embdmx.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: embDmxNrseqNew embDmxScophitsToHitlist embDmxScophitToHit embDmxScophitsAccToHitlist embDmxHitsWrite embDmxScopToScophit embDmxScopalgToScop embDmxScophitsOverlapAcc embDmxScophitsOverlap embDmxScophitMerge embDmxScophitMergeInsertOther embDmxScophitMergeInsertOtherTarget embDmxScophitMergeInsertOtherTargetBoth embDmxScophitMergeInsertThis embDmxScophitMergeInsertThisTarget embDmxScophitMergeInsertThisTargetBoth embDmxSeqNR embDmxSeqNRRange embDmxSeqCompall embDmxScophitReadAllFasta embDmxHitlistToScophits
Creates an empty non redundant sequence object
Synopsis
Prototype
EmbPDmxNrseq embDmxNrseqNew (
const AjPSeq seq
);
| Type | Name | Read/Write | Description |
|---|
| const AjPSeq | seq | Input | Sequence object |
| EmbPDmxNrseq | | RETURN | New non-redundant sequence object |
Input
| seq: | (Input) | Sequence object |
Returns
| EmbPDmxNrseq: | New non-redundant sequence object |
Description
Creates an empty non redundant sequence 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
Reads from a list of Scophit objects and writes a Hitlist object
with the next block of hits with identical SCOP classification. If the
iterator passed in is NULL it will read from the start of the list,
otherwise it will read from the current position. Memory for the Hitlist
will be allocated if necessary and must be freed by the user.
Synopsis
Prototype
AjBool embDmxScophitsToHitlist (
const AjPList in,
EmbPHitlist* out,
AjIList* iter
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | in | Input | List of pointers to Scophit objects |
| EmbPHitlist* | out | Output | Pointer to Hitlist object |
| AjIList* | iter | Modify | Pointer to iterator for list. |
| AjBool | | RETURN | True on success (lists were processed ok) |
Input
| in: | (Input) | List of pointers to Scophit objects |
Output
| out: | (Output) | Pointer to Hitlist object |
Input & Output
| iter: | (Modify) | Pointer to iterator for list. |
Returns
| AjBool: | True on success (lists were processed ok) |
Description
Reads from a list of Scophit objects and writes a Hitlist object
with the next block of hits with identical SCOP classification. If the
iterator passed in is NULL it will read from the start of the list,
otherwise it will read from the current position. Memory for the Hitlist
will be allocated if necessary and must be freed by the user.
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
Copies the contents from a Scophit to a Hit object. Creates the Hit object
if necessary.
Synopsis
Prototype
AjBool embDmxScophitToHit (
EmbPHit* to,
const AjPScophit from
);
| Type | Name | Read/Write | Description |
|---|
| EmbPHit* | to | Output | Hit object pointer |
| const AjPScophit | from | Input | Scophit object |
| AjBool | | RETURN | True if copy was successful. |
Input
| from: | (Input) | Scophit object |
Output
| to: | (Output) | Hit object pointer |
Returns
| AjBool: | True if copy was successful. |
Description
Copies the contents from a Scophit to a Hit object. Creates the Hit object
if necessary.
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
Reads from a list of Scophit objects and writes a Hitlist object
with the next block of hits with identical SCOP classification. A Hit is
only written to the Hitlist if an accession number is given. Also, only
one of any pair of duplicate hits (overlapping hits with
identical accession)
will be written to the Hitlist. An 'overlap' is defined as a shared region
of 10 or more residues.
To check for these the list is first be sorted by Accession number.
If the iterator passed in is NULL it will read from the start of the list,
otherwise it will read from the current position. Memory for the Hitlist
will be allocated if necessary and must be freed by the user.
Synopsis
Prototype
AjBool embDmxScophitsAccToHitlist (
const AjPList in,
EmbPHitlist* out,
AjIList* iter
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | in | Input | List of pointers to Scophit objects |
| EmbPHitlist* | out | Output | Pointer to Hitlist object |
| AjIList* | iter | Modify | Pointer to iterator for list. |
| AjBool | | RETURN | True on success (lists were processed ok) |
Input
| in: | (Input) | List of pointers to Scophit objects |
Output
| out: | (Output) | Pointer to Hitlist object |
Input & Output
| iter: | (Modify) | Pointer to iterator for list. |
Returns
| AjBool: | True on success (lists were processed ok) |
Description
Reads from a list of Scophit objects and writes a Hitlist object
with the next block of hits with identical SCOP classification. A Hit is
only written to the Hitlist if an accession number is given. Also, only
one of any pair of duplicate hits (overlapping hits with
identical accession)
will be written to the Hitlist. An 'overlap' is defined as a shared region
of 10 or more residues.
