ajseqdata

Enum AjEXrefType

Enumerated value(s)

Name
XREF_UNKNOWN	type not defined
XREF_DR	DR line in EMBL, SwissProt
XREF_DBXREF	db_xref in EMBL/Genbank
XREF_EC	EC= in SwissProt
XREF_DESC	Allergen= and CD_Antigen= in SwissProt DE
XREF_TAX	NCBI_TaxID
XREF_RX	RX line in EMBL or SwissProt
XREF_MAX	Beyond last defined value

Data type AjPSeqDesc

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

Alias name(s)

Name
AjSSeqDesc
AjOSeqDesc

Attributes

Name	Type	Description
Name	AjPStr	Recommended name (only one per sequence)
Short	AjPList	String list of short names
EC	AjPList	String list of EC numbers
Multi	AjPList	String list of multiple description lines
AltNames	AjPList	List of alternate description objects
SubNames	AjPList	List of submitted name objects
Includes	AjPList	List of names for included functional domains
Contains	AjPList	List of names for post-processing components
Precursor	AjBool	True if this is a precursor
Fragments	ajuint	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
AjSSeqSubdesc
AjOSeqSubdesc

Attributes

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

Attributes

Name	Type	Description
Name	AjPStr	Gene standard name
Synonyms	AjPStr	Accepted synonyms
Orf	AjPStr	Recognised open reading frame (ORF) names usually for sequencing projects in progress
Oln	AjPStr	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
AjSSeqDate
AjOSeqDate

Attributes

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

Data type AjPSeqRange

Defines the queries that map to positions in a sequence (or physical map)

Alias name(s)

Name
AjSSeqRange
AjOSeqRange

Attributes

Name	Type	Description
Query	AjPStr	Query
Start	ajulong	Start position
Length	ajulong	Length

Data type AjPSeqRef

Defines the fields needed to support various standard entry citation formats

Alias name(s)

Name
AjSSeqRef
AjOSeqRef

Attributes

Name	Type	Description
Position	AjPStr	Sequence positions
Groupname	AjPStr	Working group or consortium
Authors	AjPStr	Author list, comma-delimited
Title	AjPStr	Title
Comment	AjPStr	Comment
Xref	AjPStr	Cross reference
Location	AjPStr	Location (journal, book, submission)
Loctype	AjPStr	Location type
Number	ajuint	Reference number. This may be used in the feature table and references can disappear so the position in the list is not enough
Padding	char[4]	Padding to alignment boundary

Data type AjPSeqXref

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

Alias name(s)

Name
AjSSeqXref
AjOSeqXref

Attributes

Name	Type	Description
Db	AjPStr	Database name
Id	AjPStr	Primary identifier
Secid	AjPStr	Secondary identifier
Terid	AjPStr	Tertiary identifier
Quatid	AjPStr	Quaternary identifier
Type	ajuint	Type of cross-reference
Start	ajuint	Start position
End	ajuint	End position
Padding	char[4]	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.

Alias name(s)

Name
AjOSeq
AjSSeq

Attributes

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

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
AjSSeqset
AjOSeqset

Other related data structure(s)

Name	Description
AjPSeq	Sequences
AjPSeqall	Sequence streams

Attributes

Name	Type	Description
Size	ajuint	Number of sequences
Len	ajuint	Maximum sequence length
Begin	ajint	start position
End	ajint	end position
Offset	ajuint	offset from start
Offend	ajuint	offset from end
Rev	AjBool	true: reverse-complemented
Trimmed	AjBool	true: has been trimmed
Type	AjPStr	Type N or P
Totweight	float	total weight (usually 1.0 * Size)
EType	AjEnum	enum type obsolete
Formatstr	AjPStr	Input format name
Filename	AjPStr	Original filename
Full	AjPStr	Full name
Name	AjPStr	Name
Usa	AjPStr	USA for re-reading
Ufo	AjPStr	UFO for re-reading
Seq	AjPSeq*	Sequence array (see Size)
Seqweight	float*	Sequence weights (see also AjPSeq)
Format	AjEnum	Input format enum
Padding	char[4]	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 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.

Alias name(s)

Name
AjSSeqin
AjOSeqin

Other related data structure(s)

Name	Description
AjPSeq	Sequences
AjPSeqset	Sequence sets
AjPSeqall	Sequence streams

Attributes

Name	Type	Description
Input	AjPTextin	Text file input object
Name	AjPStr	Sequence name (replace on reading)
Acc	AjPStr	Sequence accession number (replace on reading)
Inputtype	AjPStr	Sequence type from ACD
Type	AjPStr	Sequence type N or P
Full	AjPStr	Full name
Date	AjPStr	Date
Desc	AjPStr	One-line description
Doc	AjPStr	Full text
Inseq	AjPStr	Temporary input sequence holder
DbSequence	AjPStr	Field name of sequence string
Usalist	AjPList	List of USA processing nodes
Begin	ajint	Start position
End	ajint	End position
Ufo	AjPStr	UFO for features (if any)
Fttable	AjPFeattable	Input feature table (why in AjPSeqin?)
Ftquery	AjPFeattabin	Feature table input spec
Entryname	AjPStr	Entry name
Minimal	AjBool	true: read minimal information only
Features	AjBool	true: read features if any
IsNuc	AjBool	true: known to be nucleic
IsProt	AjBool	true: known to be protein
Multiset	AjBool	true: seqsetall input
Multidone	AjBool	seqsetall input: true when set completed
Lower	AjBool	true: convert to lower case -slower
Upper	AjBool	true: convert to upper case -supper
Rev	AjBool	Reverse/complement if true
Circular	AjBool	Set sequences to be circular
SeqData	void*	Format data for reuse, e.g. multiple sequence input

