ajseqwrite.c

Datatypes:

AjPSeqout Sequence output

AjPStr Sequence output strings

Datatype: AjPSeqout

Function is for manipulating sequence output objects

Sections:

Sequence Output Constructors Constructors

destructors Destructors

AjPSeqout: Sequence Output Constructors

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

Functions:

ajSeqoutNew Creates a new sequence output object.

ajSeqoutNewFile Creates a new sequence output object using a pre-opened file.

ajSeqoutNewFormatC Creates a new sequence output object with a specified format.

ajSeqoutNewFormatS Creates a new sequence output object with a specified format.

Function ajSeqoutNew

Creates a new sequence output object.

Prototype

AjPSeqout ajSeqoutNew (
      void
);

Type Name Read/Write Description

AjPSeqout RETURN New sequence output object.

Type	Name	Read/Write	Description
`AjPSeqout`		RETURN	New sequence output object.

From EMBOSS 1.0.0

Function ajSeqoutNewFile

Creates a new sequence output object using a pre-opened file.

Prototype

AjPSeqout ajSeqoutNewFile (
      AjPFile file
);

Type Name Read/Write Description

AjPFile file Modify Open file object

AjPSeqout RETURN New sequence output object.

Type	Name	Read/Write	Description
`AjPFile`	`file`	Modify	Open file object
`AjPSeqout`		RETURN	New sequence output object.

From EMBOSS 4.1.0

Function ajSeqoutNewFormatC

Creates a new sequence output object with a specified format.

Prototype

AjPSeqout ajSeqoutNewFormatC (
      const char* txt
);

Type Name Read/Write Description

const char* txt Input Output sequence format

AjPSeqout RETURN New sequence output object.

Type	Name	Read/Write	Description
`const char*`	`txt`	Input	Output sequence format
`AjPSeqout`		RETURN	New sequence output object.

From EMBOSS 5.0.0

Function ajSeqoutNewFormatS

Creates a new sequence output object with a specified format.

Prototype

AjPSeqout ajSeqoutNewFormatS (
      const AjPStr str
);

Type Name Read/Write Description

const AjPStr str Input Output sequence format

AjPSeqout RETURN New sequence output object.

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	Output sequence format
`AjPSeqout`		RETURN	New sequence output object.

From EMBOSS 5.0.0

AjPSeqout: destructors

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

Functions:

ajSeqoutDel Destructor for AjPSeqout objects

Function ajSeqoutDel

Destructor for AjPSeqout objects

Prototype

void ajSeqoutDel (
      AjPSeqout* Pseqout
);

Type Name Read/Write Description

AjPSeqout* Pseqout Delete Sequence output object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout*`	`Pseqout`	Delete	Sequence output object
`void`		RETURN

From EMBOSS 2.9.0

AjPSeqout: Sequence Stream output

These functions output the contents of a sequence stream object. As the input is a stream they expect to be called again.

Functions:

ajSeqoutWriteSeq Write next sequence out - continue until done.

ajSeqoutWriteSet Write a set of sequences out.

Function ajSeqoutWriteSeq

Write next sequence out - continue until done.

Prototype

AjBool ajSeqoutWriteSeq (
      AjPSeqout outseq,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPSeqout outseq Modify Sequence output.

const AjPSeq seq Input Sequence.

AjBool RETURN True if sequence was successfully written. Note if the save flag is true this means it was saved to be written later when the output is closed.

Type	Name	Read/Write	Description
`AjPSeqout`	`outseq`	Modify	Sequence output.
`const AjPSeq`	`seq`	Input	Sequence.
`AjBool`		RETURN	True if sequence was successfully written. Note if the save flag is true this means it was saved to be written later when the output is closed.

From EMBOSS 4.1.0

Function ajSeqoutWriteSet

Write a set of sequences out.

Prototype

AjBool ajSeqoutWriteSet (
      AjPSeqout outseq,
      const AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqout outseq Modify Sequence output.

const AjPSeqset seq Input Sequence set.

