ajseqread.c

Section: Sequence Input Constructors

All constructors return a new sequence input object by pointer. It is the responsibility of the user to first destroy any previous sequence input object. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions: ajSeqinNew

Function ajSeqinNew

Creates a new sequence input object.

Synopsis

Prototype
AjPSeqin ajSeqinNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqin RETURNNew sequence input object.

Returns
AjPSeqin:New sequence input object.

Description

Creates a new sequence input object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Input Destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence input object.

Functions: ajSeqinDel

Function ajSeqinDel

Deletes a sequence input object.

Synopsis

Prototype
void ajSeqinDel (
      AjPSeqin* pthis
);

TypeNameRead/WriteDescription
AjPSeqin*pthisDeleteSequence input
void RETURN

Output
pthis:(Delete)Sequence input
Returns
void:No return value

Description

Deletes a sequence input object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Input Modifiers

These functions use the contents of a sequence input object and update them.

Functions: ajSeqinUsa ajSeqinSetNuc ajSeqinSetProt ajSeqinSetRange

Function ajSeqinUsa

Creates or resets a sequence input object using a new Universal Sequence Address

Synopsis

Prototype
void ajSeqinUsa (
      AjPSeqin* pthis,
      const AjPStr Usa
);

TypeNameRead/WriteDescription
AjPSeqin*pthisModifySequence input object.
const AjPStrUsaInputUSA
void RETURN

Input
Usa:(Input)USA
Input & Output
pthis:(Modify)Sequence input object.
Returns
void:No return value

Description

Creates or resets a sequence input object using a new Universal Sequence Address

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinSetNuc

Sets the type to be forced as nucleic for a sequence input object

Synopsis

Prototype
void ajSeqinSetNuc (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySequence input object to be set.
void RETURN

Input & Output
seqin:(Modify)Sequence input object to be set.
Returns
void:No return value

Description

Sets the type to be forced as nucleic for a sequence input object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinSetProt

Sets the type to be forced as protein for a sequence input object

Synopsis

Prototype
void ajSeqinSetProt (
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySequence input object to be set.
void RETURN

Input & Output
seqin:(Modify)Sequence input object to be set.
Returns
void:No return value

Description

Sets the type to be forced as protein for a sequence input object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinSetRange

Sets the start and end positions for a sequence input object

Synopsis

Prototype
void ajSeqinSetRange (
      AjPSeqin seqin,
      ajint ibegin,
      ajint iend
);

TypeNameRead/WriteDescription
AjPSeqinseqinModifySequence input object to be set.
ajintibeginInputStart position. Negative values are from the end.
ajintiendInputEnd position. Negative values are from the end.
void RETURN

Input
ibegin:(Input)Start position. Negative values are from the end.
iend:(Input)End position. Negative values are from the end.
Input & Output
seqin:(Modify)Sequence input object to be set.
Returns
void:No return value

Description

Sets the start and end positions for a sequence input object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Input Operators

These functions use the contents of a sequence input object but do not make any changes.

Functions: ajSeqAllRead ajSeqallFile ajSeqallNext ajSeqinClearPos ajSeqinClear

Function ajSeqAllRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Return the results in the AjPSeq object but leave the file open for future calls.

Synopsis

Prototype
AjBool ajSeqAllRead (
      AjPSeq thys,
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqthysOutputSequence returned.
AjPSeqinseqinModifySequence input definitions
AjBool RETURNajTrue on success.

Output
thys:(Output)Sequence returned.
Input & Output
seqin:(Modify)Sequence input definitions
Returns
AjBool:ajTrue on success.

Description

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Return the results in the AjPSeq object but leave the file open for future calls.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqallFile

Parse a USA Uniform Sequence Address

Return the results in the AjPSeqall object but leave the file open for future calls.

