ajdmx.c

Section: Constructors

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

Functions:

ajDmxScophitNew Constructor for an AJAX SCOP Hit object.

ajDmxScopalgNew Constructor for an AJAX SCOP Alignment object. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.

ajDmxScopalgRead Read an AJAX SCOP Alignment object from an AJAX File.

Function ajDmxScophitNew

Constructor for an AJAX SCOP Hit object.

Prototype

AjPScophit ajDmxScophitNew (
      void
);

Type Name Read/Write Description

AjPScophit RETURN AJAX SCOP Hit object

Type	Name	Read/Write	Description
`AjPScophit`		RETURN	AJAX SCOP Hit object

From EMBOSS 2.9.0

Function ajDmxScopalgNew

Constructor for an AJAX SCOP Alignment object. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.

Prototype

AjPScopalg ajDmxScopalgNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of sequences

AjPScopalg RETURN AJAX SCOP Alignment object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of sequences
`AjPScopalg`		RETURN	AJAX SCOP Alignment object

From EMBOSS 2.9.0

Function ajDmxScopalgRead

Read an AJAX SCOP Alignment object from an AJAX File.

Prototype

AjBool ajDmxScopalgRead (
      AjPFile inf,
      AjPScopalg* Pscopalg
);

Type Name Read/Write Description

AjPFile inf Modify Input AJAX File

AjPScopalg* Pscopalg Output AJAX SCOP Alignment address

AjBool RETURN True if the file contained any data, even an empty alignment. False if the file did not contain a 'TY' record, which is taken to indicate a domain alignment file.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input AJAX File
`AjPScopalg*`	`Pscopalg`	Output	AJAX SCOP Alignment address
`AjBool`		RETURN	True if the file contained any data, even an empty alignment. False if the file did not contain a 'TY' record, which is taken to indicate a domain alignment file.

From EMBOSS 2.9.0

Section: Structure Destructors

All destructor functions receive the address of the instance to be deleted. The original pointer is set to NULL so is ready for re-use.

Functions:

ajDmxScophitDel Destructor for an AJAX SCOP Hit object.

ajDmxScophitDelWrap Wrapper to destructor for an AJAX SCOP Hit object for use with generic functions.

ajDmxScopalgDel Destructor for an AJAX SCOP Alignment object.

Function ajDmxScophitDel

Destructor for an AJAX SCOP Hit object.

Prototype

void ajDmxScophitDel (
      AjPScophit* Pscophit
);

Type Name Read/Write Description

AjPScophit* Pscophit Output AJAX Scophit address

void RETURN

Type	Name	Read/Write	Description
`AjPScophit*`	`Pscophit`	Output	AJAX Scophit address
`void`		RETURN

From EMBOSS 2.9.0

Function ajDmxScophitDelWrap

Wrapper to destructor for an AJAX SCOP Hit object for use with generic functions.

Prototype

void ajDmxScophitDelWrap (
      void** Pitem
);

Type Name Read/Write Description

void** Pitem Delete AJAX SCOP Hit address

void RETURN

Type	Name	Read/Write	Description
`void**`	`Pitem`	Delete	AJAX SCOP Hit address
`void`		RETURN

From EMBOSS 2.9.0

Function ajDmxScopalgDel

Destructor for an AJAX SCOP Alignment object.

Prototype

void ajDmxScopalgDel (
      AjPScopalg* Pscopalg
);

Type Name Read/Write Description

AjPScopalg* Pscopalg Delete AJAX SCOP Alignment address

void RETURN

Type	Name	Read/Write	Description
`AjPScopalg*`	`Pscopalg`	Delete	AJAX SCOP Alignment address
`void`		RETURN

From EMBOSS 2.9.0

Section: Assignments

These functions overwrite the instance provided as the first argument A NULL value is always acceptable so these functions are often used to create a new instance by assignment.

Functions:

ajDmxScophitListCopy Read an AJAX List of AJAX SCOP Hit objects and return a pointer to a duplicate of the AJAX List.

ajDmxScophitCopy Copies the contents from one AJAX SCOP Hit object to another.

Function ajDmxScophitListCopy

Read an AJAX List of AJAX SCOP Hit objects and return a pointer to a duplicate of the AJAX List.

