ajdmx.c
All constructors return a pointer to a new instance. It is the
responsibility of the user to first destroy any previous instance. The
target pointer does not need to be initialised to NULL, but it is good
programming practice to do so anyway.
Functions: ajDmxScophitNew ajDmxScopalgNew ajDmxScopalgRead
Scophit object constructor.
Synopsis
Prototype
AjPScophit ajDmxScophitNew (
void
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit | | RETURN | Pointer to a Scophit object |
Returns
| AjPScophit: | Pointer to a Scophit object |
Description
Scophit object constructor.
See Also
See other functions in this section
Availability
In release 6.4.0
Scopalg object constructor. This is normally called by the ajDmxScopalgRead
function. Fore-knowledge of the number of sequences is required.
Synopsis
Prototype
AjPScopalg ajDmxScopalgNew (
ajint n
);
| Type | Name | Read/Write | Description |
|---|
| ajint | n | Input | Number of sequences |
| AjPScopalg | | RETURN | Pointer to a Scopalg object |
Input
| n: | (Input) | Number of sequences |
Returns
| AjPScopalg: | Pointer to a Scopalg object |
Description
Scopalg object constructor. This is normally called by the ajDmxScopalgRead
function. Fore-knowledge of the number of sequences is required.
See Also
See other functions in this section
Availability
In release 6.4.0
Read a Scopalg object from a file.
Synopsis
Prototype
AjBool ajDmxScopalgRead (
AjPFile inf,
AjPScopalg* thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | inf | Modify | Input file stream |
| AjPScopalg* | thys | Output | Scopalg object |
| AjBool | | RETURN | True if the file contained any data, even an empty
alignment. False if the file did not contain a 'TY' record, which is
taken to indicate a domain alignment file. |
Output
| thys: | (Output) | Scopalg object |
Input & Output
| inf: | (Modify) | Input file stream |
Returns
| AjBool: | True if the file contained any data, even an empty
alignment. False if the file did not contain a 'TY' record, which is
taken to indicate a domain alignment file. |
Description
Read a Scopalg object from a file.
See Also
See other functions in this section
Availability
In release 6.4.0
All destructor functions receive the address of the instance to be
deleted. The original pointer is set to NULL so is ready for re-use.
Functions: ajDmxScophitDel ajDmxScophitDelWrap ajDmxScopalgDel
Destructor for Scophit object.
Synopsis
Prototype
void ajDmxScophitDel (
AjPScophit* pthis
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit* | pthis | Output | Scophit object pointer |
| void | | RETURN | |
Output
| pthis: | (Output) | Scophit object pointer |
Returns
Description
Destructor for Scophit object.
See Also
See other functions in this section
Availability
In release 6.4.0
Wrapper to destructor for Scophit object for use with generic functions.
Synopsis
Prototype
void ajDmxScophitDelWrap (
void** ptr
);
| Type | Name | Read/Write | Description |
|---|
| void** | ptr | Delete | Object pointer |
| void | | RETURN | |
Output
| ptr: | (Delete) | Object pointer |
Returns
Description
Wrapper to destructor for Scophit object for use with generic functions.
See Also
See other functions in this section
Availability
In release 6.4.0
Destructor for Scopalg object.
Synopsis
Prototype
void ajDmxScopalgDel (
AjPScopalg* pthis
);
| Type | Name | Read/Write | Description |
|---|
| AjPScopalg* | pthis | Delete | Scopalg object pointer |
| void | | RETURN | |
Output
| pthis: | (Delete) | Scopalg object pointer |
Returns
Description
Destructor for Scopalg object.
See Also
See other functions in this section
Availability
In release 6.4.0
These functions overwrite the instance provided as the first argument
A NULL value is always acceptable so these functions are often used to
create a new instance by assignment.
Functions: ajDmxScophitListCopy ajDmxScophitCopy
Read a list of Scophit structures and returns a pointer to a duplicate
of the list.
Synopsis
Prototype
AjPList ajDmxScophitListCopy (
const AjPList ptr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | ptr | Input | List of Scophit objects |
| AjPList | | RETURN | True on success (list was duplicated ok) |
Input
| ptr: | (Input) | List of Scophit objects |
Returns
| AjPList: | True on success (list was duplicated ok) |
Description
Read a list of Scophit structures and returns a pointer to a duplicate
of the list.