To check for these the list is first be sorted by Accession number.
If the iterator passed in is NULL it will read from the start of the list,
otherwise it will read from the current position. Memory for the Hitlist
will be allocated if necessary and must be freed by the user.
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
Writes a list of AjOHit objects to an output file. This is intended for
displaying the results from scans of a model against a protein sequence
database. Output in a sigplot compatible format.
Synopsis
Prototype
AjBool embDmxHitsWrite (
AjPFile outf,
EmbPHitlist hits,
ajint maxhits
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | outf | Modify | Output file stream |
| EmbPHitlist | hits | Modify | Hitlist objects with hits from scan |
| ajint | maxhits | Input | Max. hits to write. |
| AjBool | | RETURN | True if file was written |
Input
| maxhits: | (Input) | Max. hits to write. |
Input & Output
| outf: | (Modify) | Output file stream |
| hits: | (Modify) | Hitlist objects with hits from scan |
Returns
| AjBool: | True if file was written |
Description
Writes a list of AjOHit objects to an output file. This is intended for
displaying the results from scans of a model against a protein sequence
database. Output in a sigplot compatible format.
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
Writes a Scophit structure with the common information in a Scop
structure. The swissprot sequence is taken in preference to the pdb
sequence.
Synopsis
Prototype
AjBool embDmxScopToScophit (
const AjPScop source,
AjPScophit* target
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScop | source | Input | The Scop object to convert |
| AjPScophit* | target | Output | Destination of the the scophit
structure to write to. |
| AjBool | | RETURN | ajTrue on the success of creating a Scophit structure. |
Input
| source: | (Input) | The Scop object to convert |
Output
| target: | (Output) | Destination of the the scophit
structure to write to. |
Returns
| AjBool: | ajTrue on the success of creating a Scophit structure. |
Description
Writes a Scophit structure with the common information in a Scop
structure. The swissprot sequence is taken in preference to the pdb
sequence.
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
Takes a Scopalg object (scop alignment) and an array of Scop objects
taken from, e.g. a scop classification file.
Extracts the scop domain codes from the alignment and compiles a list of
corresponding Scop objects from the scop classification file.
Synopsis
Prototype
AjBool embDmxScopalgToScop (
const AjPScopalg align,
AjPScop const* scop_arr,
ajint scop_dim,
AjPList* list
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScopalg | align | Input | Contains a seed alignment. |
| AjPScop const* | scop_arr | Input | Array of AjPScop objects |
| ajint | scop_dim | Input | Size of array |
| AjPList* | list | Output | List of Scop objects. |
| AjBool | | RETURN | A populated list has been returned
(a file has been written) |
Input
| align: | (Input) | Contains a seed alignment. |
| scop_arr: | (Input) | Array of AjPScop objects |
| scop_dim: | (Input) | Size of array |
Output
| list: | (Output) | List of Scop objects. |
Returns
| AjBool: | A populated list has been returned
(a file has been written) |
Description
Takes a Scopalg object (scop alignment) and an array of Scop objects
taken from, e.g. a scop classification file.
Extracts the scop domain codes from the alignment and compiles a list of
corresponding Scop objects from the scop classification file.
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
Checks for overlap and identical accession numbers between two hits.
Synopsis
Prototype
AjBool embDmxScophitsOverlapAcc (
const AjPScophit h1,
const AjPScophit h2,
ajuint n
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScophit | h1 | Input | Pointer to hit object 1 |
| const AjPScophit | h2 | Input | Pointer to hit object 2 |
| ajuint | n | Input | Threshold number of residues for overlap |
| AjBool | | RETURN | True if the overlap between the sequences is at least as
long as the threshold. False otherwise. |
Input
| h1: | (Input) | Pointer to hit object 1 |
| h2: | (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 and identical accession numbers 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
Checks for overlap between two hits.