Prototype

AjPList ajDmxScophitListCopy (
      const AjPList scophits
);

Type Name Read/Write Description

const AjPList scophits Input AJAX List of AJAX SCOP Hit objects

AjPList RETURN True on success (list was duplicated ok)

Type	Name	Read/Write	Description
`const AjPList`	`scophits`	Input	AJAX List of AJAX SCOP Hit objects
`AjPList`		RETURN	True on success (list was duplicated ok)

From EMBOSS 2.9.0

Function ajDmxScophitCopy

Copies the contents from one AJAX SCOP Hit object to another.

Prototype

AjBool ajDmxScophitCopy (
      AjPScophit* Pto,
      const AjPScophit from
);

Type Name Read/Write Description

AjPScophit* Pto Output AJAX SCOP Hit address

const AjPScophit from Input AJAX SCOP Hit

AjBool RETURN True if copy was successful.

Type	Name	Read/Write	Description
`AjPScophit*`	`Pto`	Output	AJAX SCOP Hit address
`const AjPScophit`	`from`	Input	AJAX SCOP Hit
`AjBool`		RETURN	True if copy was successful.

From EMBOSS 2.9.0

Section: Modifiers

These functions use the contents of an instance and update them.

Functions:

ajDmxScophitTargetLowPriority Sets the Target element of an AJAX SCOP Hit object to ajTrue if its Priority is low.

ajDmxScophitTarget2 Sets the Target2 element of an AJAX SCOP Hit object to ajTrue.

ajDmxScophitTarget Sets the Target element of an AJAX SCOP Hit object to ajTrue.

Function ajDmxScophitTargetLowPriority

Sets the Target element of an AJAX SCOP Hit object to ajTrue if its Priority is low.

Prototype

AjBool ajDmxScophitTargetLowPriority (
      AjPScophit* Pscophit
);

Type Name Read/Write Description

AjPScophit* Pscophit Modify AJAX SCOP Hit address

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`Pscophit`	Modify	AJAX SCOP Hit address
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Function ajDmxScophitTarget2

Sets the Target2 element of an AJAX SCOP Hit object to ajTrue.

Prototype

AjBool ajDmxScophitTarget2 (
      AjPScophit* Pscophit
);

Type Name Read/Write Description

AjPScophit* Pscophit Modify AJAX SCOP Hit address

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`Pscophit`	Modify	AJAX SCOP Hit address
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Function ajDmxScophitTarget

Sets the Target element of an AJAX SCOP Hit object to ajTrue.

Prototype

AjBool ajDmxScophitTarget (
      AjPScophit* Pscophit
);

Type Name Read/Write Description

AjPScophit* Pscophit Modify AJAX SCOP Hit address

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`Pscophit`	Modify	AJAX SCOP Hit address
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Section: Operators

These functions use the contents of an instance but do not make any changes.

Functions:

ajDmxScophitCheckTarget Checks to see if the Target element of an AJAX SCOP Hit object equals ajTrue.

Function ajDmxScophitCheckTarget

Checks to see if the Target element of an AJAX SCOP Hit object equals ajTrue.

Prototype

AjBool ajDmxScophitCheckTarget (
      const AjPScophit scophit
);

Type Name Read/Write Description

const AjPScophit scophit Input AJAX SCOP Hit

AjBool RETURN Returns ajTrue if the Target element of the AAX SCOP Hit object equals ajTrue, returns ajFalse otherwise.

Type	Name	Read/Write	Description
`const AjPScophit`	`scophit`	Input	AJAX SCOP Hit
`AjBool`		RETURN	Returns ajTrue if the Target element of the AAX SCOP Hit object equals ajTrue, returns ajFalse otherwise.

From EMBOSS 2.9.0

Section: Reporters

These functions return the contents of an instance but do not make any changes.

Functions:

ajDmxScophitCompScore Function to compare AJAX SCOP Hit objects by score member. Usually called by ajListSort.

ajDmxScophitCompPval Function to compare AJAX SCOP Hit objects by Pval member. Usually called by ajListSort.

ajDmxScophitCompAcc Function to compare AJAX SCOP Hit objects by Acc member. Usually called by ajListSort.

ajDmxScophitCompSunid Function to compare AJAX SCOP Hit objects by Sunid_Family member. Usually called by ajListSort.

ajDmxScophitCompSpr Function to compare AJAX SCOP Hit objects by Spr member. Usually called by ajListSort.

ajDmxScophitCompEnd Function to compare AJAX SCOP Hit objects by End member. Usually called by ajListSort.

ajDmxScophitCompStart Function to compare AJAX SCOP Hit objects by Start member. Usually called by ajListSort.

ajDmxScophitCompFam Function to compare AJAX SCOP Hit objects by Family member. Usually called by ajListSort.

