embsig.c

Function embSigdatNew

Sigdat object constructor. This is normally called by the embSignatureReadNew function. Fore-knowledge of the number of empirical residues and gaps is required. Important: Functions which manipulate the Sigdat object rely on data in the gap arrays (gsiz and grfq) being filled in order of increasing gap size.

Prototype

EmbPSigdat embSigdatNew (
      ajuint nres,
      ajuint ngap
);

Type Name Read/Write Description

ajuint nres Input Number of emprical residues / environments.

ajuint ngap Input Number of emprical gaps.

EmbPSigdat RETURN Pointer to a Sigdat object

Type	Name	Read/Write	Description
`ajuint`	`nres`	Input	Number of emprical residues / environments.
`ajuint`	`ngap`	Input	Number of emprical gaps.
`EmbPSigdat`		RETURN	Pointer to a Sigdat object

From EMBOSS 2.9.0

Function embSigposNew

Sigpos object constructor. This is normally called by the embSignatureCompile function. Fore-knowledge of the number of permissible gaps is required.

Prototype

EmbPSigpos embSigposNew (
      ajuint ngap
);

Type Name Read/Write Description

ajuint ngap Input Number of permissible gaps.

EmbPSigpos RETURN Pointer to a Sigpos object

Type	Name	Read/Write	Description
`ajuint`	`ngap`	Input	Number of permissible gaps.
`EmbPSigpos`		RETURN	Pointer to a Sigpos object

From EMBOSS 2.9.0

Function embSigposDel

Destructor for Sigpos object.

Prototype

void embSigposDel (
      EmbPSigpos* pthis
);

Type Name Read/Write Description

EmbPSigpos* pthis Output Sigpos object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPSigpos*`	`pthis`	Output	Sigpos object pointer
`void`		RETURN

From EMBOSS 2.9.0

Function embSigdatDel

Destructor for Sigdat object.

Prototype

void embSigdatDel (
      EmbPSigdat* pthis
);

Type Name Read/Write Description

EmbPSigdat* pthis Output Sigdat object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPSigdat*`	`pthis`	Output	Sigdat object pointer
`void`		RETURN

From EMBOSS 2.9.0

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:

embHitlistNew Hitlist object constructor. This is normally called by the embHitlistRead function. Fore-knowledge of the number of hits is required.

embHitNew Hit object constructor. This is normally called by the embHitlistNew function.

embSignatureNew Signature object constructor. This is normally called by the embSignatureReadNew function. Fore-knowledge of the number of signature positions is required.

Function embHitlistNew

Hitlist object constructor. This is normally called by the embHitlistRead function. Fore-knowledge of the number of hits is required.

Prototype

EmbPHitlist embHitlistNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of hits

EmbPHitlist RETURN Pointer to a hitlist object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of hits
`EmbPHitlist`		RETURN	Pointer to a hitlist object

From EMBOSS 2.9.0

Function embHitNew

Hit object constructor. This is normally called by the embHitlistNew function.

Prototype

EmbPHit embHitNew (
      void
);

Type Name Read/Write Description

EmbPHit RETURN Pointer to a hit object

Type	Name	Read/Write	Description
`EmbPHit`		RETURN	Pointer to a hit object

From EMBOSS 2.9.0

Function embSignatureNew

Signature object constructor. This is normally called by the embSignatureReadNew function. Fore-knowledge of the number of signature positions is required.

Prototype

EmbPSignature embSignatureNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of signature positions

EmbPSignature RETURN Pointer to a Signature object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of signature positions
`EmbPSignature`		RETURN	Pointer to a Signature object

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:

embHitlistDel Destructor for hitlist object.

embHitDel Destructor for hit object.

embSignatureDel Destructor for Signature object.

Function embHitlistDel

Destructor for hitlist object.

Prototype

void embHitlistDel (
      EmbPHitlist* ptr
);

Type Name Read/Write Description

EmbPHitlist* ptr Output Hitlist object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPHitlist*`	`ptr`	Output	Hitlist object pointer
`void`		RETURN

From EMBOSS 2.9.0

Function embHitDel

Destructor for hit object.