See Also
See other functions in this section
Availability
In release 6.4.0
Copies the contents from one Scophit object to another.
Synopsis
Prototype
AjBool ajDmxScophitCopy (
AjPScophit* to,
const AjPScophit from
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit* | to | Output | Scophit object pointer |
| const AjPScophit | from | Input | Scophit object |
| AjBool | | RETURN | True if copy was successful. |
Input
| from: | (Input) | Scophit object |
Output
| to: | (Output) | Scophit object pointer |
Returns
| AjBool: | True if copy was successful. |
Description
Copies the contents from one Scophit object to another.
See Also
See other functions in this section
Availability
In release 6.4.0
These functions use the contents of an instance and update them.
Functions: ajDmxScophitTargetLowPriority ajDmxScophitTarget2 ajDmxScophitTarget
Sets the Target element of a Scophit object to True if its Priority is low.
Synopsis
Prototype
AjBool ajDmxScophitTargetLowPriority (
AjPScophit* h
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit* | h | Modify | Pointer to Scophit object |
| AjBool | | RETURN | True on success. False otherwise. |
Input & Output
| h: | (Modify) | Pointer to Scophit object |
Returns
| AjBool: | True on success. False otherwise. |
Description
Sets the Target element of a Scophit object to True if its Priority is low.
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the Target2 element of a Scophit object to True.
Synopsis
Prototype
AjBool ajDmxScophitTarget2 (
AjPScophit* h
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit* | h | Modify | Pointer to Scophit object |
| AjBool | | RETURN | True on success. False otherwise. |
Input & Output
| h: | (Modify) | Pointer to Scophit object |
Returns
| AjBool: | True on success. False otherwise. |
Description
Sets the Target2 element of a Scophit object to True.
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the Target element of a Scophit object to True.
Synopsis
Prototype
AjBool ajDmxScophitTarget (
AjPScophit* h
);
| Type | Name | Read/Write | Description |
|---|
| AjPScophit* | h | Modify | Pointer to Scophit object |
| AjBool | | RETURN | True on success. False otherwise. |
Input & Output
| h: | (Modify) | Pointer to Scophit object |
Returns
| AjBool: | True on success. False otherwise. |
Description
Sets the Target element of a Scophit object to True.
See Also
See other functions in this section
Availability
In release 6.4.0
These functions use the contents of an instance but do not make any
changes.
Functions: ajDmxScophitCheckTarget
Checks to see if the Target element of a Scophit object == ajTrue.
Synopsis
Prototype
AjBool ajDmxScophitCheckTarget (
const AjPScophit ptr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScophit | ptr | Input | Scophit object pointer |
| AjBool | | RETURN | Returns ajTrue if the Target element of the Scophit
object == ajTrue, returns ajFalse otherwise. |
Input
| ptr: | (Input) | Scophit object pointer |
Returns
| AjBool: | Returns ajTrue if the Target element of the Scophit
object == ajTrue, returns ajFalse otherwise. |
Description
Checks to see if the Target element of a Scophit object == ajTrue.
See Also
See other functions in this section
Availability
In release 6.4.0
These functions return the contents of an instance but do not make any
changes.
Functions: ajDmxScophitCompScore ajDmxScophitCompPval ajDmxScophitCompAcc ajDmxScophitCompSunid ajDmxScophitCompSpr ajDmxScophitCompEnd ajDmxScophitCompStart ajDmxScophitCompFam ajDmxScophitCompSfam ajDmxScophitCompClass ajDmxScophitCompFold ajDmxScopalgGetseqs ajDmxScophitsWrite ajDmxScophitsWriteFasta ajDmxScophitReadFasta ajDmxScopalgWrite ajDmxScopalgWriteClustal ajDmxScopalgWriteClustal2 ajDmxScopalgWriteFasta
Function to sort Scophit objects by Score element. Usually called by
ajListSort.
Synopsis
Prototype
ajint ajDmxScophitCompScore (
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. |
Input
| hit1: | (Input) | Pointer to Hit object 1 |
| hit2: | (Input) | Pointer to Hit object 2 |
Returns
Description
Function to sort Scophit objects by Score element. Usually called by
ajListSort.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort AjOScophit objects by Pval record. Usually called by
ajListSort.
