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.

Synopsis

Prototype
EmbPSigdat embSigdatNew (
      ajuint nres,
      ajuint ngap
);

TypeNameRead/WriteDescription
ajuintnresInputNumber of emprical residues / environments.
ajuintngapInputNumber of emprical gaps.
EmbPSigdat RETURNPointer to a Sigdat object

Input
nres:(Input)Number of emprical residues / environments.
ngap:(Input)Number of emprical gaps.
Returns
EmbPSigdat:Pointer to a Sigdat object

Description

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.

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 6.4.0

Function embSigposNew

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

Synopsis

Prototype
EmbPSigpos embSigposNew (
      ajuint ngap
);

TypeNameRead/WriteDescription
ajuintngapInputNumber of permissible gaps.
EmbPSigpos RETURNPointer to a Sigpos object

Input
ngap:(Input)Number of permissible gaps.
Returns
EmbPSigpos:Pointer to a Sigpos object

Description

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

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 6.4.0

Function embSigposDel

Destructor for Sigpos object.

Synopsis

Prototype
void embSigposDel (
      EmbPSigpos* pthis
);

TypeNameRead/WriteDescription
EmbPSigpos*pthisOutputSigpos object pointer
void RETURN

Output
pthis:(Output)Sigpos object pointer
Returns
void:No return value

Description

Destructor for Sigpos 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 6.4.0

Function embSigdatDel

Destructor for Sigdat object.

Synopsis

Prototype
void embSigdatDel (
      EmbPSigdat* pthis
);

TypeNameRead/WriteDescription
EmbPSigdat*pthisOutputSigdat object pointer
void RETURN

Output
pthis:(Output)Sigdat object pointer
Returns
void:No return value

Description

Destructor for Sigdat 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 6.4.0

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 embHitNew embSignatureNew

Function embHitlistNew

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

Synopsis

Prototype
EmbPHitlist embHitlistNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of hits
EmbPHitlist RETURNPointer to a hitlist object

Input
n:(Input)Number of hits
Returns
EmbPHitlist:Pointer to a hitlist object

Description

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

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 6.4.0

Function embHitNew

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

Synopsis

Prototype
EmbPHit embHitNew (
      void
);

TypeNameRead/WriteDescription
EmbPHit RETURNPointer to a hit object

Returns
EmbPHit:Pointer to a hit object

Description

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

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 6.4.0

Function embSignatureNew

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

Synopsis

Prototype
EmbPSignature embSignatureNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of signature positions
EmbPSignature RETURNPointer to a Signature object

Input
n:(Input)Number of signature positions
Returns
EmbPSignature:Pointer to a Signature object

Description

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

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 6.4.0

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 embHitDel embSignatureDel

Function embHitlistDel

Destructor for hitlist object.

Synopsis

Prototype
void embHitlistDel (
      EmbPHitlist* ptr
);

TypeNameRead/WriteDescription
EmbPHitlist*ptrOutputHitlist object pointer
void RETURN

Output
ptr:(Output)Hitlist object pointer
Returns
void:No return value

Description

Destructor for hitlist 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 6.4.0

Function embHitDel

Destructor for hit object.

Synopsis

Prototype
void embHitDel (
      EmbPHit* ptr
);

TypeNameRead/WriteDescription
EmbPHit*ptrOutputHit object pointer
void RETURN

Output
ptr:(Output)Hit object pointer
Returns
void:No return value

Description

Destructor for hit 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 6.4.0

Function embSignatureDel

Destructor for Signature object.

Synopsis

Prototype
void embSignatureDel (
      EmbPSignature* ptr
);

TypeNameRead/WriteDescription
EmbPSignature*ptrOutputSignature object pointer
void RETURN

Output
ptr:(Output)Signature object pointer
Returns
void:No return value

Description

Destructor for Signature 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 6.4.0

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

Function embHitMerge

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

Synopsis

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

TypeNameRead/WriteDescription
const EmbPHithit1InputHit 1
const EmbPHithit2InputHit 2
EmbPHit RETURNPointer to Hit object.

Input
hit1:(Input)Hit 1
hit2:(Input)Hit 2
Returns
EmbPHit:Pointer to Hit object.

Description

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

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 6.4.0

Section: Operators

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

Functions: embHitlistMatchFold embMatchScore embMatchinvScore embMatchLigid embMatchSN

Function embHitlistMatchFold

Function to sort Hitlist object by Fold element.

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Hitlist object 1
const void*hit2InputPointer 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.