Synopsis

Prototype
AjPSeqall ajSeqallFile (
      const AjPStr usa
);

TypeNameRead/WriteDescription
const AjPStrusaInputsequence usa.
AjPSeqall RETURNseqall object

Input
usa:(Input)sequence usa.
Returns
AjPSeqall:seqall object

Description

Parse a USA Uniform Sequence Address

Return the results in the AjPSeqall object but leave the file open for future calls.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqallNext

Reads the next sequence into a sequence stream. For the first call this simply returns the sequence already loaded. For later calls a new sequence is read.

Synopsis

Prototype
AjBool ajSeqallNext (
      AjPSeqall seqall,
      AjPSeq* retseq
);

TypeNameRead/WriteDescription
AjPSeqallseqallModifySequence stream
AjPSeq*retseqOutputSequence
AjBool RETURNajTrue if a sequence was refound. ajFalse when all is done.

Output
retseq:(Output)Sequence
Input & Output
seqall:(Modify)Sequence stream
Returns
AjBool:ajTrue if a sequence was refound. ajFalse when all is done.

Description

Reads the next sequence into a sequence stream. For the first call this simply returns the sequence already loaded. For later calls a new sequence is read.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinClearPos

Clears a Sequence input object position information as possibly read from a USA that included the begni, end and direction

Synopsis

Prototype
void ajSeqinClearPos (
      AjPSeqin thys
);

TypeNameRead/WriteDescription
AjPSeqinthysModifySequence input
void RETURN

Input & Output
thys:(Modify)Sequence input
Returns
void:No return value

Description

Clears a Sequence input object position information as possibly read from a USA that included the begni, end and direction

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinClear

Clears a Sequence input object back to "as new" condition, except for the USA list and the features setting which must be preserved.

Synopsis

Prototype
void ajSeqinClear (
      AjPSeqin thys
);

TypeNameRead/WriteDescription
AjPSeqinthysOutputSequence input
void RETURN

Output
thys:(Output)Sequence input
Returns
void:No return value

Description

Clears a Sequence input object back to "as new" condition, except for the USA list and the features setting which must be preserved.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence inputs

These functions read the sequence provdied by the first argument

Functions: ajSeqRead

Function ajSeqRead

If the file is not yet open, calls seqUsaProcess to convert the USA into an open file stream.

Uses seqRead for the actual file reading.

Returns the results in the AjPSeq object.

Synopsis

Prototype
AjBool ajSeqRead (
      AjPSeq thys,
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqthysOutputSequence returned.
AjPSeqinseqinModifySequence input definitions
AjBool RETURNajTrue on success.

Output
thys:(Output)Sequence returned.
Input & Output
seqin:(Modify)Sequence input definitions
Returns
AjBool:ajTrue on success.

Description

If the file is not yet open, calls seqUsaProcess to convert the USA into an open file stream.

Uses seqRead for the actual file reading.

Returns the results in the AjPSeq object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Set Inputs

These functions read the sequence set object provided as the first argument.

Functions: ajSeqsetRead ajSeqsetallRead ajSeqsetFromList ajSeqsetFromPair ajSeqsetApp ajSeqPrintInFormat ajSeqFormatTest ajSeqUsaGetBase

Function ajSeqsetRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Read all the sequences until done

Return the results in the AjPSeqset object.

Synopsis

Prototype
AjBool ajSeqsetRead (
      AjPSeqset thys,
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqsetthysOutputSequence set returned.
AjPSeqinseqinModifySequence input definitions
AjBool RETURNajTrue on success.

Output
thys:(Output)Sequence set returned.
Input & Output
seqin:(Modify)Sequence input definitions
Returns
AjBool:ajTrue on success.

Description

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Read all the sequences until done

Return the results in the AjPSeqset object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqsetallRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Read all the sequences into sequence sets until done

Start a new set for each multiple sequence input

Return the results in the AjPList object with AjPSeqset nodes

Synopsis

Prototype
AjBool ajSeqsetallRead (
      AjPList thys,
      AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPListthysOutputList of sequence sets returned.
AjPSeqinseqinModifySequence input definitions
AjBool RETURNajTrue on success.