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqout`	`outseq`	Modify	Sequence output.
`const AjPSeqset`	`seq`	Input	Sequence set.
`AjBool`		RETURN	True on success

From EMBOSS 4.1.0

AjPSeqout: non-standard output

Writes a sequence string in SWISSPROT format with a user-defined line code

Functions:

ajSeqoutDumpSwisslike Writes a sequence in SWISSPROT format with a user-defined line code

Function ajSeqoutDumpSwisslike

Writes a sequence in SWISSPROT format with a user-defined line code

Prototype

void ajSeqoutDumpSwisslike (
      AjPSeqout outseq,
      const AjPStr seq,
      const char* prefix
);

Type Name Read/Write Description

AjPSeqout outseq Output Sequence output object

const AjPStr seq Input sequence

const char* prefix Input line prefix code - should be 2 characters

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`outseq`	Output	Sequence output object
`const AjPStr`	`seq`	Input	sequence
`const char*`	`prefix`	Input	line prefix code - should be 2 characters
`void`		RETURN

From EMBOSS 5.0.0

AjPSeqout: sequence output opening

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

Functions:

ajSeqoutClear Clears a Sequence output object back to "as new" condition

ajSeqoutClearUsa Creates or resets a sequence output object using a new Universal Sequence Address

ajSeqoutClose Close a sequence output file. For formats that save everything up and write at the end, call the Write function first.

ajSeqoutFlush Flush output to a sequence output file. For formats that save everything up and write at the end, call the Write function first.

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

ajSeqoutOpenFilename Opens an output file for sequence writing. 'stdout' and 'stderr' are special cases using standard output and standard error respectively.

ajSeqoutReset Clears a Sequence output object ready to accept further sequences

Function ajSeqoutClear

Clears a Sequence output object back to "as new" condition

Prototype

void ajSeqoutClear (
      AjPSeqout seqout
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqoutClearUsa

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

Prototype

void ajSeqoutClearUsa (
      AjPSeqout seqout,
      const AjPStr usa
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object.

const AjPStr usa Input USA

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object.
`const AjPStr`	`usa`	Input	USA
`void`		RETURN

From EMBOSS 5.0.0

Function ajSeqoutClose

Close a sequence output file. For formats that save everything up and write at the end, call the Write function first.

Prototype

void ajSeqoutClose (
      AjPSeqout seqout
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output
`void`		RETURN

From EMBOSS 4.1.0

Function ajSeqoutFlush

Flush output to a sequence output file. For formats that save everything up and write at the end, call the Write function first.

Prototype

void ajSeqoutFlush (
      AjPSeqout seqout
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output
`void`		RETURN

From EMBOSS 6.1.0

Function ajSeqoutOpen

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

Prototype

AjBool ajSeqoutOpen (
      AjPSeqout seqout
);

Type Name Read/Write Description

AjPSeqout seqout Output Sequence output object.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Output	Sequence output object.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 1.0.0

Function ajSeqoutOpenFilename

Opens an output file for sequence writing. 'stdout' and 'stderr' are special cases using standard output and standard error respectively.

Prototype

AjBool ajSeqoutOpenFilename (
      AjPSeqout seqout,
      const AjPStr name
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object.

const AjPStr name Input Output filename.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object.
`const AjPStr`	`name`	Input	Output filename.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 4.1.0

Function ajSeqoutReset

Clears a Sequence output object ready to accept further sequences

Prototype

void ajSeqoutReset (
      AjPSeqout seqout
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object
`void`		RETURN

From EMBOSS 6.1.0

AjPSeqout: set

Functions:

ajSeqoutSetFormatC Sets the output format. Currently hard coded but will be replaced in future by a variable.

ajSeqoutSetFormatS Sets the output format. Currently hard coded but will be replaced in future by a variable.

ajSeqoutSetNameDefaultC Provides a unique (for this program run) name for a sequence.

ajSeqoutSetNameDefaultS Provides a unique (for this program run) name for a sequence.

Function ajSeqoutSetFormatC

Sets the output format. Currently hard coded but will be replaced in future by a variable.

Prototype

AjBool ajSeqoutSetFormatC (
      AjPSeqout seqout,
      const char* txt
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object.

const char* txt Input Output format.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object.
`const char*`	`txt`	Input	Output format.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 5.0.0

Function ajSeqoutSetFormatS

Sets the output format. Currently hard coded but will be replaced in future by a variable.

Prototype

AjBool ajSeqoutSetFormatS (
      AjPSeqout seqout,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqout seqout Modify Sequence output object.

const AjPStr str Input Output format.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Modify	Sequence output object.
`const AjPStr`	`str`	Input	Output format.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 5.0.0

Function ajSeqoutSetNameDefaultC

Provides a unique (for this program run) name for a sequence.

Prototype

AjBool ajSeqoutSetNameDefaultC (
      AjPSeqout seqout,
      AjBool multi,
      const char* txt
);

Type Name Read/Write Description

AjPSeqout seqout Output Sequence output object

AjBool multi Input If true, appends a number to the name.

const char* txt Input Name set by caller

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Output	Sequence output object
`AjBool`	`multi`	Input	If true, appends a number to the name.
`const char*`	`txt`	Input	Name set by caller
`AjBool`		RETURN	True on success

From EMBOSS 5.0.0

Function ajSeqoutSetNameDefaultS

Provides a unique (for this program run) name for a sequence.

