ajfeat.c
All constructors return a new feature or feature table set by pointer.
It is the responsibility of the user to first destroy any previous feature.
The target pointer does not need to be initialised to NULL, but it is good
programming practice to do so anyway.
Generally, however, the AjPFeattable feature table object will first
be created, prior to creating any 'AjPFeature' objects and adding them.
To replace or reuse an existing feature object see instead
the Feature Assignments and Feature Modifiers methods.
Functions: ajFeatNew ajFeatNewSub ajFeatNewII ajFeatNewIISub ajFeatNewIIRev ajFeatNewIIRevSub ajFeatNewProt ajFeatNewProtSub ajFeatNewProtFlags ajFeatNewProtFlagsSub ajFeatCompByStart ajFeatCompByEnd ajFeatCompByGroup ajFeatCompByType ajFeatNewNuc ajFeatNewNucSub ajFeatNewNucFlags ajFeatNewNucFlagsSub
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNew (
AjPFeattable thys,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewSub (
AjPFeattable thys,
AjPFeature parent,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Simple constructor with only start and end positions
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewII (
AjPFeattable thys,
ajint Start,
ajint End
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Simple constructor with only start and end positions
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Simple constructor with only start and end positions
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewIISub (
AjPFeattable thys,
AjPFeature parent,
ajint Start,
ajint End
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Simple constructor with only start and end positions
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Simple constructor with only start and end positions, sets feature to be
on the reverse strand
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewIIRev (
AjPFeattable thys,
ajint Start,
ajint End
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Simple constructor with only start and end positions, sets feature to be
on the reverse strand
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Simple constructor with only start and end positions, sets feature to be
on the reverse strand
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewIIRevSub (
AjPFeattable thys,
AjPFeature parent,
ajint Start,
ajint End
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Simple constructor with only start and end positions, sets feature to be
on the reverse strand
User must specify associated 'ajFeattable' to which the new feature
is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewProt (
AjPFeattable thys,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewProtSub (
AjPFeattable thys,
AjPFeature parent,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewProtFlags (
AjPFeattable thys,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
ajuint flags
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| ajuint | flags | Input | flags. |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| flags: | (Input) | flags. |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
Synopsis
Prototype
AjPFeature ajFeatNewProtFlagsSub (
AjPFeattable thys,
AjPFeature parent,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
ajuint flags
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| ajuint | flags | Input | flags. |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| flags: | (Input) | flags. |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor - must specify associated 'ajFeattable'
to which the new feature is automatically added!
See Also
See other functions in this section
Availability
In release 6.4.0
Compare two features by their start.
Synopsis
Prototype
ajint ajFeatCompByStart (
const void* a,
const void* b
);
| Type | Name | Read/Write | Description |
|---|
| const void* | a | Input | feature |
| const void* | b | Input | another feature |
| ajint | | RETURN | -1 if a is less than b, 0 if a is equal to b else +1. |
Input
| a: | (Input) | feature |
| b: | (Input) | another feature |
Returns
| ajint: | -1 if a is less than b, 0 if a is equal to b else +1. |
Description
Compare two features by their start.
See Also
See other functions in this section
Availability
In release 6.4.0
Compare two features by their end.
Synopsis
Prototype
ajint ajFeatCompByEnd (
const void* a,
const void* b
);
| Type | Name | Read/Write | Description |
|---|
| const void* | a | Input | feature |
| const void* | b | Input | another feature |
| ajint | | RETURN | -1 if a is less than b, 0 if a is equal to b else +1. |
Input
| a: | (Input) | feature |
| b: | (Input) | another feature |
Returns
| ajint: | -1 if a is less than b, 0 if a is equal to b else +1. |
Description
Compare two features by their end.
See Also
See other functions in this section
Availability
In release 6.4.0
Compare two features by their group and exon numbers
Synopsis
Prototype
ajint ajFeatCompByGroup (
const void* a,
const void* b
);
| Type | Name | Read/Write | Description |
|---|
| const void* | a | Input | feature |
| const void* | b | Input | another feature |
| ajint | | RETURN | -1 if a is less than b, 0 if a is equal to b else +1. |
Input
| a: | (Input) | feature |
| b: | (Input) | another feature |
Returns
| ajint: | -1 if a is less than b, 0 if a is equal to b else +1. |
Description
Compare two features by their group and exon numbers
See Also
See other functions in this section
Availability
In release 6.4.0
Compare two features by their type (key).
Synopsis
Prototype
ajint ajFeatCompByType (
const void* a,
const void* b
);
| Type | Name | Read/Write | Description |
|---|
| const void* | a | Input | feature |
| const void* | b | Input | another feature |
| ajint | | RETURN | -1 if a is less than b, 0 if a is equal to b else +1. |
Input
| a: | (Input) | feature |
| b: | (Input) | another feature |
Returns
| ajint: | -1 if a is less than b, 0 if a is equal to b else +1. |
Description
Compare two features by their type (key).
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new feature,
automatically added to the specified table.
Synopsis
Prototype
AjPFeature ajFeatNewNuc (
AjPFeattable thys,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame,
ajint exon,
ajint Start2,
ajint End2,
const AjPStr entryid,
const AjPStr label
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| ajint | exon | Input | exon number (0 for default value) |
| ajint | Start2 | Input | 2nd Start position of the feature |
| ajint | End2 | Input | 2nd End position of the feature |
| const AjPStr | entryid | Input | Entry ID for location in
another entry |
| const AjPStr | label | Input | Label for location (non-numeric) |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
| exon: | (Input) | exon number (0 for default value) |
| Start2: | (Input) | 2nd Start position of the feature |
| End2: | (Input) | 2nd End position of the feature |
| entryid: | (Input) | Entry ID for location in
another entry |
| label: | (Input) | Label for location (non-numeric) |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor for a new feature,
automatically added to the specified table.
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new feature,
automatically added to the specified table.
Synopsis
Prototype
AjPFeature ajFeatNewNucSub (
AjPFeattable thys,
AjPFeature parent,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame,
ajint exon,
ajint Start2,
ajint End2,
const AjPStr entryid,
const AjPStr label
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| ajint | exon | Input | exon number (0 for default value) |
| ajint | Start2 | Input | 2nd Start position of the feature |
| ajint | End2 | Input | 2nd End position of the feature |
| const AjPStr | entryid | Input | Entry ID for location in
another entry |
| const AjPStr | label | Input | Label for location (non-numeric) |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
| exon: | (Input) | exon number (0 for default value) |
| Start2: | (Input) | 2nd Start position of the feature |
| End2: | (Input) | 2nd End position of the feature |
| entryid: | (Input) | Entry ID for location in
another entry |
| label: | (Input) | Label for location (non-numeric) |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor for a new feature,
automatically added to the specified table.
