TKeywordList &keywords)

Macro Definition Documentation

◆ INSDAUTHOR

#define INSDAUTHOR 59

Definition at line 103 of file fta_xml.h.

◆ INSDFEATURE

#define INSDFEATURE 32

Definition at line 76 of file fta_xml.h.

◆ INSDFEATURE_INTERVALS

#define INSDFEATURE_INTERVALS 35

Definition at line 79 of file fta_xml.h.

◆ INSDFEATURE_KEY

#define INSDFEATURE_KEY 33

Definition at line 77 of file fta_xml.h.

◆ INSDFEATURE_LOCATION

#define INSDFEATURE_LOCATION 34

Definition at line 78 of file fta_xml.h.

◆ INSDFEATURE_QUALS

#define INSDFEATURE_QUALS 36

Definition at line 80 of file fta_xml.h.

◆ INSDINTERVAL

#define INSDINTERVAL 37

Definition at line 81 of file fta_xml.h.

◆ INSDINTERVAL_ACCESSION

#define INSDINTERVAL_ACCESSION 41

Definition at line 85 of file fta_xml.h.

◆ INSDINTERVAL_FROM

#define INSDINTERVAL_FROM 38

Definition at line 82 of file fta_xml.h.

◆ INSDINTERVAL_POINT

#define INSDINTERVAL_POINT 40

Definition at line 84 of file fta_xml.h.

◆ INSDINTERVAL_TO

#define INSDINTERVAL_TO 39

Definition at line 83 of file fta_xml.h.

◆ INSDKEYWORD

#define INSDKEYWORD 31

Definition at line 75 of file fta_xml.h.

◆ INSDQUALIFIER

#define INSDQUALIFIER 42

Definition at line 86 of file fta_xml.h.

◆ INSDQUALIFIER_NAME

#define INSDQUALIFIER_NAME 43

Definition at line 87 of file fta_xml.h.

◆ INSDQUALIFIER_VALUE

#define INSDQUALIFIER_VALUE 44

Definition at line 88 of file fta_xml.h.

◆ INSDREFERENCE

#define INSDREFERENCE 45

Definition at line 89 of file fta_xml.h.

◆ INSDREFERENCE_AUTHORS

#define INSDREFERENCE_AUTHORS 48

Definition at line 92 of file fta_xml.h.

◆ INSDREFERENCE_CONSORTIUM

#define INSDREFERENCE_CONSORTIUM 49

Definition at line 93 of file fta_xml.h.

◆ INSDREFERENCE_JOURNAL

#define INSDREFERENCE_JOURNAL 51

Definition at line 95 of file fta_xml.h.

◆ INSDREFERENCE_MEDLINE

#define INSDREFERENCE_MEDLINE 52

Definition at line 96 of file fta_xml.h.

◆ INSDREFERENCE_POSITION

#define INSDREFERENCE_POSITION 47

Definition at line 91 of file fta_xml.h.

◆ INSDREFERENCE_PUBMED

#define INSDREFERENCE_PUBMED 53

Definition at line 97 of file fta_xml.h.

◆ INSDREFERENCE_REFERENCE

#define INSDREFERENCE_REFERENCE 46

Definition at line 90 of file fta_xml.h.

◆ INSDREFERENCE_REMARK

#define INSDREFERENCE_REMARK 54

Definition at line 98 of file fta_xml.h.

◆ INSDREFERENCE_TITLE

#define INSDREFERENCE_TITLE 50

Definition at line 94 of file fta_xml.h.

◆ INSDREFERENCE_XREF

#define INSDREFERENCE_XREF 55

Definition at line 99 of file fta_xml.h.

◆ INSDSECONDARY_ACCN

#define INSDSECONDARY_ACCN 30

Definition at line 74 of file fta_xml.h.

◆ INSDSEQ_ACCESSION_VERSION

#define INSDSEQ_ACCESSION_VERSION 14

Definition at line 55 of file fta_xml.h.

◆ INSDSEQ_COMMENT

#define INSDSEQ_COMMENT 23

Definition at line 64 of file fta_xml.h.