Prototype

void embHitDel (
      EmbPHit* ptr
);

Type Name Read/Write Description

EmbPHit* ptr Output Hit object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPHit*`	`ptr`	Output	Hit object pointer
`void`		RETURN

From EMBOSS 2.9.0

Function embSignatureDel

Destructor for Signature object.

Prototype

void embSignatureDel (
      EmbPSignature* ptr
);

Type Name Read/Write Description

EmbPSignature* ptr Output Signature object pointer

void RETURN

Type	Name	Read/Write	Description
`EmbPSignature*`	`ptr`	Output	Signature object pointer
`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:

embHitMerge Creates a new Hit object which corresponds to a merging of the two sequences from the Hit objects hit1 and hit2.

Function embHitMerge

Creates a new Hit object which corresponds to a merging of the two sequences from the Hit objects hit1 and hit2.

Prototype

EmbPHit embHitMerge (
      const EmbPHit hit1,
      const EmbPHit hit2
);

Type Name Read/Write Description

const EmbPHit hit1 Input Hit 1

const EmbPHit hit2 Input Hit 2

EmbPHit RETURN Pointer to Hit object.

Type	Name	Read/Write	Description
`const EmbPHit`	`hit1`	Input	Hit 1
`const EmbPHit`	`hit2`	Input	Hit 2
`EmbPHit`		RETURN	Pointer to Hit object.

From EMBOSS 2.9.0

Section: Operators

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

Functions:

embHitlistMatchFold Function to sort Hitlist object by Fold element.

embMatchScore Function to sort Hit objects by score record. Usually called by ajListSort.

embMatchinvScore Function to sort Hit objects by score record. Usually called by ajListSort. The sorting order is inverted - i.e. it returns -1 if score1 > score2 (as opposed to embMatchScore).

embMatchLigid Function to sort Hit objects by Ligid record (referenced via Sig element).

embMatchSN Function to sort Hit objects by sn element within Sig element. Usually called by ajListSort.

Function embHitlistMatchFold

Function to sort Hitlist object by Fold element.

Prototype

ajint embHitlistMatchFold (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Hitlist object 1

const void* hit2 Input Pointer to Hitlist object 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*`	`hit1`	Input	Pointer to Hitlist object 1
`const void*`	`hit2`	Input	Pointer to Hitlist object 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 embMatchScore

Function to sort Hit objects by score record. Usually called by ajListSort.

Prototype

ajint embMatchScore (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Hit object 1

const void* hit2 Input Pointer to Hit object 2

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

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	1 if score1<score2, 0 if score1==score2, else -1.

From EMBOSS 2.9.0

Function embMatchinvScore

Function to sort Hit objects by score record. Usually called by ajListSort. The sorting order is inverted - i.e. it returns -1 if score1 > score2 (as opposed to embMatchScore).

Prototype

ajint embMatchinvScore (
      const void* hit1,
      const void* hit2
);

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	1 if score1<score2, 0 if score1==score2, else -1.

From EMBOSS 2.9.0

Function embMatchLigid

Function to sort Hit objects by Ligid record (referenced via Sig element).

Prototype

ajint embMatchLigid (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Hit object 1

const void* hit2 Input Pointer to Hit object 2

ajint RETURN -1 if Ligid1 should sort before Ligid2, +1 if the Ligid2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	-1 if Ligid1 should sort before Ligid2, +1 if the Ligid2 should sort first. 0 if they are identical.

From EMBOSS 3.0.0

Function embMatchSN

Function to sort Hit objects by sn element within Sig element. Usually called by ajListSort.

Prototype

ajint embMatchSN (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Hit object 1

const void* hit2 Input Pointer to Hit object 2

ajint RETURN 1 if sn1<sn2, 0 if sn1==sn2, else -1.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	1 if sn1<sn2, 0 if sn1==sn2, else -1.

From EMBOSS 3.0.0

Section: Reporters

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

Functions:

embHitsOverlap Checks for overlap between two hits.

Function embHitsOverlap

Checks for overlap between two hits.