Synopsis
Prototype
ajint ajDmxScophitCompPval (
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 Pval1>Pval2, 0 if Pval1==Pval2, else -1. |
Input
| hit1: | (Input) | Pointer to Hit object 1 |
| hit2: | (Input) | Pointer to Hit object 2 |
Returns
| ajint: | 1 if Pval1>Pval2, 0 if Pval1==Pval2, else -1. |
Description
Function to sort AjOScophit objects by Pval record. Usually called by
ajListSort.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit objects by Acc element.
Synopsis
Prototype
ajint ajDmxScophitCompAcc (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Acc1 should sort before Acc2,
+1 if the Acc2 should sort first.
0 if they are identical in length and content. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Acc1 should sort before Acc2,
+1 if the Acc2 should sort first.
0 if they are identical in length and content. |
Description
Function to sort Scophit objects by Acc element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Sunid_Family.
Synopsis
Prototype
ajint ajDmxScophitCompSunid (
const void* entry1,
const void* entry2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | entry1 | Input | Pointer to AjOScophit object 1 |
| const void* | entry2 | Input | Pointer to AjOScophit object 2 |
| ajint | | RETURN | -1 if Sunid_Family1 < Sunid_Family2, +1 if the
Sunid_Family2 should sort first. 0 if they are identical. |
Input
| entry1: | (Input) | Pointer to AjOScophit object 1 |
| entry2: | (Input) | Pointer to AjOScophit object 2 |
Returns
| ajint: | -1 if Sunid_Family1 < Sunid_Family2, +1 if the
Sunid_Family2 should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by Sunid_Family.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Spr element.
Synopsis
Prototype
ajint ajDmxScophitCompSpr (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Spr1 should sort before Spr2,
+1 if the Spr2 should sort first.
0 if they are identical in length and content. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Spr1 should sort before Spr2,
+1 if the Spr2 should sort first.
0 if they are identical in length and content. |
Description
Function to sort Scophit object by Spr element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by End element.
Synopsis
Prototype
ajint ajDmxScophitCompEnd (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if End1 should sort before End2, +1 if the End2
should sort first. 0 if they are identical. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if End1 should sort before End2, +1 if the End2
should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by End element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Start element.
Synopsis
Prototype
ajint ajDmxScophitCompStart (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Start1 should sort before Start2, +1 if the Start2
should sort first. 0 if they are identical. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Start1 should sort before Start2, +1 if the Start2
should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by Start element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Family element.
Synopsis
Prototype
ajint ajDmxScophitCompFam (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Family1 should sort before Family2, +1 if the
Family2 should sort first. 0 if they are identical. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Family1 should sort before Family2, +1 if the
Family2 should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by Family element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Superfamily element.
Synopsis
Prototype
ajint ajDmxScophitCompSfam (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Superfamily1 should sort before Superfamily2, +1 if
the Superfamily2 should sort first. 0 if they are identical. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Superfamily1 should sort before Superfamily2, +1 if
the Superfamily2 should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by Superfamily element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Class element.
Synopsis
Prototype
ajint ajDmxScophitCompClass (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit object 2 |
| ajint | | RETURN | -1 if Class1 should sort before Class2, +1 if the Class2
should sort first. 0 if they are identical. |
Input
| hit1: | (Input) | Pointer to Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit object 2 |
Returns
| ajint: | -1 if Class1 should sort before Class2, +1 if the Class2
should sort first. 0 if they are identical. |
Description
Function to sort Scophit object by Class element.
See Also
See other functions in this section
Availability
In release 6.4.0
Function to sort Scophit object by Fold element.
Synopsis
Prototype
ajint ajDmxScophitCompFold (
const void* hit1,
const void* hit2
);
| Type | Name | Read/Write | Description |
|---|
| const void* | hit1 | Input | Pointer to Scophit object 1 |
| const void* | hit2 | Input | Pointer to Scophit 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 Scophit object 1 |
| hit2: | (Input) | Pointer to Scophit 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 Scophit object by Fold element.
See Also
See other functions in this section
Availability
In release 6.4.0
Read a Scopalg object and writes an array of AjPStr containing the
sequences without gaps.