Prototype

AjBool ajSeqoutSetNameDefaultS (
      AjPSeqout seqout,
      AjBool multi,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqout seqout Output Sequence output object

AjBool multi Input If true, appends a number to the name.

const AjPStr str Input Name set by caller

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPSeqout`	`seqout`	Output	Sequence output object
`AjBool`	`multi`	Input	If true, appends a number to the name.
`const AjPStr`	`str`	Input	Name set by caller
`AjBool`		RETURN	True on success

From EMBOSS 5.0.0

AjPSeqout: print

Functions:

ajSeqoutPrintFormat Reports the internal data structures

ajSeqoutPrintbookFormat Reports the internal data structures as EMBOSS book format

ajSeqoutPrinthtmlFormat Reports the internal data structures as wikitext

ajSeqoutPrintwikiFormat Reports the internal data structures as wikitext

Function ajSeqoutPrintFormat

Reports the internal data structures

Prototype

void ajSeqoutPrintFormat (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report (usually ajFalse)

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`AjBool`	`full`	Input	Full report (usually ajFalse)
`void`		RETURN

From EMBOSS 5.0.0

Function ajSeqoutPrintbookFormat

Reports the internal data structures as EMBOSS book format

Prototype

void ajSeqoutPrintbookFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

Function ajSeqoutPrinthtmlFormat

Reports the internal data structures as wikitext

Prototype

void ajSeqoutPrinthtmlFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

Function ajSeqoutPrintwikiFormat

Reports the internal data structures as wikitext

Prototype

void ajSeqoutPrintwikiFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

AjPSeqout: Sequence Output Casts

Functions:

ajSeqoutGetBasecount Counts the numbers of A, C, G and T in a nucleotide sequence.

ajSeqoutGetCheckgcg Calculates a GCG checksum for an output sequence.

ajSeqoutGetFilename Returns the filename for a sequence output object

Function ajSeqoutGetBasecount

Counts the numbers of A, C, G and T in a nucleotide sequence.

Prototype

void ajSeqoutGetBasecount (
      const AjPSeqout seqout,
      ajuint* bases
);

Type Name Read/Write Description

const AjPSeqout seqout Input Sequence output object

ajuint* bases Output Integer array, minimum size 5, to hold the results.

void RETURN

Type	Name	Read/Write	Description
`const AjPSeqout`	`seqout`	Input	Sequence output object
`ajuint*`	`bases`	Output	Integer array, minimum size 5, to hold the results.
`void`		RETURN

From EMBOSS 5.0.0

Function ajSeqoutGetCheckgcg

Calculates a GCG checksum for an output sequence.

Prototype

ajint ajSeqoutGetCheckgcg (
      const AjPSeqout seqout
);

Type Name Read/Write Description

const AjPSeqout seqout Input Output sequence.

ajint RETURN GCG checksum.

Type	Name	Read/Write	Description
`const AjPSeqout`	`seqout`	Input	Output sequence.
`ajint`		RETURN	GCG checksum.

From EMBOSS 5.0.0

Function ajSeqoutGetFilename

Returns the filename for a sequence output object

Prototype

const AjPStr ajSeqoutGetFilename (
      const AjPSeqout seqout
);

Type Name Read/Write Description

const AjPSeqout seqout Input Sequence output object

const AjPStr RETURN Filename

Type	Name	Read/Write	Description
`const AjPSeqout`	`seqout`	Input	Sequence output object
`const AjPStr`		RETURN	Filename

From EMBOSS 6.1.0

AjPSeqout: debugging

Functions for reporting of a string object.

Functions:

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

Function ajSeqoutTrace

Debug calls to trace the data in a sequence object.

Prototype

void ajSeqoutTrace (
      const AjPSeqout seqout
);

Type Name Read/Write Description

const AjPSeqout seqout Input Sequence output object.

void RETURN

Type	Name	Read/Write	Description
`const AjPSeqout`	`seqout`	Input	Sequence output object.
`void`		RETURN

From EMBOSS 1.0.0

AjPSeqout: exit

Functions called on exit

Functions:

ajSeqoutExit Cleans up sequence output processing internal memory

Function ajSeqoutExit

Cleans up sequence output processing internal memory

Prototype

void ajSeqoutExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 5.0.0

Datatype: AjPStr

Function is for manipulating sequence output objects

Sections:

other General use

AjPStr: other

Functions:

ajSeqoutstrGetFormatDefault Sets the default output format. Checks the _OUTFORMAT variable, and uses FASTA if no other definition is found.

ajSeqoutstrIsFormatExists Checks whether an output format name exists.

ajSeqoutstrIsFormatSingle Checks whether an output format should go to single files, rather than all sequences being written to one file. Some formats do not work when more than one sequence is written to a file. Obvious examples are plain text and GCG formats.

