ajseqdata

Data type AjPSeqDesc

Defines the gene fields needed to support various standard sequence database entry formats, especially UniProt

Alias name(s)

Name	Description
AjSSeqDesc
AjOSeqDesc

Attributes

Name	Type	Description
Name	Recommended name (only one per sequence)
Short	String list of short names
EC	String list of EC numbers
AltNames	List of alternate description objects
SubNames	List of submitted name objects
Includes	List of names for included functional domains
Contains	List of names for post-processing components
Precursor	True if this is a precursor
Fragments	1 to mark as a fragment, more to mark as fragments

Data type AjPSeqSubdesc

Defines the gene fields needed to support various standard sequence database entry formats, especially UniProt

Alias name(s)

Name	Description
AjSSeqSubdesc
AjOSeqSubdesc

Attributes

Name	Type	Description
Name	Recommended name (only one per sequence)
Short	String list of short names
EC	String list of EC numbers
Allergen	String list of Ig-E mediated atopic allergens
Biotech	String list of biotechnology context names
Cdantigen	String list of Cell Differentiation antigens
Inn	String list of International Non-proprietary Names

Data type AjPSeqGene

Defines the gene fields needed to support various standard sequence database entry formats, especially UniProt

Alias name(s)

Name	Description
AjSSeqGene
AjOSeqGene

Attributes

Name	Type	Description
Name	Gene standard name
Synonyms	Accepted synonynms
Orf	Recognized open reading frame (ORF) names usually for sequencing projects in progress
Oln	Ordered locus name(s) representing order on chromosome

Data type AjPSeqDate

Defines the date fields needed to support various standard sequence database entry formats

Alias name(s)

Name	Description
AjSSeqDate
AjOSeqDate

Attributes

Name	Type	Description
CreDate	Creation date
ModDate	Entry modification date
SeqDate	Sequence modification date
CreRel	Database release when first released
ModRel	Database release when entry last changed
SeqRel	Database release when sequence last changed
CreVer	Entry version when last changed
ModVer	Entry version when last changed
SeqVer	Entry version when sequence last changed

Data type AjPSeqRef

Defines the fields needed to support various standard entry citation formats

Alias name(s)

Name	Description
AjSSeqRef
AjOSeqRef

Attributes

Name	Type	Description
Position	Sequence positions
Groupname	Working group or consortium
Authors	Author list, comma-delimited
Title	Title
Comment	Comment
Xref	Cross reference
Location	Location (journal, book, submission)
Loctype	Location type
Number	Reference number. This may be used in the feature table and references can disappear so the position in the lst is not enough
Padding	Padding to alignment boundary

Data type AjPSeqXref

Defines the fields needed to support various standard entry cross-reference formats

Alias name(s)

Name	Description
AjSSeqXref
AjOSeqXref

Attributes

Name	Type	Description
Db	Database name
Id	Primary identifier
Secid	Secondary identifier
Terid	Tertiary identifier
Quatid	Quaternary identifier
Type	Type of cross-reference
Start	Start position
End	End position

Data type AjPSeqQuery

Holds data needed to interpret the entry specification part of a USA. This can refer to an entry name (or "id"), and accession number or other queriable items.

ajpseqquery is created with the entry specification part of a USA (Uniform Sequence Address). The syntax is currently related to that used by SRS release 5.1.

Alias name(s)

Name	Description
AjSSeqQuery
AjOSeqQuery

Other related data structure(s)

Name	Description
AjPSeqset	Sequence sets
AjPSeqall	Sequence streams

Attributes

Name	Type	Description
DbName	Database name used by EMBOSS
DbAlias	Database name used by access method
DbType	Database type
Id	ID Wildcard
Acc	Accession Wildcard
Des	Description Wildcard
Key	Keyword Wildcard
Org	Taxonomy Wildcard
Sv	SeqVersion Wildcard
Gi	GenInfo Identifier Wildcard
CaseId	True if ID match is case-sensitive
HasAcc	True if entries have acc field
Method	Name of access method
Formatstr	Name of input sequence format
IndexDir	Index directory
Directory	Data directory
Filename	Individual filename
Exclude	File wildcards to exclude (spaced)
DbFields	Query fields (plus id and acc)
DbProxy	Proxy host
DbHttpVer	HTTP Version
Field	Query field
QryString	Query term
Application	External application command
Fpos	File position from fseek
Type	Enumerated query type
QryDone	Has the query been done yet
Access	Access function : see ajseqread.h
QryData	Private data for access function
Wild	True if query contains '*' or '?'
Padding	Padding to alignment boundary