Synopsis
Prototype
ajint ajDmxScopalgGetseqs (
const AjPScopalg thys,
AjPStr** arr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | thys | Input | Scopalg object |
| AjPStr** | arr | Output | Array of AjPStr |
| ajint | | RETURN | Number of sequences read |
Input
| thys: | (Input) | Scopalg object |
Output
| arr: | (Output) | Array of AjPStr |
Returns
| ajint: | Number of sequences read |
Description
Read a Scopalg object and writes an array of AjPStr containing the
sequences without gaps.
See Also
See other functions in this section
Availability
In release 6.4.0
Write contents of a list of Scophits to an output file in embl-like format
Text for Class, Architecture, Topology, Fold, Superfamily and Family
is only written if the text is available.
Synopsis
Prototype
AjBool ajDmxScophitsWrite (
AjPFile outf,
const AjPList list
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | outf | Output | Output file stream |
| const AjPList | list | Input | List object |
| AjBool | | RETURN | True on success |
Input
Output
| outf: | (Output) | Output file stream |
Returns
Description
Write contents of a list of Scophits to an output file in embl-like format
Text for Class, Architecture, Topology, Fold, Superfamily and Family
is only written if the text is available.
See Also
See other functions in this section
Availability
In release 6.4.0
Write contents of a list of Scophits to an output file in DHF format
Text for Class, Archhitecture, Topology, Fold, Superfamily and Family
is only written if the text is available.
Synopsis
Prototype
AjBool ajDmxScophitsWriteFasta (
AjPFile outf,
const AjPList list
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | outf | Output | Output file stream |
| const AjPList | list | Input | List object |
| AjBool | | RETURN | True on success |
Input
Output
| outf: | (Output) | Output file stream |
Returns
Description
Write contents of a list of Scophits to an output file in DHF format
Text for Class, Archhitecture, Topology, Fold, Superfamily and Family
is only written if the text is available.
See Also
See other functions in this section
Availability
In release 6.4.0
Read a Scophit object from a file in extended FASTA format
(see documentation for the DOMAINATRIX "seqsearch" application).
Synopsis
Prototype
AjPScophit ajDmxScophitReadFasta (
AjPFile inf
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | inf | Modify | Input file stream |
| AjPScophit | | RETURN | Scophit 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
| AjPScophit: | Scophit 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 Scophit object from a file in extended FASTA format
(see documentation for the DOMAINATRIX "seqsearch" application).
See Also
See other functions in this section
Availability
In release 6.4.0
Write a Scopalg object to file in EMBOSS simple multiple sequence format
(same as that used by clustal) annotated with domain classification as
below (records are for SCOP domains in this example):
# TY SCOP
# XX
# CL Alpha and beta proteins (a+b)
# XX
# FO Phospholipase D/nuclease
# XX
# SF Phospholipase D/nuclease
# XX
# FA Phospholipase D
# XX
# SI 64391
# XX
d1f0ia1 1 AATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTP-GCWGDDKC 50
d1f0ia2 1 -----------------------------NVPV---------IAVG-GLG---VGIK 15
d1f0ia1 51 A-------------------------------D-RVGTKRLLAKMTENIGNATRTVD 75
d1f0ia2 16 DVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTV-NPEESALRALVASAKGHIE 65
Synopsis
Prototype
AjBool ajDmxScopalgWrite (
const AjPScopalg scop,
AjPFile outf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | scop | Input | Scopalg object |
| AjPFile | outf | Modify | Output file stream |
| AjBool | | RETURN | True on success (an alignment was written) |
Input
| scop: | (Input) | Scopalg object |
Input & Output
| outf: | (Modify) | Output file stream |
Returns
| AjBool: | True on success (an alignment was written) |
Description
Write a Scopalg object to file in EMBOSS simple multiple sequence format
(same as that used by clustal) annotated with domain classification as
below (records are for SCOP domains in this example):
# TY SCOP
# XX
# CL Alpha and beta proteins (a+b)
# XX
# FO Phospholipase D/nuclease
# XX
# SF Phospholipase D/nuclease
# XX
# FA Phospholipase D
# XX
# SI 64391
# XX
d1f0ia1 1 AATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTP-GCWGDDKC 50
d1f0ia2 1 -----------------------------NVPV---------IAVG-GLG---VGIK 15
d1f0ia1 51 A-------------------------------D-RVGTKRLLAKMTENIGNATRTVD 75
d1f0ia2 16 DVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTV-NPEESALRALVASAKGHIE 65
See Also
See other functions in this section
Availability
In release 6.4.0
Writes a Scopalg object to a specified file in CLUSTAL format (just the
alignment without the domain classification information).