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new feature,
automatically added to the specified table.
Synopsis
Prototype
AjPFeature ajFeatNewNucFlags (
AjPFeattable thys,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame,
ajint exon,
ajint Start2,
ajint End2,
const AjPStr entryid,
const AjPStr label,
ajuint flags
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| ajint | exon | Input | exon number (0 for default value) |
| ajint | Start2 | Input | 2nd Start position of the feature |
| ajint | End2 | Input | 2nd End position of the feature |
| const AjPStr | entryid | Input | Entry ID for location in
another entry |
| const AjPStr | label | Input | Label for location (non-numeric) |
| ajuint | flags | Input | flags. |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
| exon: | (Input) | exon number (0 for default value) |
| Start2: | (Input) | 2nd Start position of the feature |
| End2: | (Input) | 2nd End position of the feature |
| entryid: | (Input) | Entry ID for location in
another entry |
| label: | (Input) | Label for location (non-numeric) |
| flags: | (Input) | flags. |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor for a new feature,
automatically added to the specified table.
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new feature,
automatically added to the specified table.
Synopsis
Prototype
AjPFeature ajFeatNewNucFlagsSub (
AjPFeattable thys,
AjPFeature parent,
const AjPStr source,
const AjPStr type,
ajint Start,
ajint End,
float score,
char strand,
ajint frame,
ajint exon,
ajint Start2,
ajint End2,
const AjPStr entryid,
const AjPStr label,
ajuint flags
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Pointer to the ajFeattable which
will own the feature |
| AjPFeature | parent | Modify | Parent feature |
| const AjPStr | source | Input | Analysis basis for feature |
| const AjPStr | type | Input | Type of feature (e.g. exon) |
| ajint | Start | Input | Start position of the feature |
| ajint | End | Input | End position of the feature |
| float | score | Input | Analysis score for the feature |
| char | strand | Input | Strand of the feature |
| ajint | frame | Input | Frame of the feature |
| ajint | exon | Input | exon number (0 for default value) |
| ajint | Start2 | Input | 2nd Start position of the feature |
| ajint | End2 | Input | 2nd End position of the feature |
| const AjPStr | entryid | Input | Entry ID for location in
another entry |
| const AjPStr | label | Input | Label for location (non-numeric) |
| ajuint | flags | Input | flags. |
| AjPFeature | | RETURN | newly allocated feature object |
Input
| source: | (Input) | Analysis basis for feature |
| type: | (Input) | Type of feature (e.g. exon) |
| Start: | (Input) | Start position of the feature |
| End: | (Input) | End position of the feature |
| score: | (Input) | Analysis score for the feature |
| strand: | (Input) | Strand of the feature |
| frame: | (Input) | Frame of the feature |
| exon: | (Input) | exon number (0 for default value) |
| Start2: | (Input) | 2nd Start position of the feature |
| End2: | (Input) | 2nd End position of the feature |
| entryid: | (Input) | Entry ID for location in
another entry |
| label: | (Input) | Label for location (non-numeric) |
| flags: | (Input) | flags. |
Input & Output
| thys: | (Modify) | Pointer to the ajFeattable which
will own the feature |
| parent: | (Modify) | Parent feature |
Returns
| AjPFeature: | newly allocated feature object |
Description
Constructor for a new feature,
automatically added to the specified table.
See Also
See other functions in this section
Availability
In release 6.4.0
(Simple minded) object destruction by release of memory.
No reference counting (for now).
Functions: ajFeattableDel ajFeatDel
Destructor for ajFeattable objects.
If the given object (pointer) is NULL, or a NULL pointer, simply returns.
Synopsis
Prototype
void ajFeattableDel (
AjPFeattable* pthis
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable* | pthis | Delete | Pointer to the object to be deleted.
The pointer is always deleted. |
| void | | RETURN | |
Output
| pthis: | (Delete) | Pointer to the object to be deleted.
The pointer is always deleted. |
Returns
Description
Destructor for ajFeattable objects.
If the given object (pointer) is NULL, or a NULL pointer, simply returns.
See Also
See other functions in this section
Availability
In release 6.4.0
Destructor for AjPFeature objects.
If the given object (pointer) is NULL, or a NULL pointer, simply returns.
Synopsis
Prototype
void ajFeatDel (
AjPFeature* pthis
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature* | pthis | Delete | Pointer to the object to be deleted.
The pointer is always deleted. |
| void | | RETURN | |
Output
| pthis: | (Delete) | Pointer to the object to be deleted.
The pointer is always deleted. |
Returns
Description
Destructor for AjPFeature objects.
If the given object (pointer) is NULL, or a NULL pointer, simply returns.
See Also
See other functions in this section
Availability
In release 6.4.0
Functions: ajFeatSortByType ajFeatSortByStart ajFeatSortByEnd
Sort Feature table by Type.
Synopsis
Prototype
void ajFeatSortByType (
AjPFeattable Feattab
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | Feattab | Modify | Feature table to be sorted. |
| void | | RETURN | |
Input & Output
| Feattab: | (Modify) | Feature table to be sorted. |
Returns
Description
Sort Feature table by Type.
See Also
See other functions in this section
Availability
In release 6.4.0
Sort Feature table by Start position.
Synopsis
Prototype
void ajFeatSortByStart (
AjPFeattable Feattab
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | Feattab | Modify | Feature table to be sorted. |
| void | | RETURN | |
Input & Output
| Feattab: | (Modify) | Feature table to be sorted. |
Returns
Description
Sort Feature table by Start position.
See Also
See other functions in this section
Availability
In release 6.4.0
Sort Feature table by End position.
Synopsis
Prototype
void ajFeatSortByEnd (
AjPFeattable Feattab
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | Feattab | Modify | Feature table to be sorted. |
| void | | RETURN | |
Input & Output
| Feattab: | (Modify) | Feature table to be sorted. |
Returns
Description
Sort Feature table by End position.
See Also
See other functions in this section
Availability
In release 6.4.0
Functions: ajFeattableAdd
Method to add a new AjPFeature to a AjPFeattable
Synopsis
Prototype
void ajFeattableAdd (
AjPFeattable thys,
AjPFeature feature
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | The feature table |
| AjPFeature | feature | Modify | Feature to be added to the set |
| void | | RETURN | |
Input & Output
| thys: | (Modify) | The feature table |
| feature: | (Modify) | Feature to be added to the set |
Returns
Description
Method to add a new AjPFeature to a AjPFeattable
See Also
See other functions in this section
Availability
In release 6.4.0
These functions use the contents of a feature object,
but do not make any changes.