Prototype

AjBool embHitsOverlap (
      const EmbPHit hit1,
      const EmbPHit hit2,
      ajuint n
);

Type Name Read/Write Description

const EmbPHit hit1 Input Pointer to hit object 1

const EmbPHit hit2 Input Pointer to hit object 2

ajuint n Input Threshold number of residues for overlap

AjBool RETURN True if the overlap between the sequences is at least as long as the threshold. False otherwise.

Type	Name	Read/Write	Description
`const EmbPHit`	`hit1`	Input	Pointer to hit object 1
`const EmbPHit`	`hit2`	Input	Pointer to hit object 2
`ajuint`	`n`	Input	Threshold number of residues for overlap
`AjBool`		RETURN	True if the overlap between the sequences is at least as long as the threshold. False otherwise.

From EMBOSS 2.9.0

Section: Input & output

These functions are used for formatted input and output to file.

Functions:

embHitReadFasta Read a hit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistRead Read a hitlist object from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistReadFasta Read a hitlist object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistReadNode Reads a scop families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the scop classification provided.

embHitlistReadNodeFasta Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the domain classification provided.

embHitlistWrite Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.

embHitlistWriteSubset Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Only those hits are written for which a 1 is given in the corresponding position in array of integers. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

embHitlistWriteFasta Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.

embHitlistWriteSubsetFasta Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Only those hits are written for which a 1 is given in the corresponding position in array of integers. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

embHitlistWriteHitFasta Write contents of one Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.

embSignatureReadNew Read a Signature object from a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

embSignatureWrite Write contents of a Signature object to an output file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

embSignatureHitsRead Reads a signature hits file, allocates a Hitlist object and writes it with hits from a signature hits file (see documentation for the DOMAINATRIX "sigscan" application). In other words, this function reads the results of a scan of a signature against a protein sequence database.

embSignatureHitsWrite Writes a list of AjOHit objects to an output file (see documentation for the DOMAINATRIX "sigscan" application). This is intended for displaying the results from scans of a signature against a protein sequence database. The Hitlist must have first been classified by a call to embHitlistClassify. Hits up to the first user-specified number of false hits are written.

Function embHitReadFasta

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

Prototype

EmbPHit embHitReadFasta (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

EmbPHit RETURN 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	Input file stream
`EmbPHit`		RETURN	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 embHitlistRead

Read a hitlist object from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Prototype

EmbPHitlist embHitlistRead (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

EmbPHitlist RETURN Hitlist object

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`EmbPHitlist`		RETURN	Hitlist object

From EMBOSS 2.9.0

Function embHitlistReadFasta

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

Prototype

EmbPHitlist embHitlistReadFasta (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

EmbPHitlist RETURN Hitlist object

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`EmbPHitlist`		RETURN	Hitlist object

From EMBOSS 3.0.0

Function embHitlistReadNode

Reads a scop families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the scop classification provided.

Prototype

AjPList embHitlistReadNode (
      AjPFile inf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass
);

Type Name Read/Write Description

AjPFile inf Modify File containing multiple Hitlist objects

const AjPStr fam Input Family.

const AjPStr sfam Input Superfamily.

const AjPStr fold Input Fold.

const AjPStr klass Input Class.

AjPList RETURN List of Hitlist objects or NULL.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	File containing multiple Hitlist objects
`const AjPStr`	`fam`	Input	Family.
`const AjPStr`	`sfam`	Input	Superfamily.
`const AjPStr`	`fold`	Input	Fold.
`const AjPStr`	`klass`	Input	Class.
`AjPList`		RETURN	List of Hitlist objects or NULL.

From EMBOSS 2.9.0

Function embHitlistReadNodeFasta

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the domain classification provided.

Prototype

AjPList embHitlistReadNodeFasta (
      AjPFile inf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass
);

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	File containing multiple Hitlist objects
`const AjPStr`	`fam`	Input	Family.
`const AjPStr`	`sfam`	Input	Superfamily.
`const AjPStr`	`fold`	Input	Fold.
`const AjPStr`	`klass`	Input	Class.
`AjPList`		RETURN	List of Hitlist objects or NULL.