Synopsis
Prototype
AjBool ajDmxScopalgWriteClustal (
const AjPScopalg align,
AjPFile outf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | align | Input | Scopalg object |
| AjPFile | outf | Modify | Outfile file pointer |
| AjBool | | RETURN | True on success (a file has been written) |
Input
| align: | (Input) | Scopalg object |
Input & Output
| outf: | (Modify) | Outfile file pointer |
Returns
| AjBool: | True on success (a file has been written) |
Description
Writes a Scopalg object to a specified file in CLUSTAL format (just the
alignment without the domain classification information).
See Also
See other functions in this section
Availability
In release 6.4.0
Writes a Scopalg object to a specified file in CLUSTAL format (just the
alignment without the domain classification information).
Synopsis
Prototype
AjBool ajDmxScopalgWriteClustal2 (
const AjPScopalg align,
AjPFile outf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | align | Input | Scopalg object. |
| AjPFile | outf | Modify | Outfile file pointer. |
| AjBool | | RETURN | True on success (a file has been written) |
Input
| align: | (Input) | Scopalg object. |
Input & Output
| outf: | (Modify) | Outfile file pointer. |
Returns
| AjBool: | True on success (a file has been written) |
Description
Writes a Scopalg object to a specified file in CLUSTAL format (just the
alignment without the domain classification information).
See Also
See other functions in this section
Availability
In release 6.4.0
Writes a Scopalg object to a specified file in FASTA format (just the
alignment without the domain classification information).
Synopsis
Prototype
AjBool ajDmxScopalgWriteFasta (
const AjPScopalg align,
AjPFile outf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | align | Input | A list of hit list structures. |
| AjPFile | outf | Modify | Outfile file pointer |
| AjBool | | RETURN | True on success (a file has been written) |
Input
| align: | (Input) | A list of hit list structures. |
Input & Output
| outf: | (Modify) | Outfile file pointer |
Returns
| AjBool: | True on success (a file has been written) |
Description
Writes a Scopalg object to a specified file in FASTA format (just the
alignment without the domain classification information).
See Also
See other functions in this section
Availability
In release 6.4.0
These functions may have diverse functions that do not fit into the other
categories.
Functions: ajDmxScopSeqFromSunid ajDmxExit ajDmxDummyFunction
Writes a sequence corresponding to a Scop domain given a Sunid for the
domain. The sequence is taken from one of a list of Scop objects that is
provided. The swissprot sequence is taken in priority over the pdb
sequence.
Synopsis
Prototype
AjBool ajDmxScopSeqFromSunid (
ajint id,
AjPStr* seq,
const AjPList list
);
| Type | Name | Read/Write | Description |
|---|
| ajint | id | Input | Search term |
| AjPStr* | seq | Output | Result sequence |
| const AjPList | list | Input | Sorted list of Scop objects |
| AjBool | | RETURN | True if a swissprot identifier code was found for the
Pdb code. |
Input
| id: | (Input) | Search term |
| list: | (Input) | Sorted list of Scop objects |
Output
| seq: | (Output) | Result sequence |
Returns
| AjBool: | True if a swissprot identifier code was found for the
Pdb code. |
Description
Writes a sequence corresponding to a Scop domain given a Sunid for the
domain. The sequence is taken from one of a list of Scop objects that is
provided. The swissprot sequence is taken in priority over the pdb
sequence.
See Also
See other functions in this section
Availability
In release 6.4.0
Cleanup of Dmx function internals.
Synopsis
Prototype
void ajDmxExit (
void
);
| Type | Name | Read/Write | Description |
|---|
| void | | RETURN | |
Returns
Description
Cleanup of Dmx function internals.
See Also
See other functions in this section
Availability
In release 6.4.0
Dummy function to catch all unused functions defined in the ajdmx
source file.
Synopsis
Prototype
void ajDmxDummyFunction (
void
);
| Type | Name | Read/Write | Description |
|---|
| void | | RETURN | |
Returns
Description
Dummy function to catch all unused functions defined in the ajdmx
source file.
See Also
See other functions in this section
Availability
In release 6.4.0