Functions: ajFeattableClear ajFeatTypeGetCategory ajFeattableGetEntry ajFeattableGetQryC ajFeattableGetQryS ajFeattableGetTypeC ajFeattableGetTypeS ajFeattableGetXrefs ajFeatframeGetFrame ajFeatframeGetFrameNuc ajFeatstrandGetStrand ajFeattableIsNuc ajFeattableIsProt ajFeattableGetBegin ajFeattableGetEnd ajFeattableGetLen ajFeattableGetName ajFeattableGetSize ajFeatGetFlags ajFeatGetSeq ajFeatGetSeqJoin ajFeatGetRemoteseq ajFeatGetXrefs ajFeatLocMark ajFeatGetNoteC ajFeatGetNoteCI ajFeatGetNoteSI ajFeatGetNoteS ajFeatGetTagC ajFeatGetTagS ajFeatGetType ajFeatGetSource ajFeatGetStart ajFeatGetStrand ajFeatGetEnd ajFeatGetLength ajFeatGetScore ajFeatGetForward ajFeatGetFrame ajFeatGetTranslation ajFeatTest ajFeatVocabGetTags ajFeatVocabGetTagsNuc ajFeatVocabGetTagsProt ajFeatVocabGetTypes ajFeatVocabGetTypesNuc ajFeatVocabGetTypesProt ajFeatVocabInit ajFeatVocabInitNuc ajFeatVocabInitProt ajFeatSetDescApp ajFeatSetDesc ajFeatSetSource ajFeatSetScore ajFeatSetStrand ajFeatTagSetC ajFeatTagSet ajFeattagSpecialGff2 ajFeattagSpecialGff3 ajFeatTagAddCC ajFeatTagAddC ajFeatTagAdd ajFeattagSpecial ajFeattableNew ajFeattableSetDefname ajFeattableSetLength ajFeattableSetNuc ajFeattableSetProt ajFeattableSetRange ajFeattableReverse ajFeatReverse ajFeattableNewDna ajFeattableNewSeq ajFeattableNewProt ajFeatGfftagAddC ajFeatGfftagAdd ajFeattableNewFtable ajFeattableNewFtableLimit ajFeatNewFeat ajFeatTrace ajFeatTagTrace ajFeatGfftagsNew ajFeatGfftagsDel ajFeatGetGfftags ajFeatGetParent ajFeatTagIter ajFeatSubIter ajFeatTagval ajFeattableTrace ajFeatTypeNuc ajFeatTypeProt ajFeattypeGetExternal ajFeattypeGetInternal ajFeattypeGetInternalEmbl ajFeattypeGetInternalNuc ajFeattypeGetInternalPir ajFeattypeGetInternalProt ajFeattypeGetInternalRefseqp ajFeattagGetNameC ajFeattagGetNameS ajFeattagFormat ajFeattagGetLimit ajFeatUnused ajFeatTypeIsCds ajFeatTypeMatchC ajFeatTypeMatchS ajFeatTypeMatchWildS ajFeatIsLocal ajFeatIsLocalRange ajFeatIsChild ajFeatIsMultiple ajFeatIsCompMult ajFeattablePos ajFeattablePosI ajFeattablePosII ajFeattableTrimOff ajFeattableTrim ajFeatTrimOffRange ajFeattagIsNote ajFeatExit ajFeatWarn
Clears a feature table of all features
Synopsis
Prototype
void ajFeattableClear (
AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table |
| void | | RETURN | |
Input & Output
| thys: | (Modify) | Feature table |
Returns
Description
Clears a feature table of all features
See Also
See other functions in this section
Availability
In release 6.4.0
returns the category name for a feature type
Used to identify category for DASGFF output
Synopsis
Prototype
const AjPStr ajFeatTypeGetCategory (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Feature type |
| const AjPStr | | RETURN | Feature category |
Input
Returns
| const AjPStr: | Feature category |
Description
returns the category name for a feature type
Used to identify category for DASGFF output
See Also
See other functions in this section
Availability
In release 6.4.0
Return the full text
Synopsis
Prototype
const AjPStr ajFeattableGetEntry (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table object |
| const AjPStr | | RETURN | Returned full text |
Input
| thys: | (Input) | Feature table object |
Returns
| const AjPStr: | Returned full text |
Description
Return the full text
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the query string of a feature table data object.
Because this is a pointer to the real internal string
the caller must take care not to change the character string in any way.
If the string is to be changed (case for example) then it must first
be copied.
Synopsis
Prototype
const char* ajFeattableGetQryC (
const AjPFeattable ftable
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | ftable | Input | Feature table data object. |
| const char* | | RETURN | Query as a character string. |
Input
| ftable: | (Input) | Feature table data object. |
Returns
| const char*: | Query as a character string. |
Description
Returns the query string of a feature table data object.
Because this is a pointer to the real internal string
the caller must take care not to change the character string in any way.
If the string is to be changed (case for example) then it must first
be copied.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the query string of a feature table data object.
Because this is a pointer to the real internal string
the caller must take care not to change the character string in any way.
If the string is to be changed (case for example) then it must first
be copied.
Synopsis
Prototype
const AjPStr ajFeattableGetQryS (
const AjPFeattable ftable
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | ftable | Input | Feature table data object. |
| const AjPStr | | RETURN | Query as a string. |
Input
| ftable: | (Input) | Feature table data object. |
Returns
| const AjPStr: | Query as a string. |
Description
Returns the query string of a feature table data object.
Because this is a pointer to the real internal string
the caller must take care not to change the character string in any way.