Output
thys:(Output)List of sequence sets returned.
Input & Output
seqin:(Modify)Sequence input definitions
Returns
AjBool:ajTrue on success.

Description

Parse a USA Uniform Sequence Address into format, access, file and entry

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Read all the sequences into sequence sets until done

Start a new set for each multiple sequence input

Return the results in the AjPList object with AjPSeqset nodes

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqsetFromList

Builds a sequence set from a list of sequences

Synopsis

Prototype
ajint ajSeqsetFromList (
      AjPSeqset thys,
      const AjPList list
);

TypeNameRead/WriteDescription
AjPSeqsetthysOutputSequence set
const AjPListlistInputList of sequence objects
ajint RETURNNumber of sequences in the set.

Input
list:(Input)List of sequence objects
Output
thys:(Output)Sequence set
Returns
ajint:Number of sequences in the set.

Description

Builds a sequence set from a list of sequences

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqsetFromPair

Builds a sequence set from a pair of sequences

Synopsis

Prototype
ajint ajSeqsetFromPair (
      AjPSeqset thys,
      const AjPSeq seqa,
      const AjPSeq seqb
);

TypeNameRead/WriteDescription
AjPSeqsetthysOutputSequence set
const AjPSeqseqaInputSequence 1
const AjPSeqseqbInputSequence 2
ajint RETURNNumber of sequences in the set.

Input
seqa:(Input)Sequence 1
seqb:(Input)Sequence 2
Output
thys:(Output)Sequence set
Returns
ajint:Number of sequences in the set.

Description

Builds a sequence set from a pair of sequences

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqsetApp

Adds a sequence to a sequence set

Synopsis

Prototype
ajint ajSeqsetApp (
      AjPSeqset thys,
      const AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqsetthysOutputSequence set
const AjPSeqseqInputSequence
ajint RETURNNumber of sequences in the set.

Input
seq:(Input)Sequence
Output
thys:(Output)Sequence set
Returns
ajint:Number of sequences in the set.

Description

Adds a sequence to a sequence set

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqPrintInFormat

Reports the internal data structures

Synopsis

Prototype
void ajSeqPrintInFormat (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report (usually ajFalse)
void RETURN

Input
full:(Input)Full report (usually ajFalse)
Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the internal data structures

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqFormatTest

tests whether a named format is known

Synopsis

Prototype
AjBool ajSeqFormatTest (
      const AjPStr format
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if formats was accepted

Input
format:(Input)Format
Returns
AjBool:ajTrue if formats was accepted

Description

tests whether a named format is known

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqUsaGetBase

Extracts the base part from a USA, suitable for use in fetching other sequences from the same source

Synopsis

Prototype
AjBool ajSeqUsaGetBase (
      const AjPStr usa,
      AjPStr* Pbaseusa
);

TypeNameRead/WriteDescription
const AjPStrusaInputOriginal USA
AjPStr*PbaseusaModifyBase part of USA
AjBool RETURNTrue on success

Input
usa:(Input)Original USA
Input & Output
Pbaseusa:(Modify)Base part of USA
Returns
AjBool:True on success

Description

Extracts the base part from a USA, suitable for use in fetching other sequences from the same source

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Query Constructors

All constructors return a new sequence query object by pointer. It is the responsibility of the user to first destroy any previous sequenceoutput object. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions: ajSeqQueryNew

Function ajSeqQueryNew

Creates a new sequence query object

Synopsis

Prototype
AjPSeqQuery ajSeqQueryNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqQuery RETURNNew sequence query object.

Returns
AjPSeqQuery:New sequence query object.

Description

Creates a new sequence query object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Query Destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence query object.

Functions: ajSeqQueryDel

Function ajSeqQueryDel

Deletes a sequence query object

Synopsis

Prototype
void ajSeqQueryDel (
      AjPSeqQuery* pthis
);

TypeNameRead/WriteDescription
AjPSeqQuery*pthisDeleteAddress of sequence query object
void RETURN

Output
pthis:(Delete)Address of sequence query object
Returns
void:No return value

Description

Deletes a sequence query object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Query Modifiers

These functions use the contents of a sequence query object and update them.