ajDmxScophitCompSfam Function to compare AJAX SCOP Hit objects by Superfamily member. Usually called by ajListSort.

ajDmxScophitCompClass Function to compare AJAX SCOP Hit objects by Class member. Usually called by ajListSort.

ajDmxScophitCompFold Function to compare AJAX SCOP Hit objects by Fold member. Usually called by ajListSort.

ajDmxScopalgGetseqs Read an AJAX SCOP Alignment object and write an array of AJAX Strong objects containing the sequences without gaps.

ajDmxScophitsWrite Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in EMBL-like format. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

ajDmxScophitsWriteFasta Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in DHF format. Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.

ajDmxScophitReadFasta Read an AJAX SCOP Hit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

ajDmxScopalgWrite Write an AJAX SCOP Alignment object to an AJAX FIle in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):

ajDmxScopalgWriteClustal Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).

ajDmxScopalgWriteClustal2 Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).

ajDmxScopalgWriteFasta Write an AJAX SCOP Alignment object to an AJAX File in FASTA format (just the alignment without the domain classification information).

Function ajDmxScophitCompScore

Function to compare AJAX SCOP Hit objects by score member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompScore (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN 1 if score1 < score2, 0 if score1 == score2, else -1.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	1 if score1 < score2, 0 if score1 == score2, else -1.

From EMBOSS 2.9.0

Function ajDmxScophitCompPval

Function to compare AJAX SCOP Hit objects by Pval member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompPval (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN 1 if Pval1 > Pval2, 0 if Pval1 == Pval2, else -1.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	1 if Pval1 > Pval2, 0 if Pval1 == Pval2, else -1.

From EMBOSS 2.9.0

Function ajDmxScophitCompAcc

Function to compare AJAX SCOP Hit objects by Acc member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompAcc (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Acc1 should sort before Acc2, +1 if the Acc2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Acc1 should sort before Acc2, +1 if the Acc2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajDmxScophitCompSunid

Function to compare AJAX SCOP Hit objects by Sunid_Family member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompSunid (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Sunid_Family1 < Sunid_Family2, +1 if the Sunid_Family2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Sunid_Family1 < Sunid_Family2, +1 if the Sunid_Family2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompSpr

Function to compare AJAX SCOP Hit objects by Spr member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompSpr (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Spr1 should sort before Spr2, +1 if the Spr2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Spr1 should sort before Spr2, +1 if the Spr2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajDmxScophitCompEnd

Function to compare AJAX SCOP Hit objects by End member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompEnd (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if End1 should sort before End2, +1 if the End2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if End1 should sort before End2, +1 if the End2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompStart

Function to compare AJAX SCOP Hit objects by Start member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompStart (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Start1 should sort before Start2, +1 if the Start2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Start1 should sort before Start2, +1 if the Start2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompFam

Function to compare AJAX SCOP Hit objects by Family member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompFam (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Family1 should sort before Family2, +1 if the Family2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Family1 should sort before Family2, +1 if the Family2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompSfam

Function to compare AJAX SCOP Hit objects by Superfamily member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompSfam (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Superfamily1 should sort before Superfamily2, +1 if the Superfamily2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Superfamily1 should sort before Superfamily2, +1 if the Superfamily2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompClass

Function to compare AJAX SCOP Hit objects by Class member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompClass (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Class1 should sort before Class2, +1 if the Class2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Class1 should sort before Class2, +1 if the Class2 should sort first. 0 if they are identical.

From EMBOSS 3.0.0

Function ajDmxScophitCompFold

Function to compare AJAX SCOP Hit objects by Fold member. Usually called by ajListSort.

Prototype

ajint ajDmxScophitCompFold (
      const void* item1,
      const void* item2
);

Type Name Read/Write Description

const void* item1 Input AJAX SCOP Hit address 1

const void* item2 Input AJAX SCOP Hit address 2

ajint RETURN -1 if Fold1 should sort before Fold2, +1 if the Fold2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`item1`	Input	AJAX SCOP Hit address 1
`const void*`	`item2`	Input	AJAX SCOP Hit address 2
`ajint`		RETURN	-1 if Fold1 should sort before Fold2, +1 if the Fold2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScopalgGetseqs

Read an AJAX SCOP Alignment object and write an array of AJAX Strong objects containing the sequences without gaps.