Constructor(s)

Name	Description
ajSeqQueryNew	Default constructor

Destructor(s)

Name	Description
ajSeqQueryDel	Default destructor

Modifier(s)

Name	Description
ajSeqQueryClear	Clears all contents

Operator(s)

Name	Description
seqQueryMatch	Compares an AjPSeq to a query.

Modifier(s)

Name	Description
ajSeqQueryStarclear	Clears fully wild elements of a query because empty elements are the same.

Operator(s)

Name	Description
ajSeqQueryWild	Tests whether a query includes wildcards
ajSeqQueryIs	Tests whether a query has been defined

Data type AjPSeqin

Holds the sequence specification and information needed to read the sequence and possible further sequences.

Also holds information on a selected sequence range and other options.

Constructor(s)

Name	Description
ajSeqinNew	Default constructor

Destructor(s)

Name	Description
ajSeqinDel	Default destructor

Modifier(s)

Name	Description
ajSeqinUsa	Resets using a new USA
ajSeqinClear	Resets ready for reuse.
ajSeqinSetRange	Sets a sequence range for all input sequences

Other related data structure(s)

Name	Description
AjPSeq	Sequences
AjPSeqset	Sequence sets
AjPSeqall	Sequence streams

Attributes

Name	Type	Description
Name	Sequence name (replace on reading)
Acc	Sequence accession number (replace on reading)
Inputtype	Sequence type from ACD
Type	Sequence type N or P
Db	Database name (from commandline, replace on reading)
Full	Full name
Date	Date
Desc	One-line description
Doc	Full text
Inseq	Temporary input sequence holder
Begin	Start position
End	End position
List	List of USAs to be read
Usa	USA for the sequence
Ufo	UFO for features (if any)
Fttable	Input feature table (why in AjPSeqin?)
Ftquery	Feature table input spec
Formatstr	Sequence input format name
Filename	Original filename
Entryname	Entry name
Filebuff	Input sequence buffered file
Search	Search for more entries (always true?)
Single	Read single entries
CaseId	Id case sensitive (default false)
Features	true: read features if any
IsNuc	true: known to be nucleic
IsProt	true: known to be protein
multi	???? see also Single
multiset	true: seqsetall input
multidone	seqsetall input: true when set completed
Lower	true: convert to lower case -slower
Upper	true: convert to upper case -supper
Text	true: save full text of entry
Count	count of entries so far. Used when ACD reads first sequence and we need to reuse it in a Next loop
Filecount	Number of files read - used by seqsetall input
Fileseqs	Number of seqs in file - used by seqsetall input
Rev	Reverse/complement if true
Fpos	File position (fseek) for building USA
Query	Query data - see AjPSeqQuery
Data	Format data for reuse, e.g. multiple sequence input
Format	Sequence input format enum
Padding	Padding to alignment boundary

Data type AjPSeq

Holds the sequence itself, plus associated information such as a sequence name, accession number, format, type.

Also holds information on a selected sequence range and other options.

Sequence features can also be stored, but for efficiency reasons features are turned off by default.