Functions: ajSeqQueryClear

Function ajSeqQueryClear

Resets a Sequence query object to a clean state for reuse

Synopsis

Prototype
void ajSeqQueryClear (
      AjPSeqQuery thys
);

TypeNameRead/WriteDescription
AjPSeqQuerythysModifySequence query object
void RETURN

Input & Output
thys:(Modify)Sequence query object
Returns
void:No return value

Description

Resets a Sequence query object to a clean state for reuse

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Query Operators

These functions use the contents of a sequence query object but do not make any changes.

Functions: ajSeqQueryWild ajSeqQueryStarclear ajSeqQueryIs ajSeqQueryTrace

Function ajSeqQueryWild

Tests whether a query includes wild cards in any element, or can return more than one entry (keyword and some other search terms will find multiple entries)

Synopsis

Prototype
AjBool ajSeqQueryWild (
      AjPSeqQuery qry
);

TypeNameRead/WriteDescription
AjPSeqQueryqryModifyQuery object.
AjBool RETURNajTrue if query had wild cards.

Input & Output
qry:(Modify)Query object.
Returns
AjBool:ajTrue if query had wild cards.

Description

Tests whether a query includes wild cards in any element, or can return more than one entry (keyword and some other search terms will find multiple entries)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqQueryStarclear

Clears elements of a query object if they are simply "*" because this is equivalent to a null string.

Synopsis

Prototype
void ajSeqQueryStarclear (
      AjPSeqQuery qry
);

TypeNameRead/WriteDescription
AjPSeqQueryqryModifyQuery object.
void RETURN

Input & Output
qry:(Modify)Query object.
Returns
void:No return value

Description

Clears elements of a query object if they are simply "*" because this is equivalent to a null string.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqQueryIs

Tests whether any element of a query has been set. Elements which are simply '*' are cleared as this has the same meaning.

Synopsis

Prototype
AjBool ajSeqQueryIs (
      const AjPSeqQuery qry
);

TypeNameRead/WriteDescription
const AjPSeqQueryqryInputQuery object.
AjBool RETURNajTrue if query should be made. ajFalse if the query includes all entries.

Input
qry:(Input)Query object.
Returns
AjBool:ajTrue if query should be made. ajFalse if the query includes all entries.

Description

Tests whether any element of a query has been set. Elements which are simply '*' are cleared as this has the same meaning.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqQueryTrace

Debug calls to trace the data in a sequence query object.

Synopsis

Prototype
void ajSeqQueryTrace (
      const AjPSeqQuery thys
);

TypeNameRead/WriteDescription
const AjPSeqQuerythysInputSequence query object.
void RETURN

Input
thys:(Input)Sequence query object.
Returns
void:No return value

Description

Debug calls to trace the data in a sequence query object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Section: Sequence Query Casts

These functions examine the contents of a sequence query object and return some derived information. Some of them provide access to the internal components of a sequence query object. They are provided for programming convenience but should be used with caution.

Functions: ajSeqParseFasta ajSeqParseNcbi ajSeqParseFastq ajSeqGetFromUsa ajSeqsetGetFromUsa ajSeqReadExit ajSeqinTrace

Function ajSeqParseFasta

Parse an NCBI format fasta line. Return id acc sv and description

Synopsis

Prototype
AjBool ajSeqParseFasta (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* acc,
      AjPStr* sv,
      AjPStr* desc
);

TypeNameRead/WriteDescription
const AjPStrinstrInputfasta line.
AjPStr*idOutputid.
AjPStr*accOutputaccession number.
AjPStr*svOutputsequence version number.
AjPStr*descOutputdescription.
AjBool RETURNajTrue if fasta format

Input
instr:(Input)fasta line.
Output
id:(Output)id.
acc:(Output)accession number.
sv:(Output)sequence version number.
desc:(Output)description.
Returns
AjBool:ajTrue if fasta format

Description

Parse an NCBI format fasta line. Return id acc sv and description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqParseNcbi

Parse an NCBI format fasta line. Return id acc and description.