If the string is to be changed (case for example) then it must first
be copied.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
Synopsis
Prototype
const char* ajFeattableGetTypeC (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| const char* | | RETURN | Feature table type. |
Input
| thys: | (Input) | Feature table |
Returns
| const char*: | Feature table type. |
Description
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
Synopsis
Prototype
const AjPStr ajFeattableGetTypeS (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| const AjPStr | | RETURN | Feature table name. |
Input
| thys: | (Input) | Feature table |
Returns
| const AjPStr: | Feature table name. |
Description
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns all cross-references from a feature table
Synopsis
Prototype
AjBool ajFeattableGetXrefs (
const AjPFeattable thys,
AjPList* Pxreflist,
ajuint* Ptaxid
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| AjPList* | Pxreflist | Modify | List of sequence cross-reference objects |
| ajuint* | Ptaxid | Output | Taxon ID |
| AjBool | | RETURN | True on success |
Input
| thys: | (Input) | Feature table |
Output
Input & Output
| Pxreflist: | (Modify) | List of sequence cross-reference objects |
Returns
Description
Returns all cross-references from a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a frame number in the range 0 to 3 to a GFF frame character
or '.' as the general default
Synopsis
Prototype
char ajFeatframeGetFrame (
ajint frame
);
| Type | Name | Read/Write | Description |
|---|
| ajint | frame | Input | Feature frame number |
| char | | RETURN | character for this frame in GFF |
Input
| frame: | (Input) | Feature frame number |
Returns
| char: | character for this frame in GFF |
Description
Converts a frame number in the range 0 to 3 to a GFF frame character
or '.' as the general default
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a frame number in the range 0 to 3 to a GFF frame character
or '0' for the nucleotide default
Synopsis
Prototype
char ajFeatframeGetFrameNuc (
ajint frame
);
| Type | Name | Read/Write | Description |
|---|
| ajint | frame | Input | Feature frame number |
| char | | RETURN | character for this frame in GFF |
Input
| frame: | (Input) | Feature frame number |
Returns
| char: | character for this frame in GFF |
Description
Converts a frame number in the range 0 to 3 to a GFF frame character
or '0' for the nucleotide default
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a strand number to a GFF strand character. NULL characters
are converted to '+' All other values are simply cast to character.
Synopsis
Prototype
char ajFeatstrandGetStrand (
ajint strand
);
| Type | Name | Read/Write | Description |
|---|
| ajint | strand | Input | Strand |
| char | | RETURN | GFF character for this strand. |
Input
Returns
| char: | GFF character for this strand. |
Description
Converts a strand number to a GFF strand character. NULL characters
are converted to '+' All other values are simply cast to character.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns ajTrue if a feature table is nucleotide
Synopsis
Prototype
AjBool ajFeattableIsNuc (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| AjBool | | RETURN | ajTrue for a protein feature table |
Input
| thys: | (Input) | Feature table |
Returns
| AjBool: | ajTrue for a protein feature table |
Description
Returns ajTrue if a feature table is nucleotide
See Also
See other functions in this section
Availability
In release 6.4.0
Returns ajTrue if a feature table is protein
Synopsis
Prototype
AjBool ajFeattableIsProt (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| AjBool | | RETURN | ajTrue for a protein feature table |
Input
| thys: | (Input) | Feature table |
Returns
| AjBool: | ajTrue for a protein feature table |
Description
Returns ajTrue if a feature table is protein
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the feature table start position, or 1 if no start has been set.
Synopsis
Prototype
ajint ajFeattableGetBegin (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | feature table object |
| ajint | | RETURN | Start position. |
Input
| thys: | (Input) | feature table object |
Returns
Description
Returns the feature table start position, or 1 if no start has been set.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the features table end position, or the feature table length if
no end has been set.
Synopsis
Prototype
ajint ajFeattableGetEnd (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | feature table object |
| ajint | | RETURN | End position. |
Input
| thys: | (Input) | feature table object |
Returns
Description
Returns the features table end position, or the feature table length if
no end has been set.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the sequence length of a feature table
Synopsis
Prototype
ajint ajFeattableGetLen (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| ajint | | RETURN | Length in bases or residues |
Input
| thys: | (Input) | Feature table |
Returns
| ajint: | Length in bases or residues |
Description
Returns the sequence length of a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
Synopsis
Prototype
const AjPStr ajFeattableGetName (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| const AjPStr | | RETURN | Feature table name. |
Input
| thys: | (Input) | Feature table |
Returns
| const AjPStr: | Feature table name. |
Description
Returns the name of a feature table object. This is a copy of the
pointer to the name, and is still owned by the feature table
and is not to be destroyed.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the size of a feature table object.
Synopsis
Prototype
ajuint ajFeattableGetSize (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| ajuint | | RETURN | Feature table size. |
Input
| thys: | (Input) | Feature table |
Returns
| ajuint: | Feature table size. |
Description
Returns the size of a feature table object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the sequence matching a feature. For multiple location features
(joins in an EMBL/GenBank feature table) the full feature table is used
to find all exons.
The database name is used to retrieve sequences from other entries
Synopsis
Prototype
AjBool ajFeatGetFlags (
const AjPFeature thys,
AjPStr* Pflagstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjPStr* | Pflagstr | Modify | Sequence for this feature |
| AjBool | | RETURN | True on success |
Input
Input & Output
| Pflagstr: | (Modify) | Sequence for this feature |
Returns
Description
Returns the sequence matching a feature. For multiple location features
(joins in an EMBL/GenBank feature table) the full feature table is used
to find all exons.
The database name is used to retrieve sequences from other entries
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the sequence matching a feature.
The database name is used to retrieve sequences from other entries
Synopsis
Prototype
AjBool ajFeatGetSeq (
const AjPFeature thys,
const AjPSeq seq,
AjPStr* Pseqstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| const AjPSeq | seq | Input | Sequence for the current feature table |
| AjPStr* | Pseqstr | Modify | Sequence for this feature |
| AjBool | | RETURN | True on success |
Input
| thys: | (Input) | Feature |
| seq: | (Input) | Sequence for the current feature table |
Input & Output
| Pseqstr: | (Modify) | Sequence for this feature |
Returns
Description
Returns the sequence matching a feature.
The database name is used to retrieve sequences from other entries
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the sequence matching a feature. For multiple location features
(joins in an EMBL/GenBank feature table) the full feature table is used
to find all exons.
The database name is used to retrieve sequences from other entries
Synopsis
Prototype
AjBool ajFeatGetSeqJoin (
const AjPFeature thys,
const AjPSeq seq,
AjPStr* Pseqstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| const AjPSeq | seq | Input | Sequence for the current feature table |
| AjPStr* | Pseqstr | Modify | Sequence for this feature |
| AjBool | | RETURN | True on success |
Input
| thys: | (Input) | Feature |
| seq: | (Input) | Sequence for the current feature table |
Input & Output
| Pseqstr: | (Modify) | Sequence for this feature |
Returns
Description
Returns the sequence matching a feature. For multiple location features
(joins in an EMBL/GenBank feature table) the full feature table is used
to find all exons.