Synopsis
Prototype
AjBool embDmxScophitsOverlap (
const AjPScophit h1,
const AjPScophit h2,
ajuint n
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScophit | h1 | Input | Pointer to hit object 1 |
| const AjPScophit | h2 | Input | Pointer to hit object 2 |
| ajuint | n | Input | Threshold number of residues for overlap |
| AjBool | | RETURN | True if the overlap between the sequences is at least as
long as the threshold. False otherwise. |
Input
| h1: | (Input) | Pointer to hit object 1 |
| h2: | (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
Creates a new Scophit object which corresponds to a merging of the two
sequences from the Scophit objects hit1 and hit2.
The Typeobj of the merged hit is set. The merged hit is classified
as follows :
If hit1 or hit2 is a SEED, the merged hit is classified as a SEED.
Otherwise, if hit1 or hit2 is HIT, the merged hit is clsasified as a HIT.
If hit1 and hit2 are both OTHER, the merged hit remains classified as
OTHER.
Synopsis
Prototype
AjPScophit embDmxScophitMerge (
const AjPScophit hit1,
const AjPScophit hit2
);
| Type | Name | Read/Write | Description |
|---|
| const AjPScophit | hit1 | Input | Scophit 1 |
| const AjPScophit | hit2 | Input | Scophit 2 |
| AjPScophit | | RETURN | Pointer to Scophit object. |
Input
| hit1: | (Input) | Scophit 1 |
| hit2: | (Input) | Scophit 2 |
Returns
| AjPScophit: | Pointer to Scophit object. |
Description
Creates a new Scophit object which corresponds to a merging of the two
sequences from the Scophit objects hit1 and hit2.
The Typeobj of the merged hit is set. The merged hit is classified
as follows :
If hit1 or hit2 is a SEED, the merged hit is classified as a SEED.
Otherwise, if hit1 or hit2 is HIT, the merged hit is clsasified as a HIT.
If hit1 and hit2 are both OTHER, the merged hit remains classified as
OTHER.
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertOther (
AjPList list,
AjPScophit hit1,
AjPScophit hit2
);
| Type | Name | Read/Write | Description |
|---|
| AjPList | list | Modify | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjBool | | RETURN | True on success. |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| list: | (Modify) | List of Scophit objects |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertOtherTarget (
AjPList list,
AjPScophit hit1,
AjPScophit hit2
);
| Type | Name | Read/Write | Description |
|---|
| AjPList | list | Modify | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjBool | | RETURN | True on success. |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| list: | (Modify) | List of Scophit objects |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertOtherTargetBoth (
AjPList list,
AjPScophit hit1,
AjPScophit hit2
);
| Type | Name | Read/Write | Description |
|---|
| AjPList | list | Modify | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjBool | | RETURN | True on success. |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| list: | (Modify) | List of Scophit objects |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Appends the new Scophit onto a list. Target
hit1 and hit2 for removal (set the Target element to ajTrue).
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1 and hit2 for removal (set the Target element to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertThis (
const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | list | Input | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjIList | iter | Modify | List iterator |
| AjBool | | RETURN | True on success. |
Input
| list: | (Input) | List of Scophit objects |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| iter: | (Modify) | List iterator |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1 and hit2 for removal (set the Target element to ajTrue).
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1, hit2 and the new Scophit for removal
(set the Target element to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertThisTarget (
const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | list | Input | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjIList | iter | Modify | List iterator |
| AjBool | | RETURN | True on success. |
Input
| list: | (Input) | List of Scophit objects |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| iter: | (Modify) | List iterator |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1, hit2 and the new Scophit for removal
(set the Target element to ajTrue).
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
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1, hit2 and the new Scophit for removal (both the Target and
Target2 elements are set to ajTrue).
Synopsis
Prototype
AjBool embDmxScophitMergeInsertThisTargetBoth (
const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | list | Input | List of Scophit objects |
| AjPScophit | hit1 | Delete | Scophit object 1 |
| AjPScophit | hit2 | Delete | Scophit object 2 |
| AjIList | iter | Modify | List iterator |
| AjBool | | RETURN | True on success. |
Input
| list: | (Input) | List of Scophit objects |
Output
| hit1: | (Delete) | Scophit object 1 |
| hit2: | (Delete) | Scophit object 2 |
Input & Output
| iter: | (Modify) | List iterator |
Returns
Description
Creates a new Scophit object which corresponds to a merging of two Scophit
objects hit1 and hit2. Insert the new Scophit immediately after hit2.