Input
hit1:(Input)Pointer to Hitlist object 1
hit2:(Input)Pointer to Hitlist object 2
Returns
ajint:-1 if Fold1 should sort before Fold2, +1 if the Fold2 should sort first. 0 if they are identical.

Description

Function to sort Hitlist object by Fold element.

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 6.4.0

Function embMatchScore

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

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Hit object 1
const void*hit2InputPointer to Hit object 2
ajint RETURN1 if score1<score2, 0 if score1==score2, else -1.

Input
hit1:(Input)Pointer to Hit object 1
hit2:(Input)Pointer to Hit object 2
Returns
ajint:1 if score1

Description

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

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 6.4.0

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).

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Hit object 1
const void*hit2InputPointer to Hit object 2
ajint RETURN1 if score1<score2, 0 if score1==score2, else -1.

Input
hit1:(Input)Pointer to Hit object 1
hit2:(Input)Pointer to Hit object 2
Returns
ajint:1 if score1

Description

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).

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 6.4.0

Function embMatchLigid

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

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Hit object 1
const void*hit2InputPointer 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.

Input
hit1:(Input)Pointer to Hit object 1
hit2:(Input)Pointer to Hit object 2
Returns
ajint:-1 if Ligid1 should sort before Ligid2, +1 if the Ligid2 should sort first. 0 if they are identical.

Description

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

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 6.4.0

Function embMatchSN

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

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Hit object 1
const void*hit2InputPointer to Hit object 2
ajint RETURN1 if sn1<sn2, 0 if sn1==sn2, else -1.

Input
hit1:(Input)Pointer to Hit object 1
hit2:(Input)Pointer to Hit object 2
Returns
ajint:1 if sn1

Description

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

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 6.4.0

Section: Reporters

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

Functions: embHitsOverlap

Function embHitsOverlap

Checks for overlap between two hits.

Synopsis

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

TypeNameRead/WriteDescription
const EmbPHithit1InputPointer to hit object 1
const EmbPHithit2InputPointer to hit object 2
ajuintnInputThreshold number of residues for overlap
AjBool RETURNTrue if the overlap between the sequences is at least as long as the threshold. False otherwise.

Input
hit1:(Input)Pointer to hit object 1
hit2:(Input)Pointer to hit object 2
n:(Input)Threshold number of residues for overlap
Returns
AjBool:True if the overlap between the sequences is at least as long as the threshold. False otherwise.

Description

Checks for overlap between two hits.

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 6.4.0

Section: Input & output

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

Functions: embHitReadFasta embHitlistRead embHitlistReadFasta embHitlistReadNode embHitlistReadNodeFasta embHitlistWrite embHitlistWriteSubset embHitlistWriteFasta embHitlistWriteSubsetFasta embHitlistWriteHitFasta embSignatureReadNew embSignatureWrite embSignatureHitsRead embSignatureHitsWrite

Function embHitReadFasta

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

Synopsis

Prototype
EmbPHit embHitReadFasta (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
EmbPHit RETURNHit object, or NULL if the file was not in extended FASTA (DHF) format (indicated by a token count of the the lines beginning with '>').

Input & Output
inf:(Modify)Input file stream
Returns
EmbPHit: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 '>').

Description

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

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 6.4.0

Function embHitlistRead

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

Synopsis

Prototype
EmbPHitlist embHitlistRead (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
EmbPHitlist RETURNHitlist object

Input & Output
inf:(Modify)Input file stream
Returns
EmbPHitlist:Hitlist object

Description

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

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 6.4.0

Function embHitlistReadFasta

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

Synopsis

Prototype
EmbPHitlist embHitlistReadFasta (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
EmbPHitlist RETURNHitlist object

Input & Output
inf:(Modify)Input file stream
Returns
EmbPHitlist:Hitlist object

Description

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

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileinfModifyFile containing multiple Hitlist objects
const AjPStrfamInputFamily.
const AjPStrsfamInputSuperfamily.
const AjPStrfoldInputFold.
const AjPStrklassInputClass.
AjPList RETURNList of Hitlist objects or NULL.

Input
fam:(Input)Family.
sfam:(Input)Superfamily.
fold:(Input)Fold.
klass:(Input)Class.
Input & Output
inf:(Modify)File containing multiple Hitlist objects
Returns
AjPList:List of Hitlist objects or NULL.

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileinfModifyFile containing multiple Hitlist objects
const AjPStrfamInputFamily.
const AjPStrsfamInputSuperfamily.
const AjPStrfoldInputFold.
const AjPStrklassInputClass.
AjPList RETURNList of Hitlist objects or NULL.