Data type AjPSeqall

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

Alias name(s)

Name
AjSSeqall
AjOSeqall

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	AjPSeq	Current sequence
Seqin	AjPSeqin	Sequence input for reading next
Totseqs	ajlong	Count of sequences so far
Totlength	ajlong	Count of sequence lengths so far
Count	ajint	Count of sequences so far
Begin	ajint	start position
End	ajint	end position
Rev	AjBool	if true: reverse-complement
Returned	AjBool	if true: Seq object has been returned to a new owner and is not to be deleted by the destructor
Padding	char[4]	Padding to alignment boundary

Data type AjPSeqAccess

Holds information needed to read a sequence from a database. Access methods are defined for each known database type.

Sequences are read from the database using the defined database access function, which is usually a static function within ajtextdb.c ajseqdb.c

This should be a static data object but is needed for the definition of AjPSeqin.

Alias name(s)

Name
AjSSeqAccess
AjOSeqAccess

Attributes

Name	Type	Description
Name	const char*	Access method name used in emboss.default
Access	AjBool function	Access function
AccessFree	AjBool function	Access cleanup function
Qlink	const char*	Supported query link operators
Desc	const char*	Description
Alias	AjBool	Alias for another name
Entry	AjBool	Supports retrieval of single entries
Query	AjBool	Supports retrieval of selected entries
All	AjBool	Supports retrieval of all entries
Chunked	AjBool	Supports retrieval of entries in chunks
Padding	AjBool	Padding to alignment boundary

Data type AjPSeqout

Holds definition of sequence output.

Alias name(s)

Name
AjSSeqout
AjOSeqout

Attributes

Name	Type	Description
Name	AjPStr	Name (ID)
Acc	AjPStr	Accession number (primary only)
Sv	AjPStr	SeqVersion number
Gi	AjPStr	GI NCBI version number
Desc	AjPStr	One-line description
Tax	AjPStr	Main taxonomy (species)
Taxcommon	AjPStr	Main taxonomy (species) common name
Taxid	AjPStr	Main taxonomy (species) id in NCBI taxonomy
Organelle	AjPStr	Organelle taxonomy
Type	AjPStr	Type N or P
Outputtype	AjPStr	Output sequence known type
Molecule	AjPStr	Molecule type
Class	AjPStr	Class of entry
Division	AjPStr	Database division
Evidence	AjPStr	Experimental evidence (e.g. from UniProt)
Db	AjPStr	Database name from input name
Setdb	AjPStr	Database name from input command line
Setoutdb	AjPStr	Database name from command line
Full	AjPStr	Full name
Date	AjPSeqDate	Dates
Fulldesc	AjPSeqDesc	Dates
Doc	AjPStr	Obsolete - see TextPtr
Usa	AjPStr	USA for re-reading
Ufo	AjPStr	UFO for re-reading
Fttable	AjPFeattable	Feature table
Ftquery	AjPFeattabOut	Feature table output
FtFormat	AjPStr	Feature output format (if not in UFO)
FtFilename	AjPStr	Feature output filename (if not in UFO)
Informatstr	AjPStr	Input format
Formatstr	AjPStr	Output format
EType	AjEnum	unused, obsolete
Format	AjEnum	Output format index
Filename	AjPStr	Output filename (if not in USA)
Directory	AjPStr	Output directory
Entryname	AjPStr	Entry name
Acclist	AjPList	Secondary accessions
Keylist	AjPList	Keyword list
Taxlist	AjPList	Taxonomy list
Genelist	AjPList	Gene list
Reflist	AjPList	References (citations)
Cmtlist	AjPList	Comment block list
Xreflist	AjPList	Database cross reference list
Seq	AjPStr	The sequence
File	AjPFile	Output file
Knownfile	AjPFile	Already open output file (we don't close this one)
Extension	AjPStr	File extension
Savelist	AjPList	Previous sequences saved for later output (e.g. MSF format)
Accuracy	float*	Accuracy values (one per base) from base calling
Data	void*	Format data for reuse, e.g. multiple sequence output
Cleanup	void function	Function to write remaining lines on closing
Rev	AjBool	true: to be reverse-complemented
Circular	AjBool	true: circular nucleotide molecule
Single	AjBool	If true, single sequence in each file (-ossingle)
Features	AjBool	If true, save features with sequence or in file
Qualsize	ajuint	Size of Accuracy array
Count	ajint	Number of sequences
Offset	ajint	offset from start

Constructor(s)

Name	Description
ajSeqoutNew	Default constructor

Destructor(s)

Name	Description
ajSeqoutDel	Default destructor

Modifier(s)

Name	Description
ajSeqoutUsa	Resets using a new USA
ajSeqoutClear	Resets ready for reuse.
ajSeqoutOpen	If the file is not yet open, calls seqoutUsaProcess

Cast(s)

Name	Description
ajSeqoutCheckGcg	Calculates the GCG checksum for a sequence set.

Modifier(s)

Name	Description
ajSeqWrite	Master sequence output routine
ajSeqsetWrite	Master sequence set output routine
ajSeqFileNewOut	Opens an output file for sequence writing.

Other related data structure(s)

Name	Description
AjPSeq	Sequences

Attributes

Name	Type	Description
Padding	char[4]	Padding to alignment boundary