◆ INSDSEQ_CONTIG

#define INSDSEQ_CONTIG 29

Definition at line 70 of file fta_xml.h.

◆ INSDSEQ_CREATE_DATE

#define INSDSEQ_CREATE_DATE 8

Definition at line 49 of file fta_xml.h.

◆ INSDSEQ_CREATE_RELEASE

#define INSDSEQ_CREATE_RELEASE 10

Definition at line 51 of file fta_xml.h.

◆ INSDSEQ_DATABASE_REFERENCE

#define INSDSEQ_DATABASE_REFERENCE 26

Definition at line 67 of file fta_xml.h.

◆ INSDSEQ_DEFINITION

#define INSDSEQ_DEFINITION 11

Definition at line 52 of file fta_xml.h.

◆ INSDSEQ_DIVISION

#define INSDSEQ_DIVISION 6

Definition at line 47 of file fta_xml.h.

◆ INSDSEQ_END

#define INSDSEQ_END "</INSDSeq>"

Definition at line 40 of file fta_xml.h.

◆ INSDSEQ_ENTRY_VERSION

#define INSDSEQ_ENTRY_VERSION 13

Definition at line 54 of file fta_xml.h.

◆ INSDSEQ_FEATURE_TABLE

#define INSDSEQ_FEATURE_TABLE 27

Definition at line 68 of file fta_xml.h.

◆ INSDSEQ_KEYWORDS

#define INSDSEQ_KEYWORDS 17

Definition at line 58 of file fta_xml.h.

◆ INSDSEQ_LENGTH

#define INSDSEQ_LENGTH 2

Definition at line 43 of file fta_xml.h.

◆ INSDSEQ_LOCUS

#define INSDSEQ_LOCUS 1

Definition at line 42 of file fta_xml.h.

◆ INSDSEQ_MOLTYPE

#define INSDSEQ_MOLTYPE 4

Definition at line 45 of file fta_xml.h.

◆ INSDSEQ_ORGANISM

#define INSDSEQ_ORGANISM 20

Definition at line 61 of file fta_xml.h.

◆ INSDSEQ_OTHER_SEQIDS

#define INSDSEQ_OTHER_SEQIDS 15

Definition at line 56 of file fta_xml.h.

◆ INSDSEQ_PRIMARY

#define INSDSEQ_PRIMARY 24

Definition at line 65 of file fta_xml.h.

◆ INSDSEQ_PRIMARY_ACCESSION

#define INSDSEQ_PRIMARY_ACCESSION 12

Definition at line 53 of file fta_xml.h.

◆ INSDSEQ_REFERENCES

#define INSDSEQ_REFERENCES 22

Definition at line 63 of file fta_xml.h.

◆ INSDSEQ_SECONDARY_ACCESSIONS

#define INSDSEQ_SECONDARY_ACCESSIONS 16

Definition at line 57 of file fta_xml.h.

◆ INSDSEQ_SEGMENT

#define INSDSEQ_SEGMENT 18

Definition at line 59 of file fta_xml.h.

◆ INSDSEQ_SEQUENCE

#define INSDSEQ_SEQUENCE 28

Definition at line 69 of file fta_xml.h.

◆ INSDSEQ_SOURCE

#define INSDSEQ_SOURCE 19

Definition at line 60 of file fta_xml.h.

◆ INSDSEQ_SOURCE_DB

#define INSDSEQ_SOURCE_DB 25

Definition at line 66 of file fta_xml.h.

◆ INSDSEQ_START

#define INSDSEQ_START "<INSDSeq>"

Definition at line 39 of file fta_xml.h.

◆ INSDSEQ_STRANDEDNESS

#define INSDSEQ_STRANDEDNESS 3

Definition at line 44 of file fta_xml.h.

◆ INSDSEQ_TAXONOMY

#define INSDSEQ_TAXONOMY 21

Definition at line 62 of file fta_xml.h.

◆ INSDSEQ_TOPOLOGY

#define INSDSEQ_TOPOLOGY 5

Definition at line 46 of file fta_xml.h.

◆ INSDSEQ_UPDATE_DATE

#define INSDSEQ_UPDATE_DATE 7

Definition at line 48 of file fta_xml.h.