From EMBOSS 3.0.0

Function embHitlistWrite

Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool embHitlistWrite (
      AjPFile outf,
      const EmbPHitlist obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const EmbPHitlist obj Input Hitlist object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const EmbPHitlist`	`obj`	Input	Hitlist object
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Function embHitlistWriteSubset

Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Only those hits are written for which a 1 is given in the corresponding position in array of integers. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool embHitlistWriteSubset (
      AjPFile outf,
      const EmbPHitlist obj,
      const AjPUint ok
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const EmbPHitlist obj Input Hitlist object

const AjPUint ok Input Whether hits are to be printed or not

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const EmbPHitlist`	`obj`	Input	Hitlist object
`const AjPUint`	`ok`	Input	Whether hits are to be printed or not
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Function embHitlistWriteFasta

Prototype

AjBool embHitlistWriteFasta (
      AjPFile outf,
      const EmbPHitlist obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const EmbPHitlist obj Input Hitlist object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const EmbPHitlist`	`obj`	Input	Hitlist object
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function embHitlistWriteSubsetFasta

Prototype

AjBool embHitlistWriteSubsetFasta (
      AjPFile outf,
      const EmbPHitlist obj,
      const AjPUint ok
);

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const EmbPHitlist`	`obj`	Input	Hitlist object
`const AjPUint`	`ok`	Input	Whether hits are to be printed or not
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function embHitlistWriteHitFasta

Write contents of one Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool embHitlistWriteHitFasta (
      AjPFile outf,
      ajuint n,
      const EmbPHitlist obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

ajuint n Input Number of hit

const EmbPHitlist obj Input Hitlist object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`ajuint`	`n`	Input	Number of hit
`const EmbPHitlist`	`obj`	Input	Hitlist object
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function embSignatureReadNew

Read a Signature object from a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Prototype

EmbPSignature embSignatureReadNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

EmbPSignature RETURN Signature object

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`EmbPSignature`		RETURN	Signature object

From EMBOSS 2.9.0

Function embSignatureWrite

Write contents of a Signature object to an output file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Prototype

AjBool embSignatureWrite (
      AjPFile outf,
      const EmbPSignature obj
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const EmbPSignature obj Input Signature object

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	Output file stream
`const EmbPSignature`	`obj`	Input	Signature object
`AjBool`		RETURN	ajTrue on success

From EMBOSS 2.9.0

Function embSignatureHitsRead

Reads a signature hits file, allocates a Hitlist object and writes it with hits from a signature hits file (see documentation for the DOMAINATRIX "sigscan" application). In other words, this function reads the results of a scan of a signature against a protein sequence database.

Prototype

EmbPHitlist embSignatureHitsRead (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

EmbPHitlist RETURN Hitlist object that was allocated.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`EmbPHitlist`		RETURN	Hitlist object that was allocated.

From EMBOSS 2.9.0

Function embSignatureHitsWrite

Writes a list of AjOHit objects to an output file (see documentation for the DOMAINATRIX "sigscan" application). This is intended for displaying the results from scans of a signature against a protein sequence database. The Hitlist must have first been classified by a call to embHitlistClassify. Hits up to the first user-specified number of false hits are written.

Prototype

AjBool embSignatureHitsWrite (
      AjPFile outf,
      const EmbPSignature sig,
      const EmbPHitlist hitlist,
      ajuint n
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const EmbPSignature sig Input Signature object

const EmbPHitlist hitlist Input Hitlist objects with hits from scan

ajuint n Input Max. no. false hits to output

AjBool RETURN True if file was written

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const EmbPSignature`	`sig`	Input	Signature object
`const EmbPHitlist`	`hitlist`	Input	Hitlist objects with hits from scan
`ajuint`	`n`	Input	Max. no. false hits to output
`AjBool`		RETURN	True if file was written

From EMBOSS 2.9.0

Section: Miscellaneous

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

Functions:

embHitlistClassify Classifies a list of signature-sequence hits (held in a Hitlist object) according to list of target sequences (a list of Hitlist objects).

embSignatureCompile Function to compile a signature: calls embSigposNew to allocate an array of AjOSigpos objects within an AjOSignature object, and then writes this array. The signature must first have been allocated by using the embSignatureNew function.

embSignatureAlignSeq Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling the embSignatureCompile function. A Hit object is written.

embSignatureAlignSeqall Aligns a signature to a set of sequences and writes a Hitlist object with the results. The top-scoring <n> hits are written. The signature must have first been compiled by calling the embSignatureCompile function. Memory for an Hitlist object must be allocated beforehand by using the Hitlist constructor with an arg. of 0.

embSigExit Cleanup of signature function internals.