The database name is used to retrieve sequences from other entries
See Also
See other functions in this section
Availability
In release 6.4.0
Returns a sequence entry from a feature location which points to
another entry
Synopsis
Prototype
AjBool ajFeatGetRemoteseq (
const AjPFeature thys,
const AjPStr usa,
AjPSeq seq
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| const AjPStr | usa | Input | usa of query |
| AjPSeq | seq | Modify | Sequence object for results |
| AjBool | | RETURN | True on success |
Input
| thys: | (Input) | Feature |
| usa: | (Input) | usa of query |
Input & Output
| seq: | (Modify) | Sequence object for results |
Returns
Description
Returns a sequence entry from a feature location which points to
another entry
See Also
See other functions in this section
Availability
In release 6.4.0
Returns all cross-references from a feature
Synopsis
Prototype
AjBool ajFeatGetXrefs (
const AjPFeature thys,
AjPList* Pxreflist
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjPList* | Pxreflist | Modify | List of sequence cross-reference objects |
| AjBool | | RETURN | True on success |
Input
Input & Output
| Pxreflist: | (Modify) | List of sequence cross-reference objects |
Returns
Description
Returns all cross-references from a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Returns a sequence entry converted to lower case where a feature
location matches.
Synopsis
Prototype
AjBool ajFeatLocMark (
const AjPFeature thys,
const AjPFeattable table,
AjPStr* Pseqstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| const AjPFeattable | table | Input | Feature table |
| AjPStr* | Pseqstr | Modify | Sequence to be marked in lower case |
| AjBool | | RETURN | true on success |
Input
| thys: | (Input) | Feature |
| table: | (Input) | Feature table |
Input & Output
| Pseqstr: | (Modify) | Sequence to be marked in lower case |
Returns
Description
Returns a sequence entry converted to lower case where a feature
location matches.
See Also
See other functions in this section
Availability
In release 6.4.0
Finds a named note tag (with a * prefix)
Synopsis
Prototype
AjBool ajFeatGetNoteC (
const AjPFeature thys,
const char* name,
AjPStr* val
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const char* | name | Input | Tag name |
| AjPStr* | val | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| name: | (Input) | Tag name |
Output
| val: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Finds a named note tag (with a * prefix)
See Also
See other functions in this section
Availability
In release 6.4.0
Finds a named note tag (with a * prefix)
Synopsis
Prototype
AjBool ajFeatGetNoteCI (
const AjPFeature thys,
const char* name,
ajint count,
AjPStr* val
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const char* | name | Input | Tag name |
| ajint | count | Input | Tag count: zero for any, 1 for first, 2 for second |
| AjPStr* | val | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| name: | (Input) | Tag name |
| count: | (Input) | Tag count: zero for any, 1 for first, 2 for second |
Output
| val: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Finds a named note tag (with a * prefix)
See Also
See other functions in this section
Availability
In release 6.4.0
Finds a named note tag (with a * prefix)
Synopsis
Prototype
AjBool ajFeatGetNoteSI (
const AjPFeature thys,
const AjPStr name,
ajint count,
AjPStr* val
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const AjPStr | name | Input | Tag name |
| ajint | count | Input | Tag count: zero for any, 1 for first, 2 for second |
| AjPStr* | val | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| name: | (Input) | Tag name |
| count: | (Input) | Tag count: zero for any, 1 for first, 2 for second |
Output
| val: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Finds a named note tag (with a * prefix)
See Also
See other functions in this section
Availability
In release 6.4.0
Finds a named note tag (with a * prefix)
Synopsis
Prototype
AjBool ajFeatGetNoteS (
const AjPFeature thys,
const AjPStr name,
AjPStr* val
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const AjPStr | name | Input | Tag name |
| AjPStr* | val | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| name: | (Input) | Tag name |
Output
| val: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Finds a named note tag (with a * prefix)
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the nth value of a named feature tag.
If not found as a tag, also searches for a named note
Synopsis
Prototype
AjBool ajFeatGetTagC (
const AjPFeature thys,
const char* tname,
ajint num,
AjPStr* Pval
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const char* | tname | Input | Tag name |
| ajint | num | Input | Tag number |
| AjPStr* | Pval | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| tname: | (Input) | Tag name |
| num: | (Input) | Tag number |
Output
| Pval: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Returns the nth value of a named feature tag.
If not found as a tag, also searches for a named note
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the nth value of a named feature tag.
If not found as a tag, also searches for a named note
Synopsis
Prototype
AjBool ajFeatGetTagS (
const AjPFeature thys,
const AjPStr name,
ajint num,
AjPStr* val
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const AjPStr | name | Input | Tag name |
| ajint | num | Input | Tag number |
| AjPStr* | val | Output | Tag value (if found) |
| AjBool | | RETURN | ajTrue on success (feature tag found) |
Input
| thys: | (Input) | Feature object |
| name: | (Input) | Tag name |
| num: | (Input) | Tag number |
Output
| val: | (Output) | Tag value (if found) |
Returns
| AjBool: | ajTrue on success (feature tag found) |
Description
Returns the nth value of a named feature tag.
If not found as a tag, also searches for a named note
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the type (key) of a feature object. This is a copy of the
pointer to the type, and is still owned by the feature
and is not to be destroyed.
Synopsis
Prototype
const AjPStr ajFeatGetType (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const AjPStr | | RETURN | Feature type, read only |
Input
| thys: | (Input) | Feature object |
Returns
| const AjPStr: | Feature type, read only |
Description
Returns the type (key) of a feature object. This is a copy of the
pointer to the type, and is still owned by the feature
and is not to be destroyed.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the source name of a feature object.
Synopsis
Prototype
const AjPStr ajFeatGetSource (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| const AjPStr | | RETURN | Feature source name |
Input
| thys: | (Input) | Feature object |
Returns
| const AjPStr: | Feature source name |
Description
Returns the source name of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the start position of a feature object.
Synopsis
Prototype
ajuint ajFeatGetStart (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| ajuint | | RETURN | Feature start position |
Input
| thys: | (Input) | Feature object |
Returns
| ajuint: | Feature start position |
Description
Returns the start position of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the strand of a feature object.
Synopsis
Prototype
char ajFeatGetStrand (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| char | | RETURN | Feature strand code |
Input
| thys: | (Input) | Feature object |
Returns
Description
Returns the strand of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the end position of a feature object.
Synopsis
Prototype
ajuint ajFeatGetEnd (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| ajuint | | RETURN | Feature end position |
Input
| thys: | (Input) | Feature object |
Returns
| ajuint: | Feature end position |
Description
Returns the end position of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the sequence length of a feature object.
Synopsis
Prototype
ajuint ajFeatGetLength (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| ajuint | | RETURN | Feature length |
Input
| thys: | (Input) | Feature object |
Returns
Description
Returns the sequence length of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the score of a feature object.
Synopsis
Prototype
float ajFeatGetScore (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| float | | RETURN | Feature score |
Input
| thys: | (Input) | Feature object |
Returns
Description
Returns the score of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the direction of a feature object.