◆ INSDSEQ_UPDATE_RELEASE

#define INSDSEQ_UPDATE_RELEASE 9

Definition at line 50 of file fta_xml.h.

◆ INSDXREF

#define INSDXREF 56

Definition at line 100 of file fta_xml.h.

◆ INSDXREF_DBNAME

#define INSDXREF_DBNAME 57

Definition at line 101 of file fta_xml.h.

◆ INSDXREF_ID

#define INSDXREF_ID 58

Definition at line 102 of file fta_xml.h.

◆ XML_FEATURES

#define XML_FEATURES 1

Definition at line 105 of file fta_xml.h.

Function Documentation

◆ XMLBuildRefDataBlk()

DataBlkPtr XMLBuildRefDataBlk	(	char *	entry,
		const XmlIndex *	xip,
		int	type
	)

Definition at line 1471 of file xm_index.cpp.

References INSDSEQ_REFERENCES, DataBlk::mOffset, DataBlk::mpData, DataBlk::mpNext, DataBlk::mType, XmlIndex::next, XmlIndex::subtags, XmlIndex::tag, and XmlIndex::type.

Referenced by ImpFeatPub(), SeqFeatPub(), and XMLGetDescr().

◆ XMLConcatSubTags()

unique_ptr<string> XMLConcatSubTags	(	const char *	entry,
		const XmlIndex *	xip,
		Int4	tag,
		Char	sep
	)

Definition at line 1527 of file xm_index.cpp.

References buf, XmlIndex::end, i, XmlIndex::next, XmlIndex::start, XmlIndex::subtags, tag, XmlIndex::tag, and XMLRestoreSpecialCharacters().

Referenced by XMLGetEMBLBlock(), XMLGetGBBlock(), and XMLRefs().

◆ XMLFindTagValue()

unique_ptr<string> XMLFindTagValue	(	const char *	entry,
		const XmlIndex *	xip,
		Int4	tag
	)

Definition at line 214 of file xm_index.cpp.

References XmlIndex::next, tag, XmlIndex::tag, and XMLGetTagValue().

Referenced by GetEmblBlockXref(), GetSeqData(), SeqFeatPub(), XMLDefVsHTGKeywords(), XMLGetDescr(), XMLGetDivision(), XMLGetEMBLBlock(), XMLGetGBBlock(), XMLGetInstContig(), XMLGetMolInfo(), and XMLRefs().

◆ XMLGetKeywords()

void XMLGetKeywords	(	const char *	entry,
		const XmlIndex *	xip,
		TKeywordList &	keywords
	)

Definition at line 1504 of file xm_index.cpp.

References INSDSEQ_KEYWORDS, XmlIndex::next, XmlIndex::subtags, XmlIndex::tag, and XMLGetTagValue().

Referenced by CollectGapFeats(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ XMLGetTagValue()

unique_ptr<string> XMLGetTagValue	(	const char *	entry,
		const XmlIndex *	xip
	)

Definition at line 202 of file xm_index.cpp.

References buf, XmlIndex::end, XmlIndex::start, and XMLRestoreSpecialCharacters().

Referenced by XMLAccessionsCheck(), XMLFakeBioSources(), XMLFindTagValue(), XMLGetInst(), XMLGetKeywords(), XMLGetQuals(), XMLGetSegment(), XMLGetXrefs(), XMLIndexReferences(), XMLInitialEntry(), XMLKeywordsCheck(), and XMLLoadFeatBlk().

◆ XMLLoadEntry()

char* XMLLoadEntry	(	ParserPtr	pp,
		bool	err
	)

Definition at line 953 of file xm_index.cpp.

References Char, Parser::curindx, Parser::entrylist, ERR_FORMAT_NonAsciiChar, ErrPostEx, i, Indexblk::len, Indexblk::linenum, MemFree(), Indexblk::offset, s_GetCharAndAdvance(), s_HasInput(), s_SetPointer(), SEV_WARNING, and StringNew().

Referenced by XMLAscii(), and XMLIndex().

Macros

Functions