Function embHitlistClassify

Classifies a list of signature-sequence hits (held in a Hitlist object) according to list of target sequences (a list of Hitlist objects).

Prototype

AjBool embHitlistClassify (
      EmbPHitlist hitlist,
      const AjPList targets,
      ajuint thresh
);

Type Name Read/Write Description

EmbPHitlist hitlist Modify Hitlist object with hits

const AjPList targets Input List of AjOHitlist objects with targets

ajuint thresh Input Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit.

AjBool RETURN True on success, else False

Type	Name	Read/Write	Description
`EmbPHitlist`	`hitlist`	Modify	Hitlist object with hits
`const AjPList`	`targets`	Input	List of AjOHitlist objects with targets
`ajuint`	`thresh`	Input	Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit.
`AjBool`		RETURN	True on success, else False

From EMBOSS 2.9.0

Function embSignatureCompile

Function to compile a signature: calls embSigposNew to allocate an array of AjOSigpos objects within an AjOSignature object, and then writes this array. The signature must first have been allocated by using the embSignatureNew function.

Prototype

AjBool embSignatureCompile (
      EmbPSignature* S,
      float gapo,
      float gape,
      const AjPMatrixf matrix
);

Type Name Read/Write Description

EmbPSignature* S Output Signature object

float gapo Input Gap opening penalty

float gape Input Gap extension penalty

const AjPMatrixf matrix Input Residue substitution matrix

AjBool RETURN True if array was written succesfully.

Type	Name	Read/Write	Description
`EmbPSignature*`	`S`	Output	Signature object
`float`	`gapo`	Input	Gap opening penalty
`float`	`gape`	Input	Gap extension penalty
`const AjPMatrixf`	`matrix`	Input	Residue substitution matrix
`AjBool`		RETURN	True if array was written succesfully.

From EMBOSS 2.9.0

Function embSignatureAlignSeq

Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling the embSignatureCompile function. A Hit object is written.

Prototype

AjBool embSignatureAlignSeq (
      const EmbPSignature S,
      const AjPSeq seq,
      EmbPHit* hit,
      ajuint nterm
);

Type Name Read/Write Description

const EmbPSignature S Input Signature object

const AjPSeq seq Input Protein sequence

EmbPHit* hit Output Hit object pointer

ajuint nterm Input N-terminal matching option

AjBool RETURN True if a signature-sequence alignment was successful and the Hit object was written. Returns False if there was an internal error, bad arg's etc. or in cases where a sequence is rejected because of N-terminal matching options).

Type	Name	Read/Write	Description
`const EmbPSignature`	`S`	Input	Signature object
`const AjPSeq`	`seq`	Input	Protein sequence
`EmbPHit*`	`hit`	Output	Hit object pointer
`ajuint`	`nterm`	Input	N-terminal matching option
`AjBool`		RETURN	True if a signature-sequence alignment was successful and the Hit object was written. Returns False if there was an internal error, bad arg's etc. or in cases where a sequence is rejected because of N-terminal matching options).

From EMBOSS 2.9.0

Function embSignatureAlignSeqall

Aligns a signature to a set of sequences and writes a Hitlist object with the results. The top-scoring <n> hits are written. The signature must have first been compiled by calling the embSignatureCompile function. Memory for an Hitlist object must be allocated beforehand by using the Hitlist constructor with an arg. of 0.