Attributes

Name	Type	Description
Name	Name (ID)
Acc	Accession number (primary only)
Sv	SeqVersion number
Gi	GI NCBI version number
Tax	Main taxonomy (species)
Taxid	Main taxonomy (species) id in NCBI taxonomy
Organelle	Organelle taxonomy
Type	Type N or P
Molecule	Molecule type
Class	Class of entry
Division	Database division
Evidence	Experimental evidence (e.g. from UniProt)
Db	Database name from input
Setdb	Database name from command line
Full	Full name
Date	Creation, modification and sequence mod dates
Desc	One-line description
Fulldesc	Detailed description
Doc	Obsolete - see TextPtr
Rev	true: to be reverse-complemented
Reversed	true: has been reverse-complemented
Trimmed	true: has been trimmed
Circular	true: circular nucleotide molecule
Begin	start position (processed on reading)
End	end position (processed on reading)
Offset	offset from start
Offend	offset from end
Fpos	File position (fseek) for USA
Usa	USA for re-reading
Ufo	UFO for re-reading
Formatstr	Input format name
Filename	Original filename
Entryname	Entryname (ID)
TextPtr	Full text
Acclist	Secondary accessions
Keylist	Keyword list
Taxlist	Taxonomy list (organelle, species, taxa)
Genelist	Gene names list
Reflist	Reference citation list
Cmtlist	Comment block list
Xreflist	Cross reference list
Seq	The sequence
Fttable	Feature table
Accuracy	Accuracy values (one per base) from base calling
Format	Input format enum
EType	unused, obsolete
Weight	Weight from multiple alignment
Padding	Padding to alignment boundary

Data type AjPSeqset

Holds the sequence set itself, plus associated information such as a sequence names, accession number, format, type.

Also holds information on a selected sequence range and other options.

Sequence set features can also be stored, but for efficiency reasons features are turned off by default.

Alias name(s)

Name	Description
AjSSeqset
AjOSeqset

Other related data structure(s)

Name	Description
AjPSeq	Sequences
AjPSeqall	Sequence streams

Attributes

Name	Type	Description
Size	Number of sequences
Len	Maximum sequence length
Begin	start position
End	end position
Offset	offset from start
Offend	offset from end
Rev	true: reverse-complemented
Trimmed	true: has been trimmed
Type	Type N or P
Totweight	total weight (usually 1.0 * Size)
EType	enum type obsolete
Formatstr	Input format name
Filename	Original filename
Full	Full name
Name	Name
Usa	USA for re-reading
Ufo	UFO for re-reading
Seq	Sequence array (see Size)
Seqweight	Sequence weights (see also AjPSeq)
Format	Input format enum
Padding	Padding to alignment boundary

Constructor(s)

Name	Description
ajSeqsetNew	Default constructor

Destructor(s)

Name	Description
ajSeqsetDel	Default destructor

Input

Name	Description
ajSeqsetRead	Master input routine for a sequence set

Modifier(s)

Name	Description
ajSeqsetToLower	Converts a sequence set to lower case
ajSeqsetToUpper	Converts a sequence set to upper case

Cast(s)

Name	Description
ajSeqsetLen	Returns the maximum length of a sequence set
ajSeqsetSize	Returns the number of sequences in a sequence set
ajSeqsetAcc	Returns the accession number of a sequence in a set
ajSeqsetName	Returns the name of a sequence in a set
ajSeqsetSeq	Returns the char* pointer to a sequence in a set
ajSeqsetIsNuc	Tests whether the sequence set is nucleotide
ajSeqsetIsProt	Tests whether the sequence set is protein
ajSeqsetGetFilename	Returns the filename of a sequence set

Output

Name	Description
ajSeqsetWrite	Writes out all sequences in a set

Data type AjPSeqall

Inherits an AjPSeq but allows more sequences to be read from the same input by also inheriting the AjPSeqin input object.

Constructor(s)

Name	Description
ajSeqallNew	Default constructor

Destructor(s)

Name	Description
ajSeqallDel	Default destructor

Modifier(s)

Name	Description
ajSeqallNext	Master sequence stream input, reads next sequence from an open input stream.

Cast(s)

Name	Description
ajSeqallGetFilename	Returns the filename of a seqall object.

Other related data structure(s)

Name	Description
AjPSeq	Sequences
AjPSeqin	Sequence input
AjPSeqset	Sequence sets

Attributes

Name	Type	Description
Seq	Current sequence
Seqin	Sequence input for reading next
Totseqs	Count of sequences so far
Totlength	Count of sequence lengths so far
Count	Count of sequences so far
Begin	start position
End	end position
Rev	if true: reverse-complement
Returned	if true: Seq object has been returned to a new owner and is not to be deleted by the destructor
Padding	Padding to alignment boundary