Function ajSeqoutstrGetFormatDefault

Sets the default output format. Checks the _OUTFORMAT variable, and uses FASTA if no other definition is found.

Prototype

AjBool ajSeqoutstrGetFormatDefault (
      AjPStr* Pformat
);

Type Name Read/Write Description

AjPStr* Pformat Output Default output format.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPStr*`	`Pformat`	Output	Default output format.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 5.0.0

Function ajSeqoutstrIsFormatExists

Checks whether an output format name exists.

Prototype

AjBool ajSeqoutstrIsFormatExists (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Output format required.

AjBool RETURN ajTrue if format is known.

Type	Name	Read/Write	Description
`const AjPStr`	`format`	Input	Output format required.
`AjBool`		RETURN	ajTrue if format is known.

From EMBOSS 5.0.0

Function ajSeqoutstrIsFormatSingle

Checks whether an output format should go to single files, rather than all sequences being written to one file. Some formats do not work when more than one sequence is written to a file. Obvious examples are plain text and GCG formats.

Prototype

AjBool ajSeqoutstrIsFormatSingle (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Output format required.

AjBool RETURN ajTrue if separate file is needed for each sequence.

Type	Name	Read/Write	Description
`const AjPStr`	`format`	Input	Output format required.
`AjBool`		RETURN	ajTrue if separate file is needed for each sequence.

From EMBOSS 5.0.0

Sequence Output Constructors	Constructors
destructors	Destructors

ajSeqoutNew	Creates a new sequence output object.
ajSeqoutNewFile	Creates a new sequence output object using a pre-opened file.
ajSeqoutNewFormatC	Creates a new sequence output object with a specified format.
ajSeqoutNewFormatS	Creates a new sequence output object with a specified format.

ajSeqoutWriteSeq	Write next sequence out - continue until done.
ajSeqoutWriteSet	Write a set of sequences out.

ajSeqoutClear	Clears a Sequence output object back to "as new" condition
ajSeqoutClearUsa	Creates or resets a sequence output object using a new Universal Sequence Address
ajSeqoutClose	Close a sequence output file. For formats that save everything up and write at the end, call the Write function first.
ajSeqoutFlush	Flush output to a sequence output file. For formats that save everything up and write at the end, call the Write function first.
ajSeqoutOpen	If the file is not yet open, calls seqoutUsaProcess to convert the USA into an open output file stream.
ajSeqoutOpenFilename	Opens an output file for sequence writing. 'stdout' and 'stderr' are special cases using standard output and standard error respectively.
ajSeqoutReset	Clears a Sequence output object ready to accept further sequences

ajSeqoutSetFormatC	Sets the output format. Currently hard coded but will be replaced in future by a variable.
ajSeqoutSetFormatS	Sets the output format. Currently hard coded but will be replaced in future by a variable.
ajSeqoutSetNameDefaultC	Provides a unique (for this program run) name for a sequence.
ajSeqoutSetNameDefaultS	Provides a unique (for this program run) name for a sequence.

ajSeqoutPrintFormat	Reports the internal data structures
ajSeqoutPrintbookFormat	Reports the internal data structures as EMBOSS book format
ajSeqoutPrinthtmlFormat	Reports the internal data structures as wikitext
ajSeqoutPrintwikiFormat	Reports the internal data structures as wikitext

ajSeqoutGetBasecount	Counts the numbers of A, C, G and T in a nucleotide sequence.
ajSeqoutGetCheckgcg	Calculates a GCG checksum for an output sequence.
ajSeqoutGetFilename	Returns the filename for a sequence output object

ajSeqoutstrGetFormatDefault	Sets the default output format. Checks the _OUTFORMAT variable, and uses FASTA if no other definition is found.
ajSeqoutstrIsFormatExists	Checks whether an output format name exists.
ajSeqoutstrIsFormatSingle	Checks whether an output format should go to single files, rather than all sequences being written to one file. Some formats do not work when more than one sequence is written to a file. Obvious examples are plain text and GCG formats.