Synopsis
Prototype
AjBool ajFeatGetForward (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| AjBool | | RETURN | ajTrue for a forward direction, ajFalse for reverse |
Input
| thys: | (Input) | Feature object |
Returns
| AjBool: | ajTrue for a forward direction, ajFalse for reverse |
Description
Returns the direction of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the reading frame of a feature object.
Synopsis
Prototype
ajint ajFeatGetFrame (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature object |
| ajint | | RETURN | Feature reading frame (zero for undefined) |
Input
| thys: | (Input) | Feature object |
Returns
| ajint: | Feature reading frame (zero for undefined) |
Description
Returns the reading frame of a feature object.
See Also
See other functions in this section
Availability
In release 6.4.0
Returns translation tag value
Synopsis
Prototype
AjBool ajFeatGetTranslation (
const AjPFeature thys,
AjPStr* Ptrans
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjPStr* | Ptrans | Output | Translations |
| AjBool | | RETURN | True if translation tag was found |
Input
Output
| Ptrans: | (Output) | Translations |
Returns
| AjBool: | True if translation tag was found |
Description
Returns translation tag value
See Also
See other functions in this section
Availability
In release 6.4.0
Temporary testing function for feature handling
to be deleted when all is working happily
Synopsis
Prototype
void ajFeatTest (
void
);
| Type | Name | Read/Write | Description |
|---|
| void | | RETURN | |
Returns
Description
Temporary testing function for feature handling
to be deleted when all is working happily
See Also
See other functions in this section
Availability
In release 6.4.0
Returns tags table for a named feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTags (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Tags table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Tags table on success
NULL on failure |
Description
Returns tags table for a named feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Returns tags table for a named nucleotide feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTagsNuc (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Tags table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Tags table on success
NULL on failure |
Description
Returns tags table for a named nucleotide feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Returns tags table for a named protein feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTagsProt (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Tags table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Tags table on success
NULL on failure |
Description
Returns tags table for a named protein feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Returns types table for a named feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTypes (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Returns types table for a named feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Returns types table for a named nucleotide feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTypesNuc (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Returns types table for a named nucleotide feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Returns types table for a named protein feature format
Synopsis
Prototype
const AjPTable ajFeatVocabGetTypesProt (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Returns types table for a named protein feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Initialises feature table internals for a named feature format
Synopsis
Prototype
const AjPTable ajFeatVocabInit (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Initialises feature table internals for a named feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Initialises feature table internals for a named feature format
Synopsis
Prototype
const AjPTable ajFeatVocabInitNuc (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Initialises feature table internals for a named feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Initialises feature table internals for a named feature format
Synopsis
Prototype
const AjPTable ajFeatVocabInitProt (
const char* name
);
| Type | Name | Read/Write | Description |
|---|
| const char* | name | Input | Feature format name |
| const AjPTable | | RETURN | Type table on success
NULL on failure |
Input
| name: | (Input) | Feature format name |
Returns
| const AjPTable: | Type table on success
NULL on failure |
Description
Initialises feature table internals for a named feature format
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the description for a feature
Synopsis
Prototype
void ajFeatSetDescApp (
AjPFeature thys,
const AjPStr desc
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | desc | Input | Feature description (simple text) |
| void | | RETURN | |
Input
| desc: | (Input) | Feature description (simple text) |
Input & Output
Returns
Description
Sets the description for a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the description for a feature
Synopsis
Prototype
void ajFeatSetDesc (
AjPFeature thys,
const AjPStr desc
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | desc | Input | Feature description (simple text) |
| void | | RETURN | |
Input
| desc: | (Input) | Feature description (simple text) |
Input & Output
Returns
Description
Sets the description for a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the source for a feature
Synopsis
Prototype
void ajFeatSetSource (
AjPFeature thys,
const AjPStr source
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | source | Input | Feature source |
| void | | RETURN | |
Input
| source: | (Input) | Feature source |
Input & Output
Returns
Description
Sets the source for a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the score for a feature
Synopsis
Prototype
void ajFeatSetScore (
AjPFeature thys,
float score
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| float | score | Input | Score value |
| void | | RETURN | |
Input
Input & Output
Returns
Description
Sets the score for a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the strand for a feature
Synopsis
Prototype
void ajFeatSetStrand (
AjPFeature thys,
AjBool rev
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| AjBool | rev | Input | True if reverse strand |
| void | | RETURN | |
Input
| rev: | (Input) | True if reverse strand |
Input & Output
Returns
Description
Sets the strand for a feature
See Also
See other functions in this section
Availability
In release 6.4.0
Sets a feature tag value
Synopsis
Prototype
AjBool ajFeatTagSetC (
AjPFeature thys,
const char* tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const char* | tag | Input | Feature tag |
| const AjPStr | value | Input | Feature tag value |
| AjBool | | RETURN | ajTrue is value was valid
ajFalse if it was "corrected" |
Input
| tag: | (Input) | Feature tag |
| value: | (Input) | Feature tag value |
Input & Output
Returns
| AjBool: | ajTrue is value was valid
ajFalse if it was "corrected" |
Description
Sets a feature tag value
See Also
See other functions in this section
Availability
In release 6.4.0
Sets a feature tag value
Synopsis
Prototype
AjBool ajFeatTagSet (
AjPFeature thys,
const AjPStr tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | tag | Input | Feature tag |
| const AjPStr | value | Input | Feature tag value |
| AjBool | | RETURN | ajTrue is value was valid
ajFalse if it was "corrected" |
Input
| tag: | (Input) | Feature tag |
| value: | (Input) | Feature tag value |
Input & Output
Returns
| AjBool: | ajTrue is value was valid
ajFalse if it was "corrected" |
Description
Sets a feature tag value
See Also
See other functions in this section
Availability
In release 6.4.0
Special processing for known GFF tags
This function will be very similar to featTagSpecial, with scope
for future GFF-specific extensions
Synopsis
Prototype
AjBool ajFeattagSpecialGff2 (
const AjPStr tag,
AjPStr* pval
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | tag | Input | original tag name |
| AjPStr* | pval | Modify | tag value |
| AjBool | | RETURN | ajTrue on success |
Input
| tag: | (Input) | original tag name |
Input & Output
Returns
Description
Special processing for known GFF tags
This function will be very similar to featTagSpecial, with scope
for future GFF-specific extensions
See Also
See other functions in this section
Availability
In release 6.4.0
Special processing for known GFF3 tags
This function will be very similar to featTagSpecial, with scope
for future GFF3-specific extensions
Synopsis
Prototype
AjBool ajFeattagSpecialGff3 (
const AjPStr tag,
AjPStr* pval
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | tag | Input | original tag name |
| AjPStr* | pval | Modify | tag value |
| AjBool | | RETURN | ajTrue on success |
Input
| tag: | (Input) | original tag name |
Input & Output
Returns
Description
Special processing for known GFF3 tags
This function will be very similar to featTagSpecial, with scope
for future GFF3-specific extensions
See Also
See other functions in this section
Availability
In release 6.4.0
Sets a feature tag value, creating a new feature tag even if one
already exists.