Prototype

ajuint ajDmxScopalgGetseqs (
      const AjPScopalg scopalg,
      AjPStr** array
);

Type Name Read/Write Description

const AjPScopalg scopalg Input AJAX SCOP Alignment

AjPStr** array Output Array of AJAX String objects

ajuint RETURN Number of sequences read

Type	Name	Read/Write	Description
`const AjPScopalg`	`scopalg`	Input	AJAX SCOP Alignment
`AjPStr**`	`array`	Output	Array of AJAX String objects
`ajuint`		RETURN	Number of sequences read

From EMBOSS 2.9.0

Function ajDmxScophitsWrite

Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in EMBL-like format. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool ajDmxScophitsWrite (
      AjPFile outf,
      const AjPList scophits
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const AjPList scophits Input AJAX List of AJAX SCOP Hit objects

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	Output file stream
`const AjPList`	`scophits`	Input	AJAX List of AJAX SCOP Hit objects
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Function ajDmxScophitsWriteFasta

Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in DHF format. Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool ajDmxScophitsWriteFasta (
      AjPFile outf,
      const AjPList scophits
);

Type Name Read/Write Description

AjPFile outf Output AJAX Output File stream

const AjPList scophits Input AJAX List of AJAX SCOP Hit objects

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	AJAX Output File stream
`const AjPList`	`scophits`	Input	AJAX List of AJAX SCOP Hit objects
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function ajDmxScophitReadFasta

Read an AJAX SCOP Hit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Prototype

AjPScophit ajDmxScophitReadFasta (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify AJAX Input file stream

AjPScophit RETURN AJAX SCOP Hit object, or NULL if the file was not in extended FASTA (DHF) format (indicated by a token count of the the lines beginning with '>').

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	AJAX Input file stream
`AjPScophit`		RETURN	AJAX SCOP Hit object, or NULL if the file was not in extended FASTA (DHF) format (indicated by a token count of the the lines beginning with '>').

From EMBOSS 3.0.0

Function ajDmxScopalgWrite

Write an AJAX SCOP Alignment object to an AJAX FIle in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):

Prototype

AjBool ajDmxScopalgWrite (
      const AjPScopalg scopalg,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg scopalg Input AJAX SCOP Alignment

AjPFile outf Modify AJAX Output file stream

AjBool RETURN True on success (an alignment was written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`scopalg`	Input	AJAX SCOP Alignment
`AjPFile`	`outf`	Modify	AJAX Output file stream
`AjBool`		RETURN	True on success (an alignment was written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteClustal

Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteClustal (
      const AjPScopalg scopalg,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg scopalg Input AJAX SCOP Alignment

AjPFile outf Modify AJAX Outfile file

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`scopalg`	Input	AJAX SCOP Alignment
`AjPFile`	`outf`	Modify	AJAX Outfile file
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteClustal2

Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteClustal2 (
      const AjPScopalg scopalg,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg scopalg Input AJAX SCOP Alignment

AjPFile outf Modify AJAX Outfile file

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`scopalg`	Input	AJAX SCOP Alignment
`AjPFile`	`outf`	Modify	AJAX Outfile file
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteFasta

Write an AJAX SCOP Alignment object to an AJAX File in FASTA format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteFasta (
      const AjPScopalg scopalg,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg scopalg Input AJAX SCOP Alignment

AjPFile outf Modify AJAX Outfile file

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`scopalg`	Input	AJAX SCOP Alignment
`AjPFile`	`outf`	Modify	AJAX Outfile file
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Section: Miscellaneous

These functions may have diverse functions that do not fit into the other categories.

Functions:

ajDmxScopSeqFromSunid Write a sequence corresponding to an AJAX SCOP domain given a Sunid for the domain. The sequence is taken from one of an AJAX List of AJAX SCOP objects that is provided. The SWISS-Prot sequence is taken in priority over the PDB sequence.

ajDmxExit Cleanup of Dmx function internals.

ajDmxDummyFunction Dummy function to catch all unused functions defined in the ajdmx source file.

Function ajDmxScopSeqFromSunid

Write a sequence corresponding to an AJAX SCOP domain given a Sunid for the domain. The sequence is taken from one of an AJAX List of AJAX SCOP objects that is provided. The SWISS-Prot sequence is taken in priority over the PDB sequence.

Prototype

AjBool ajDmxScopSeqFromSunid (
      ajint identifier,
      AjPStr* seq,
      const AjPList scops
);

Type Name Read/Write Description

ajint identifier Input Search term

AjPStr* seq Output Result sequence

const AjPList scops Input Sorted AJAX List of AJAX SCOP objects

AjBool RETURN True if a SWISS-Prot identifier code was found for the PDB code.