Target hit1, hit2 and the new Scophit for removal (both the Target and
Target2 elements are set to ajTrue).
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
Reads a list of AjPSeq's and writes an array describing the redundancy in
the list. Elements in the array correspond to sequences in the list, i.e.
the array[0] corresponds to the first sequence in the list.
Sequences are classed as redundant (0 in the array, i.e. they are possibly
to be discarded later) if they exceed a threshold (%) level of sequence
similarity to any other in the set (the shortest sequence of the current
pair will be discarded). If, however, the CheckGarbage argument
is set ON (True) then the the sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If the CheckGarbage argument is set OFF (False)
the shortest sequence is marked as redundant as normal.
The set output will always contain at least 1 sequence.
Synopsis
Prototype
AjBool embDmxSeqNR (
const AjPList input,
AjPUint* keep,
ajint* nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh,
AjBool CheckGarbage
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | input | Input | List of EmbPDmxNrseq objects |
| AjPUint* | keep | Output | 0: rejected (redundant) sequence, 1: the
sequence was retained |
| ajint* | nset | Output | Number of non-garbage sequences in nr set |
| const AjPMatrixf | matrix | Input | Residue substitution matrix |
| float | gapopen | Input | Gap insertion penalty |
| float | gapextend | Input | Gap extension penalty |
| float | thresh | Input | Threshold residue id. for "redundancy" |
| AjBool | CheckGarbage | Input | If True, when two sequences are compared
and deemed redundant, then the Sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If False, the shortest sequence is marked as
redundant as normal. |
| AjBool | | RETURN | ajTrue on success |
Input
| input: | (Input) | List of EmbPDmxNrseq objects |
| matrix: | (Input) | Residue substitution matrix |
| gapopen: | (Input) | Gap insertion penalty |
| gapextend: | (Input) | Gap extension penalty |
| thresh: | (Input) | Threshold residue id. for "redundancy" |
| CheckGarbage: | (Input) | If True, when two sequences are compared
and deemed redundant, then the Sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If False, the shortest sequence is marked as
redundant as normal. |
Output
| keep: | (Output) | 0: rejected (redundant) sequence, 1: the
sequence was retained |
| nset: | (Output) | Number of non-garbage sequences in nr set |
Returns
Description
Reads a list of AjPSeq's and writes an array describing the redundancy in
the list. Elements in the array correspond to sequences in the list, i.e.
the array[0] corresponds to the first sequence in the list.
Sequences are classed as redundant (0 in the array, i.e. they are possibly
to be discarded later) if they exceed a threshold (%) level of sequence
similarity to any other in the set (the shortest sequence of the current
pair will be discarded). If, however, the CheckGarbage argument
is set ON (True) then the the sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If the CheckGarbage argument is set OFF (False)
the shortest sequence is marked as redundant as normal.
The set output will always contain at least 1 sequence.
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
Reads a list of AjPSeq's and writes an array describing the redundancy in
the list. Elements in the array correspond to sequences in the list, i.e.
the array[0] corresponds to the first sequence in the list.
Sequences are classed as redundant (0 in the array, i.e. they are possibly
to be discarded later) if they lie outside a range of threshold (%)
sequence similarity to others in the set (the shortest sequence of the
current pair will be discarded). If, however, the CheckGarbage argument
is set ON (True) then the the sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If the CheckGarbage argument is set OFF (False)
the shortest sequence is marked as redundant as normal.
Synopsis
Prototype
AjBool embDmxSeqNRRange (
const AjPList input,
AjPUint* keep,
ajint* nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float threshlow,
float threshup,
AjBool CheckGarbage
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | input | Input | List of EmbPDmxNrseq objects |
| AjPUint* | keep | Output | 0: rejected (redundant) sequence, 1: the
sequence was retained |
| ajint* | nset | Output | Number of non-garbage sequences in nr set. |
| const AjPMatrixf | matrix | Input | Residue substitution matrix |
| float | gapopen | Input | Gap insertion penalty |
| float | gapextend | Input | Gap extension penalty |
| float | threshlow | Input | Threshold lower limit |
| float | threshup | Input | Threshold upper limit |
| AjBool | CheckGarbage | Input | If True, when two sequences are compared
and deemed redundant, then the Sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If False, the shortest sequence is marked as
redundant as normal. |
| AjBool | | RETURN | ajTrue on success |
Input
| input: | (Input) | List of EmbPDmxNrseq objects |
| matrix: | (Input) | Residue substitution matrix |
| gapopen: | (Input) | Gap insertion penalty |
| gapextend: | (Input) | Gap extension penalty |
| threshlow: | (Input) | Threshold lower limit |
| threshup: | (Input) | Threshold upper limit |
| CheckGarbage: | (Input) | If True, when two sequences are compared
and deemed redundant, then the Sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If False, the shortest sequence is marked as
redundant as normal. |
Output
| keep: | (Output) | 0: rejected (redundant) sequence, 1: the
sequence was retained |
| nset: | (Output) | Number of non-garbage sequences in nr set. |
Returns
Description
Reads a list of AjPSeq's and writes an array describing the redundancy in
the list. Elements in the array correspond to sequences in the list, i.e.