Synopsis
Prototype
AjBool ajFeatTagAddCC (
AjPFeature thys,
const char* tag,
const char* value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const char* | tag | Input | Feature tag |
| const char* | value | Input | Feature tag value |
| AjBool | | RETURN | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Input
| tag: | (Input) | Feature tag |
| value: | (Input) | Feature tag value |
Input & Output
Returns
| AjBool: | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Description
Sets a feature tag value, creating a new feature tag even if one
already exists.
See Also
See other functions in this section
Availability
In release 6.4.0
Sets a feature tag value, creating a new feature tag even if one
already exists.
Synopsis
Prototype
AjBool ajFeatTagAddC (
AjPFeature thys,
const char* tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const char* | tag | Input | Feature tag |
| const AjPStr | value | Input | Feature tag value |
| AjBool | | RETURN | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Input
| tag: | (Input) | Feature tag |
| value: | (Input) | Feature tag value |
Input & Output
Returns
| AjBool: | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Description
Sets a feature tag value, creating a new feature tag even if one
already exists.
See Also
See other functions in this section
Availability
In release 6.4.0
Sets a feature tag value, creating a new feature tag even if one
already exists.
Synopsis
Prototype
AjBool ajFeatTagAdd (
AjPFeature thys,
const AjPStr tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | tag | Input | Feature tag |
| const AjPStr | value | Input | Feature tag value |
| AjBool | | RETURN | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Input
| tag: | (Input) | Feature tag |
| value: | (Input) | Feature tag value |
Input & Output
Returns
| AjBool: | ajTrue if value was valid
ajFalse if it was bad and was "corrected" |
Description
Sets a feature tag value, creating a new feature tag even if one
already exists.
See Also
See other functions in this section
Availability
In release 6.4.0
Special processing for known internal (EMBL) tags
Synopsis
Prototype
AjBool ajFeattagSpecial (
const AjPStr tag,
AjPStr* pval
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | tag | Input | original tag name |
| AjPStr* | pval | Modify | parameter value |
| AjBool | | RETURN | ajTrue on success |
Input
| tag: | (Input) | original tag name |
Input & Output
| pval: | (Modify) | parameter value |
Returns
Description
Special processing for known internal (EMBL) tags
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new (generic) feature table.
Does not define the feature table type.
Synopsis
Prototype
AjPFeattable ajFeattableNew (
const AjPStr name
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | name | Input | Name for new feature table
(or NULL for unnamed) |
| AjPFeattable | | RETURN | Pointer to a new (empty) feature table |
Input
| name: | (Input) | Name for new feature table
(or NULL for unnamed) |
Returns
| AjPFeattable: | Pointer to a new (empty) feature table |
Description
Constructor for a new (generic) feature table.
Does not define the feature table type.
See Also
See other functions in this section
Availability
In release 6.4.0
Provides a unique (for this program run) name for a feature table.
Synopsis
Prototype
void ajFeattableSetDefname (
AjPFeattable thys,
const AjPStr setname
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Output | Feature table |
| const AjPStr | setname | Input | Name set by caller |
| void | | RETURN | |
Input
| setname: | (Input) | Name set by caller |
Output
| thys: | (Output) | Feature table |
Returns
Description
Provides a unique (for this program run) name for a feature table.
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the length of a feature table with the length of the source sequence.
This is needed to reverse the table correctly
Synopsis
Prototype
void ajFeattableSetLength (
AjPFeattable thys,
ajuint len
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table object |
| ajuint | len | Input | Length |
| void | | RETURN | |
Input
Input & Output
| thys: | (Modify) | Feature table object |
Returns
Description
Sets the length of a feature table with the length of the source sequence.
This is needed to reverse the table correctly
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the type of a feature table as nucleotide
Synopsis
Prototype
void ajFeattableSetNuc (
AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table object |
| void | | RETURN | |
Input & Output
| thys: | (Modify) | Feature table object |
Returns
Description
Sets the type of a feature table as nucleotide
See Also
See other functions in this section
Availability
In release 6.4.0
Sets the type of a feature table as Protein
Synopsis
Prototype
void ajFeattableSetProt (
AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table object |
| void | | RETURN | |
Input & Output
| thys: | (Modify) | Feature table object |
Returns
Description
Sets the type of a feature table as Protein
See Also
See other functions in this section
Availability
In release 6.4.0
Set the begin and end range for a feature table
Synopsis
Prototype
void ajFeattableSetRange (
AjPFeattable thys,
ajint fbegin,
ajint fend
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table object |
| ajint | fbegin | Input | Begin position |
| ajint | fend | Input | End position |
| void | | RETURN | |
Input
| fbegin: | (Input) | Begin position |
| fend: | (Input) | End position |
Input & Output
| thys: | (Modify) | Feature table object |
Returns
Description
Set the begin and end range for a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Reverse the features in a feature table by iterating through and
reversing all positions and strands.
Synopsis
Prototype
void ajFeattableReverse (
AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Feature table object |
| void | | RETURN | |
Input & Output
| thys: | (Modify) | Feature table object |
Returns
Description
Reverse the features in a feature table by iterating through and
reversing all positions and strands.
See Also
See other functions in this section
Availability
In release 6.4.0
Reverse one feature by reversing all positions and strand.
Synopsis
Prototype
void ajFeatReverse (
AjPFeature thys,
ajint ilen
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature object |
| ajint | ilen | Input | Sequence length |
| void | | RETURN | |
Input
| ilen: | (Input) | Sequence length |
Input & Output
| thys: | (Modify) | Feature object |
Returns
Description
Reverse one feature by reversing all positions and strand.
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new DNA feature table
Synopsis
Prototype
AjPFeattable ajFeattableNewDna (
const AjPStr name
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | name | Input | Name for new feature table
(or NULL for unnamed) |
| AjPFeattable | | RETURN | Pointer to a new (empty) feature table |
Input
| name: | (Input) | Name for new feature table
(or NULL for unnamed) |
Returns
| AjPFeattable: | Pointer to a new (empty) feature table |
Description
Constructor for a new DNA feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new feature table for an existing sequence.
The feature table type is determined by the sequence type.
