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

AjPSigdat embSigdatNew (
      ajint nres,
      ajint ngap
);

Input

nres:(Input)Number of emprical residues / environments.
ngap:(Input)Number of emprical gaps.

Returns

AjPSigdat: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 3.0.0

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

AjPSigpos embSigposNew (
      ajint ngap
);

Input

ngap:(Input)Number of permissible gaps.

Returns

AjPSigpos: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 3.0.0

Function embSigposDel

Destructor for Sigpos object.

Synopsis

Prototype

void embSigposDel (
      AjPSigpos* pthis
);

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 3.0.0

Function embSigdatDel

Destructor for Sigdat object.

Synopsis

Prototype

void embSigdatDel (
      AjPSigdat* pthis
);

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 3.0.0

Function embHitidxNew

Hitidx object constructor. This is normally called by the embHitlistClassify function.

Synopsis

Prototype

EmbPHitidx embHitidxNew (
      void
);

Returns

EmbPHitidx:Pointer to a Hitidx object

Description

Hitidx object constructor. This is normally called by the embHitlistClassify 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 3.0.0

Function embHitidxDel

Destructor for Hitidx object.

Synopsis

Prototype

void embHitidxDel (
      EmbPHitidx* pthis
);

Output

pthis:(Output)Hitidx object pointer

Returns

void:No return value

Description

Destructor for Hitidx 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 3.0.0

Function embHitidxBinSearch

Performs a binary search for an accession number over an array of Hitidx structures (which of course must first have been sorted). This is a case-insensitive search.

Synopsis

Prototype

ajint embHitidxBinSearch (
      const AjPStr id,
      EmbPHitidx const* arr,
      ajint siz
);

Input

id:(Input)Search term
arr:(Input)Array of EmbOHitidx objects
siz:(Input)Size of array

Returns

ajint:Index of first Hitidx object found with an Id element matching id, or -1 if id is not found.

Description

Performs a binary search for an accession number over an array of Hitidx structures (which of course must first have been sorted). This is a case-insensitive search.

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 3.0.0

Function embHitidxMatchId

Function to sort Hitidx objects by Id element. Usually called by embHitlistClassify.

Synopsis

Prototype

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

Input

hit1:(Input)Pointer to Hitidx object 1
hit2:(Input)Pointer to Hitidx object 2

Returns

ajint:-1 if Id1 should sort before Id2, +1 if the Id2 should sort first. 0 if they are identical in length and content.

Description

Function to sort Hitidx objects by Id element. Usually called by embHitlistClassify.

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 3.0.0

Function embHitlistReadFam

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified family, and create a list of Hitlist structures. Only the first familiy in the scop families file matching the specified classification is read (the file should not normally contain duplicate families).

Synopsis

Prototype

AjBool embHitlistReadFam (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

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

Description

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified family, and create a list of Hitlist structures. Only the first familiy in the scop families file matching the specified classification is read (the file should not normally contain duplicate families).

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 3.0.0

Function embHitlistReadSfam

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified superfamily, and create a list of Hitlist structures.

Synopsis

Prototype

AjBool embHitlistReadSfam (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

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

Description

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified superfamily, and create a list of Hitlist structures.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embHitlistReadFold

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified fold, and create a list of Hitlist structures.

Synopsis

Prototype

AjBool embHitlistReadFold (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

AjBool:ajTrue on success

Description

Reads a domain families file (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified fold, and create a list of Hitlist structures.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embHitlistReadFamFasta

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified family, and create a list of Hitlist structures. Only the first familiy in the scop families file matching the specified classification is read (the file should not normally contain duplicate families).

Synopsis

Prototype

AjBool embHitlistReadFamFasta (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

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

Description

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified family, and create a list of Hitlist structures. Only the first familiy in the scop families file matching the specified classification is read (the file should not normally contain duplicate families).

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 3.0.0

Function embHitlistReadSfamFasta

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified superfamily, and create a list of Hitlist structures.

Synopsis

Prototype

AjBool embHitlistReadSfamFasta (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

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

Description

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified superfamily, and create a list of Hitlist structures.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embHitlistReadFoldFasta

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified fold, and create a list of Hitlist structures.