Input
fam:(Input)Family.
sfam:(Input)Superfamily.
fold:(Input)Fold.
klass:(Input)Class.
Input & Output
inf:(Modify)File containing multiple Hitlist objects
Returns
AjPList:List of Hitlist objects or NULL.

Description

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.

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 6.4.0

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.

Synopsis

Prototype
AjBool embHitlistWrite (
      AjPFile outf,
      const EmbPHitlist obj
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const EmbPHitlistobjInputHitlist object
AjBool RETURNTrue on success

Input
obj:(Input)Hitlist object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True on success

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const EmbPHitlistobjInputHitlist object
const AjPUintokInputWhether hits are to be printed or not
AjBool RETURNTrue on success

Input
obj:(Input)Hitlist object
ok:(Input)Whether hits are to be printed or not
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True on success

Description

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.

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 6.4.0

Function 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.

Synopsis

Prototype
AjBool embHitlistWriteFasta (
      AjPFile outf,
      const EmbPHitlist obj
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const EmbPHitlistobjInputHitlist object
AjBool RETURNTrue on success

Input
obj:(Input)Hitlist object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True on success

Description

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.

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 6.4.0

Function 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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const EmbPHitlistobjInputHitlist object
const AjPUintokInputWhether hits are to be printed or not
AjBool RETURNTrue on success

Input
obj:(Input)Hitlist object
ok:(Input)Whether hits are to be printed or not
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True on success

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
ajuintnInputNumber of hit
const EmbPHitlistobjInputHitlist object
AjBool RETURNTrue on success

Input
n:(Input)Number of hit
obj:(Input)Hitlist object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True on success

Description

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.

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 6.4.0

Function embSignatureReadNew

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

Synopsis

Prototype
EmbPSignature embSignatureReadNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
EmbPSignature RETURNSignature object

Input & Output
inf:(Modify)Input file stream
Returns
EmbPSignature:Signature object

Description

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

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 6.4.0

Function embSignatureWrite

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

Synopsis

Prototype
AjBool embSignatureWrite (
      AjPFile outf,
      const EmbPSignature obj
);

TypeNameRead/WriteDescription
AjPFileoutfOutputOutput file stream
const EmbPSignatureobjInputSignature object
AjBool RETURNajTrue on success

Input
obj:(Input)Signature object
Output
outf:(Output)Output file stream
Returns
AjBool:ajTrue on success

Description

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

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 6.4.0

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.

Synopsis

Prototype
EmbPHitlist embSignatureHitsRead (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
EmbPHitlist RETURNHitlist object that was allocated.

Input & Output
inf:(Modify)Input file stream
Returns
EmbPHitlist:Hitlist object that was allocated.

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const EmbPSignaturesigInputSignature object
const EmbPHitlisthitlistInputHitlist objects with hits from scan
ajuintnInputMax. no. false hits to output
AjBool RETURNTrue if file was written

Input
sig:(Input)Signature object
hitlist:(Input)Hitlist objects with hits from scan
n:(Input)Max. no. false hits to output
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True if file was written

Description

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.

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 6.4.0

Section: Miscellaneous

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

Functions: embHitlistClassify embSignatureCompile embSignatureAlignSeq embSignatureAlignSeqall embSigExit

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).

The following classification of hits is taken from the documentation for the DOMAINATRIX "sigscan" application : Definition of classes of hit The primary classification is an objective definition of the hit and has one of the following values: SEED - the sequence was included in the original alignment from which the signature was generated. HIT - A protein which was detected by psiblast (see psiblasts.c) to be a homologue to at least one of the proteins in the family from which the signature was derived. Such proteins are identified by the 'HIT' record in the scop families file. OTHER - A true member of the family but not a homologue as detected by psi-blast. Such proteins may have been found from the literature and manually added to the scop families file or may have been detected by the EMBOSS program swissparse (see swissparse.c). They are identified in the scop families file by the 'OTHER' record. CROSS - A protein which is homologous to a protein of the same fold, but differnt family, of the proteins from which the signature was derived. FALSE - A homologue to a protein with a different fold to the family of the signature. UNKNOWN - The protein is not known to be CROSS, FALSE or a true hit (a SEED, HIT or OTHER). The secondary classification is provided for convenience and a value as follows: Hits of SEED, HIT and OTHER classification are all listed as TRUE. Hits of CROSS, FALSE or UNKNOWN objective classification are listed as CROSS, FALSE or UNKNOWN respectively.