Prototype

AjBool embSignatureAlignSeqall (
      const EmbPSignature sig,
      AjPSeqall db,
      ajuint n,
      EmbPHitlist* hitlist,
      ajuint nterm
);

Type Name Read/Write Description

const EmbPSignature sig Input Signature object

AjPSeqall db Modify Protein sequences

ajuint n Input Max. number of top-scoring hits to store

EmbPHitlist* hitlist Output Hitlist object pointer

ajuint nterm Input N-terminal matching option

AjBool RETURN True if Hitlist object was written succesfully.

Type	Name	Read/Write	Description
`const EmbPSignature`	`sig`	Input	Signature object
`AjPSeqall`	`db`	Modify	Protein sequences
`ajuint`	`n`	Input	Max. number of top-scoring hits to store
`EmbPHitlist*`	`hitlist`	Output	Hitlist object pointer
`ajuint`	`nterm`	Input	N-terminal matching option
`AjBool`		RETURN	True if Hitlist object was written succesfully.

From EMBOSS 2.9.0

Function embSigExit

Cleanup of signature function internals.

Prototype

void embSigExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.1.0

embHitlistNew	Hitlist object constructor. This is normally called by the embHitlistRead function. Fore-knowledge of the number of hits is required.
embHitNew	Hit object constructor. This is normally called by the embHitlistNew function.
embSignatureNew	Signature object constructor. This is normally called by the embSignatureReadNew function. Fore-knowledge of the number of signature positions is required.

embHitlistDel	Destructor for hitlist object.
embHitDel	Destructor for hit object.
embSignatureDel	Destructor for Signature object.

embHitlistMatchFold	Function to sort Hitlist object by Fold element.
embMatchScore	Function to sort Hit objects by score record. Usually called by ajListSort.
embMatchinvScore	Function to sort Hit objects by score record. Usually called by ajListSort. The sorting order is inverted - i.e. it returns -1 if score1 > score2 (as opposed to embMatchScore).
embMatchLigid	Function to sort Hit objects by Ligid record (referenced via Sig element).
embMatchSN	Function to sort Hit objects by sn element within Sig element. Usually called by ajListSort.

embHitReadFasta	Read a hit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistRead	Read a hitlist object from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistReadFasta	Read a hitlist object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistReadNode	Reads a scop families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the scop classification provided.
embHitlistReadNodeFasta	Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package) and writes a list of Hitlist objects containing all domains matching the domain classification provided.
embHitlistWrite	Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.
embHitlistWriteSubset	Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Only those hits are written for which a 1 is given in the corresponding position in array of integers. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.
embHitlistWriteFasta	Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.
embHitlistWriteSubsetFasta	Write contents of a Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Only those hits are written for which a 1 is given in the corresponding position in array of integers. Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.
embHitlistWriteHitFasta	Write contents of one Hitlist object to an output file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application). Text for Class, Fold, Superfamily and Family is only written if the text is available.
embSignatureReadNew	Read a Signature object from a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).
embSignatureWrite	Write contents of a Signature object to an output file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).
embSignatureHitsRead	Reads a signature hits file, allocates a Hitlist object and writes it with hits from a signature hits file (see documentation for the DOMAINATRIX "sigscan" application). In other words, this function reads the results of a scan of a signature against a protein sequence database.
embSignatureHitsWrite	Writes a list of AjOHit objects to an output file (see documentation for the DOMAINATRIX "sigscan" application). This is intended for displaying the results from scans of a signature against a protein sequence database. The Hitlist must have first been classified by a call to embHitlistClassify. Hits up to the first user-specified number of false hits are written.

embHitlistClassify	Classifies a list of signature-sequence hits (held in a Hitlist object) according to list of target sequences (a list of Hitlist objects).
embSignatureCompile	Function to compile a signature: calls embSigposNew to allocate an array of AjOSigpos objects within an AjOSignature object, and then writes this array. The signature must first have been allocated by using the embSignatureNew function.
embSignatureAlignSeq	Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling the embSignatureCompile function. A Hit object is written.
embSignatureAlignSeqall	Aligns a signature to a set of sequences and writes a Hitlist object with the results. The top-scoring <n> hits are written. The signature must have first been compiled by calling the embSignatureCompile function. Memory for an Hitlist object must be allocated beforehand by using the Hitlist constructor with an arg. of 0.
embSigExit	Cleanup of signature function internals.