Type	Name	Read/Write	Description
`ajint`	`identifier`	Input	Search term
`AjPStr*`	`seq`	Output	Result sequence
`const AjPList`	`scops`	Input	Sorted AJAX List of AJAX SCOP objects
`AjBool`		RETURN	True if a SWISS-Prot identifier code was found for the PDB code.

From EMBOSS 2.9.0

Function ajDmxExit

Cleanup of Dmx function internals.

Prototype

void ajDmxExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.1.0

Function ajDmxDummyFunction

Dummy function to catch all unused functions defined in the ajdmx source file.

Prototype

void ajDmxDummyFunction (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 2.9.0

ajDmxScophitNew	Constructor for an AJAX SCOP Hit object.
ajDmxScopalgNew	Constructor for an AJAX SCOP Alignment object. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.
ajDmxScopalgRead	Read an AJAX SCOP Alignment object from an AJAX File.

ajDmxScophitDel	Destructor for an AJAX SCOP Hit object.
ajDmxScophitDelWrap	Wrapper to destructor for an AJAX SCOP Hit object for use with generic functions.
ajDmxScopalgDel	Destructor for an AJAX SCOP Alignment object.

ajDmxScophitListCopy	Read an AJAX List of AJAX SCOP Hit objects and return a pointer to a duplicate of the AJAX List.
ajDmxScophitCopy	Copies the contents from one AJAX SCOP Hit object to another.

ajDmxScophitTargetLowPriority	Sets the Target element of an AJAX SCOP Hit object to ajTrue if its Priority is low.
ajDmxScophitTarget2	Sets the Target2 element of an AJAX SCOP Hit object to ajTrue.
ajDmxScophitTarget	Sets the Target element of an AJAX SCOP Hit object to ajTrue.

ajDmxScophitCompScore	Function to compare AJAX SCOP Hit objects by score member. Usually called by ajListSort.
ajDmxScophitCompPval	Function to compare AJAX SCOP Hit objects by Pval member. Usually called by ajListSort.
ajDmxScophitCompAcc	Function to compare AJAX SCOP Hit objects by Acc member. Usually called by ajListSort.
ajDmxScophitCompSunid	Function to compare AJAX SCOP Hit objects by Sunid_Family member. Usually called by ajListSort.
ajDmxScophitCompSpr	Function to compare AJAX SCOP Hit objects by Spr member. Usually called by ajListSort.
ajDmxScophitCompEnd	Function to compare AJAX SCOP Hit objects by End member. Usually called by ajListSort.
ajDmxScophitCompStart	Function to compare AJAX SCOP Hit objects by Start member. Usually called by ajListSort.
ajDmxScophitCompFam	Function to compare AJAX SCOP Hit objects by Family member. Usually called by ajListSort.
ajDmxScophitCompSfam	Function to compare AJAX SCOP Hit objects by Superfamily member. Usually called by ajListSort.
ajDmxScophitCompClass	Function to compare AJAX SCOP Hit objects by Class member. Usually called by ajListSort.
ajDmxScophitCompFold	Function to compare AJAX SCOP Hit objects by Fold member. Usually called by ajListSort.
ajDmxScopalgGetseqs	Read an AJAX SCOP Alignment object and write an array of AJAX Strong objects containing the sequences without gaps.
ajDmxScophitsWrite	Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in EMBL-like format. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.
ajDmxScophitsWriteFasta	Write contents of an AJAX List of AJAX SCOP Hit objects to an AJAX File in DHF format. Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.
ajDmxScophitReadFasta	Read an AJAX SCOP Hit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
ajDmxScopalgWrite	Write an AJAX SCOP Alignment object to an AJAX FIle in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):
ajDmxScopalgWriteClustal	Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).
ajDmxScopalgWriteClustal2	Write an AJAX SCOP Alignment object to an AJAX File in CLUSTAL format (just the alignment without the domain classification information).
ajDmxScopalgWriteFasta	Write an AJAX SCOP Alignment object to an AJAX File in FASTA format (just the alignment without the domain classification information).

ajDmxScopSeqFromSunid	Write a sequence corresponding to an AJAX SCOP domain given a Sunid for the domain. The sequence is taken from one of an AJAX List of AJAX SCOP objects that is provided. The SWISS-Prot sequence is taken in priority over the PDB sequence.
ajDmxExit	Cleanup of Dmx function internals.
ajDmxDummyFunction	Dummy function to catch all unused functions defined in the ajdmx source file.