The Group element is copied from the target sequence for 'TRUE' objective hits, whereas 'NOT_APPLICABLE' is given for other types of hit.

The subjective column allows for hand-annotation of the hits files so that proteins of UNKNOWN objective classification can re-classified by a human expert as TRUE, FALSE, CROSS or otherwise left as UNKNOWN for the purpose of generating signature performance plots with the EMBOSS application sigplot.

Writes the Group, Typeobj (primary classification) & Typesbj (secondary classification) elements depending on how the SCOP classification records of the Hit object and target sequence in question compare.

Synopsis

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

TypeNameRead/WriteDescription
EmbPHitlisthitlistModifyHitlist object with hits
const AjPListtargetsInputList of AjOHitlist objects with targets
ajuintthreshInputMinimum length (residues) of overlap required for two hits with the same code to be counted as the same hit.
AjBool RETURNTrue on success, else False

Input
targets:(Input)List of AjOHitlist objects with targets
thresh:(Input)Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit.
Input & Output
hitlist:(Modify)Hitlist object with hits
Returns
AjBool:True on success, else False

Description

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

The following classification of hits is taken from the documentation for the DOMAINATRIX "sigscan" application : Definition of classes of hit The primary classification is an objective definition of the hit and has one of the following values: SEED - the sequence was included in the original alignment from which the signature was generated. HIT - A protein which was detected by psiblast (see psiblasts.c) to be a homologue to at least one of the proteins in the family from which the signature was derived. Such proteins are identified by the 'HIT' record in the scop families file. OTHER - A true member of the family but not a homologue as detected by psi-blast. Such proteins may have been found from the literature and manually added to the scop families file or may have been detected by the EMBOSS program swissparse (see swissparse.c). They are identified in the scop families file by the 'OTHER' record. CROSS - A protein which is homologous to a protein of the same fold, but differnt family, of the proteins from which the signature was derived. FALSE - A homologue to a protein with a different fold to the family of the signature. UNKNOWN - The protein is not known to be CROSS, FALSE or a true hit (a SEED, HIT or OTHER). The secondary classification is provided for convenience and a value as follows: Hits of SEED, HIT and OTHER classification are all listed as TRUE. Hits of CROSS, FALSE or UNKNOWN objective classification are listed as CROSS, FALSE or UNKNOWN respectively.

The Group element is copied from the target sequence for 'TRUE' objective hits, whereas 'NOT_APPLICABLE' is given for other types of hit.

The subjective column allows for hand-annotation of the hits files so that proteins of UNKNOWN objective classification can re-classified by a human expert as TRUE, FALSE, CROSS or otherwise left as UNKNOWN for the purpose of generating signature performance plots with the EMBOSS application sigplot.

Writes the Group, Typeobj (primary classification) & Typesbj (secondary classification) elements depending on how the SCOP classification records of the Hit object and target sequence in question compare.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
EmbPSignature*SOutputSignature object
floatgapoInputGap opening penalty
floatgapeInputGap extension penalty
const AjPMatrixfmatrixInputResidue substitution matrix
AjBool RETURNTrue if array was written succesfully.

Input
gapo:(Input)Gap opening penalty
gape:(Input)Gap extension penalty
matrix:(Input)Residue substitution matrix
Output
S:(Output)Signature object
Returns
AjBool:True if array was written succesfully.

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
const EmbPSignatureSInputSignature object
const AjPSeqseqInputProtein sequence
EmbPHit*hitOutputHit object pointer
ajuintntermInputN-terminal matching option
AjBool RETURNTrue 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).

Input
S:(Input)Signature object
seq:(Input)Protein sequence
nterm:(Input)N-terminal matching option
Output
hit:(Output)Hit object pointer
Returns
AjBool: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).

Description

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.

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 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
const EmbPSignaturesigInputSignature object
AjPSeqalldbModifyProtein sequences
ajuintnInputMax. number of top-scoring hits to store
EmbPHitlist*hitlistOutputHitlist object pointer
ajuintntermInputN-terminal matching option
AjBool RETURNTrue if Hitlist object was written succesfully.

Input
sig:(Input)Signature object
n:(Input)Max. number of top-scoring hits to store
nterm:(Input)N-terminal matching option
Output
hitlist:(Output)Hitlist object pointer
Input & Output
db:(Modify)Protein sequences
Returns
AjBool:True if Hitlist object was written succesfully.

Description

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.

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 6.4.0

Function embSigExit

Cleanup of signature function internals.

Synopsis

Prototype
void embSigExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleanup of signature function internals.

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 6.4.0