the array[0] corresponds to the first sequence in the list.
Sequences are classed as redundant (0 in the array, i.e. they are possibly
to be discarded later) if they lie outside a range of threshold (%)
sequence similarity to others in the set (the shortest sequence of the
current pair will be discarded). If, however, the CheckGarbage argument
is set ON (True) then the the sequence that is *not* garbage is marked
up as redundant. A sequence is "garbage" if the Garbage element of the
data structure is set. If the CheckGarbage argument is set OFF (False)
the shortest sequence is marked as redundant as normal.
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
Reads a list of AjPSeq's and writes an array of sequence similarity values
for an all-versus-all comparison of the sequences. The rows and columns
in the array correspond to the order of the sequences in the list.
Synopsis
Prototype
AjBool embDmxSeqCompall (
const AjPList input,
AjPFloat2d* scores,
const AjPMatrixf matrix,
float gapopen,
float gapextend
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | input | Input | List of ajPSeq's |
| AjPFloat2d* | scores | Output | Sequence similarity values |
| const AjPMatrixf | matrix | Input | Residue substitution matrix |
| float | gapopen | Input | Gap insertion penalty |
| float | gapextend | Input | Gap extension penalty |
| AjBool | | RETURN | ajTrue on success |
Input
| input: | (Input) | List of ajPSeq's |
| matrix: | (Input) | Residue substitution matrix |
| gapopen: | (Input) | Gap insertion penalty |
| gapextend: | (Input) | Gap extension penalty |
Output
| scores: | (Output) | Sequence similarity values |
Returns
Description
Reads a list of AjPSeq's and writes an array of sequence similarity values
for an all-versus-all comparison of the sequences. The rows and columns
in the array correspond to the order of the sequences in the list.
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
Reads a DHF file and returns a list of Scophit objects.
Parsing routine is identical to embHitlistReadFasta.
Synopsis
Prototype
AjPList embDmxScophitReadAllFasta (
AjPFile inf
);
| Type | Name | Read/Write | Description |
|---|
| AjPFile | inf | Modify | DHF file. |
| AjPList | | RETURN | List of Scophit object pointers, or NULL (error). |
Input & Output
Returns
| AjPList: | List of Scophit object pointers, or NULL (error). |
Description
Reads a DHF file and returns a list of Scophit objects.
Parsing routine is identical to embHitlistReadFasta.
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
Read from a list of Hitlist structures and writes a list of Scophit
structures.
Synopsis
Prototype
AjBool embDmxHitlistToScophits (
const AjPList in,
AjPList out
);
| Type | Name | Read/Write | Description |
|---|
| const AjPList | in | Input | List of pointers to Hitlist structures |
| AjPList | out | Output | List of Scophit structures |
| AjBool | | RETURN | True on success (lists were processed ok) |
Input
| in: | (Input) | List of pointers to Hitlist structures |
Output
| out: | (Output) | List of Scophit structures |
Returns
| AjBool: | True on success (lists were processed ok) |
Description
Read from a list of Hitlist structures and writes a list of Scophit
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 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: embDmxNrseqDel
Creates an empty non redundant sequence object
Synopsis
Prototype
void embDmxNrseqDel (
EmbPDmxNrseq* Pnrseq
);
| Type | Name | Read/Write | Description |
|---|
| EmbPDmxNrseq* | Pnrseq | Delete | Non-redundant sequence object |
| void | | RETURN | |
Output
| Pnrseq: | (Delete) | Non-redundant sequence object |
Returns
Description
Creates an empty non redundant sequence 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