Synopsis

Prototype

AjBool embHitlistReadFoldFasta (
      AjPFile scopf,
      const AjPStr fam,
      const AjPStr sfam,
      const AjPStr fold,
      const AjPStr klass,
      AjPList* list
);

Input

fam:(Input)Family
sfam:(Input)Superfamily
fold:(Input)Fold
klass:(Input)Class

Output

list:(Output)A list of hitlist structures.

Input & Output

scopf:(Modify)The scop families file.

Returns

AjBool:ajTrue on success

Description

Reads a domain families file in extended FASTA format (see documentation for the EMBASSY DOMAINATRIX package), selects the entries with the specified fold, and create a list of Hitlist structures.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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.

Function embHitlistNew

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

Synopsis

Prototype

AjPHitlist embHitlistNew (
      ajint n
);

Input

n:(Input)Number of hits

Returns

AjPHitlist: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 3.0.0

Function embHitNew

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

Synopsis

Prototype

AjPHit embHitNew (
      void
);

Returns

AjPHit: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 3.0.0

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

AjPSignature embSignatureNew (
      ajint n
);

Input

n:(Input)Number of signature positions

Returns

AjPSignature: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 3.0.0

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.

Function embHitlistDel

Destructor for hitlist object.

Synopsis

Prototype

void embHitlistDel (
      AjPHitlist* ptr
);

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 3.0.0

Function embHitDel

Destructor for hit object.

Synopsis

Prototype

void embHitDel (
      AjPHit* ptr
);

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 3.0.0

Function embSignatureDel

Destructor for Signature object.

Synopsis

Prototype

void embSignatureDel (
      AjPSignature* ptr
);

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 3.0.0

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.

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

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

Input

hit1:(Input)Hit 1
hit2:(Input)Hit 2

Returns

AjPHit: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 3.0.0

Operators

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

Function embHitlistMatchFold

Function to sort Hitlist object by Fold element.

Synopsis

Prototype

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

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 3.0.0

Function embMatchScore

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

Synopsis

Prototype

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

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 3.0.0

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
);

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 3.0.0

Function embMatchLigid

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

Synopsis

Prototype

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

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 3.0.0

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
);

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 3.0.0

Reporters

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

Function embHitsOverlap

Checks for overlap between two hits.

Synopsis

Prototype

AjBool embHitsOverlap (
      const AjPHit hit1,
      const AjPHit hit2,
      ajint n
);

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 3.0.0

Input & output

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

Function embHitReadFasta

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

Synopsis

Prototype

AjPHit embHitReadFasta (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPHit: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 3.0.0

Function embHitlistRead

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

Synopsis

Prototype

AjPHitlist embHitlistRead (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPHitlist: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 3.0.0

Function embHitlistReadFasta

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

Synopsis

Prototype

AjPHitlist embHitlistReadFasta (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPHitlist: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 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.

Synopsis

Prototype

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

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 3.0.0

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
);

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 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.

Synopsis

Prototype

AjBool embHitlistWrite (
      AjPFile outf,
      const AjPHitlist obj
);

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 3.0.0

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 AjPHitlist obj,
      const AjPInt ok
);

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 3.0.0

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 AjPHitlist obj
);

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 3.0.0

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 AjPHitlist obj,
      const AjPInt ok
);

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 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.

Synopsis

Prototype

AjBool embHitlistWriteHitFasta (
      AjPFile outf,
      ajint n,
      const AjPHitlist obj
);

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 3.0.0

Function embSignatureReadNew

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

Synopsis

Prototype

AjPSignature embSignatureReadNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPSignature: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 3.0.0

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 AjPSignature obj
);

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 3.0.0

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

AjPHitlist embSignatureHitsRead (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPHitlist: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 3.0.0

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 AjPSignature sig,
      const AjPHitlist hitlist,
      ajint n
);

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 3.0.0

Miscellaneous

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

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 (
      const AjPHitlist* hits,
      const AjPList targets,
      ajint thresh
);

Input

hits:(Input)Pointer to Hitlist object with hits
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.

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 3.0.0

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 (
      AjPSignature* S,
      float gapo,
      float gape,
      const AjPMatrixf matrix
);

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 3.0.0

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 AjPSignature S,
      const AjPSeq seq,
      AjPHit* hit,
      ajint nterm
);

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 3.0.0

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 AjPSignature sig,
      AjPSeqall db,
      ajint n,
      AjPHitlist* hitlist,
      ajint nterm
);

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 3.0.0