Tries to cope with the amazing variety of identifiers NCBI inflicts on us all - see the BLAST document README.formatdb from NCBI for some of the gory detail, and look at some real files for clues to what can really happen. Sadly,'real files' also includes internal IDs in blast databases reformatted by formatdb.

Synopsis

Prototype
AjBool ajSeqParseNcbi (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* acc,
      AjPStr* sv,
      AjPStr* gi,
      AjPStr* db,
      AjPStr* desc
);

TypeNameRead/WriteDescription
const AjPStrinstrInputfasta line.
AjPStr*idOutputid.
AjPStr*accOutputaccession number.
AjPStr*svOutputsequence version number.
AjPStr*giOutputGI version number.
AjPStr*dbOutputNCBI database name
AjPStr*descOutputdescription.
AjBool RETURNajTrue if ncbi format

Input
instr:(Input)fasta line.
Output
id:(Output)id.
acc:(Output)accession number.
sv:(Output)sequence version number.
gi:(Output)GI version number.
db:(Output)NCBI database name
desc:(Output)description.
Returns
AjBool:ajTrue if ncbi format

Description

Parse an NCBI format fasta line. Return id acc and description.

Tries to cope with the amazing variety of identifiers NCBI inflicts on us all - see the BLAST document README.formatdb from NCBI for some of the gory detail, and look at some real files for clues to what can really happen. Sadly,'real files' also includes internal IDs in blast databases reformatted by formatdb.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqParseFastq

Parse a fastq id line. Return id acc sv and description

Synopsis

Prototype
AjBool ajSeqParseFastq (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* acc,
      AjPStr* sv,
      AjPStr* desc
);

TypeNameRead/WriteDescription
const AjPStrinstrInputfastq line.
AjPStr*idOutputid.
AjPStr*accOutputaccession number.
AjPStr*svOutputsequence version number.
AjPStr*descOutputdescription.
AjBool RETURNajTrue if fastq format

Input
instr:(Input)fastq line.
Output
id:(Output)id.
acc:(Output)accession number.
sv:(Output)sequence version number.
desc:(Output)description.
Returns
AjBool:ajTrue if fastq format

Description

Parse a fastq id line. Return id acc sv and description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqGetFromUsa

Returns a sequence given a USA

Synopsis

Prototype
AjBool ajSeqGetFromUsa (
      const AjPStr thys,
      AjBool protein,
      AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPStrthysInputUSA
AjBoolproteinInputTrue if protein
AjPSeqseqModifysequence
AjBool RETURNajTrue on success

Input
thys:(Input)USA
protein:(Input)True if protein
Input & Output
seq:(Modify)sequence
Returns
AjBool:ajTrue on success

Description

Returns a sequence given a USA

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqsetGetFromUsa

Return a seqset given a usa

Synopsis

Prototype
AjBool ajSeqsetGetFromUsa (
      const AjPStr thys,
      AjPSeqset* seq
);

TypeNameRead/WriteDescription
const AjPStrthysInputusa
AjPSeqset*seqOutputseqset
AjBool RETURNajTrue on success

Input
thys:(Input)usa
Output
seq:(Output)seqset
Returns
AjBool:ajTrue on success

Description

Return a seqset given a usa

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqReadExit

Cleans up sequence reading internal memory

Synopsis

Prototype
void ajSeqReadExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up sequence reading internal memory

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0

Function ajSeqinTrace

Debug calls to trace the data in a sequence input object.

Synopsis

Prototype
void ajSeqinTrace (
      const AjPSeqin thys
);

TypeNameRead/WriteDescription
const AjPSeqinthysInputSequence input object.
void RETURN

Input
thys:(Input)Sequence input object.
Returns
void:No return value

Description

Debug calls to trace the data in a sequence input object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 5.0.0