Synopsis
Prototype
AjPFeattable ajFeattableNewSeq (
const AjPSeq seq
);
| Type | Name | Read/Write | Description |
|---|
| const AjPSeq | seq | Input | Sequence object to provide the name and type |
| AjPFeattable | | RETURN | Pointer to a new (empty) feature table |
Input
| seq: | (Input) | Sequence object to provide the name and type |
Returns
| AjPFeattable: | Pointer to a new (empty) feature table |
Description
Constructor for a new feature table for an existing sequence.
The feature table type is determined by the sequence type.
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a new protein feature table
Synopsis
Prototype
AjPFeattable ajFeattableNewProt (
const AjPStr name
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | name | Input | Name for new feature table
(or NULL for unnamed) |
| AjPFeattable | | RETURN | Pointer to a new (empty) feature table |
Input
| name: | (Input) | Name for new feature table
(or NULL for unnamed) |
Returns
| AjPFeattable: | Pointer to a new (empty) feature table |
Description
Constructor for a new protein feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a feature GFF3 tag-value pair
Synopsis
Prototype
ajuint ajFeatGfftagAddC (
AjPFeature thys,
const char* tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const char* | tag | Input | Tag name |
| const AjPStr | value | Input | Tag value list |
| ajuint | | RETURN | Number of values added |
Input
| tag: | (Input) | Tag name |
| value: | (Input) | Tag value list |
Input & Output
Returns
| ajuint: | Number of values added |
Description
Constructor for a feature GFF3 tag-value pair
See Also
See other functions in this section
Availability
In release 6.4.0
Constructor for a feature GFF3 tag-value pair
Synopsis
Prototype
ajuint ajFeatGfftagAdd (
AjPFeature thys,
const AjPStr tag,
const AjPStr value
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | thys | Modify | Feature |
| const AjPStr | tag | Input | Tag name |
| const AjPStr | value | Input | Tag value list |
| ajuint | | RETURN | Number of values added |
Input
| tag: | (Input) | Tag name |
| value: | (Input) | Tag value list |
Input & Output
Returns
| ajuint: | Number of values added |
Description
Constructor for a feature GFF3 tag-value pair
See Also
See other functions in this section
Availability
In release 6.4.0
Makes a copy of a feature table.
For cases where we need a copy we can safely change and/or delete.
Synopsis
Prototype
AjPFeattable ajFeattableNewFtable (
const AjPFeattable orig
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | orig | Input | Original feature table |
| AjPFeattable | | RETURN | Feature table copy of the original |
Input
| orig: | (Input) | Original feature table |
Returns
| AjPFeattable: | Feature table copy of the original |
Description
Makes a copy of a feature table.
For cases where we need a copy we can safely change and/or delete.
See Also
See other functions in this section
Availability
In release 6.4.0
Makes a copy of a feature table using only a limited number of features.
For cases where we need a copy we can safely change and/or delete.
Synopsis
Prototype
AjPFeattable ajFeattableNewFtableLimit (
const AjPFeattable orig,
ajint limit
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | orig | Input | Original feature table |
| ajint | limit | Input | Limit to number of features copied |
| AjPFeattable | | RETURN | Feature table copy of the original |
Input
| orig: | (Input) | Original feature table |
| limit: | (Input) | Limit to number of features copied |
Returns
| AjPFeattable: | Feature table copy of the original |
Description
Makes a copy of a feature table using only a limited number of features.
For cases where we need a copy we can safely change and/or delete.
See Also
See other functions in this section
Availability
In release 6.4.0
Makes a copy of a feature.
For cases where we need a copy we can safely change and/or delete.
Synopsis
Prototype
AjPFeature ajFeatNewFeat (
const AjPFeature orig
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | orig | Input | Original feature |
| AjPFeature | | RETURN | Feature copy of the original |
Input
| orig: | (Input) | Original feature |
Returns
| AjPFeature: | Feature copy of the original |
Description
Makes a copy of a feature.
For cases where we need a copy we can safely change and/or delete.
See Also
See other functions in this section
Availability
In release 6.4.0
Traces (to the debug file) a feature object
Synopsis
Prototype
void ajFeatTrace (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| void | | RETURN | |
Input
Returns
Description
Traces (to the debug file) a feature object
See Also
See other functions in this section
Availability
In release 6.4.0
Traces (to the debug file) the tag-value pairs of a feature object
Synopsis
Prototype
void ajFeatTagTrace (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| void | | RETURN | |
Input
Returns
Description
Traces (to the debug file) the tag-value pairs of a feature object
See Also
See other functions in this section
Availability
In release 6.4.0
Creates a structure holding GFF tag value pairs
Synopsis
Prototype
AjPFeatGfftags ajFeatGfftagsNew (
void
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeatGfftags | | RETURN | GFF tag-values structure |
Returns
| AjPFeatGfftags: | GFF tag-values structure |
Description
Creates a structure holding GFF tag value pairs
See Also
See other functions in this section
Availability
In release 6.4.0
Destroys a structure holding GFF tag value pairs
Synopsis
Prototype
void ajFeatGfftagsDel (
AjPFeatGfftags* Pthys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeatGfftags* | Pthys | Delete | GFF tag-values structure |
| void | | RETURN | |
Output
| Pthys: | (Delete) | GFF tag-values structure |
Returns
Description
Destroys a structure holding GFF tag value pairs
See Also
See other functions in this section
Availability
In release 6.4.0
Returns an object with all feature GFF tag-value pairs
Synopsis
Prototype
AjPFeatGfftags ajFeatGetGfftags (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjPFeatGfftags | | RETURN | Gff tags object |
Input
Returns
| AjPFeatGfftags: | Gff tags object |
Description
Returns an object with all feature GFF tag-value pairs
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the GFF Parent tag of a feature with GFF tag-value pairs
Synopsis
Prototype
const AjPStr ajFeatGetParent (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| const AjPStr | | RETURN | Parent tag |
Input
Returns
Description
Returns the GFF Parent tag of a feature with GFF tag-value pairs
See Also
See other functions in this section
Availability
In release 6.4.0
Returns an iterator over all feature tag-value pairs
Synopsis
Prototype
AjIList ajFeatTagIter (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjIList | | RETURN | List iterator |
Input
Returns
Description
Returns an iterator over all feature tag-value pairs
See Also
See other functions in this section
Availability
In release 6.4.0
Returns an iterator over all subfeaturers
Synopsis
Prototype
AjIList ajFeatSubIter (
const AjPFeature thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | thys | Input | Feature |
| AjIList | | RETURN | List iterator |
Input
Returns
Description
Returns an iterator over all subfeaturers
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the tag-value pairs of a feature object
Synopsis
Prototype
AjBool ajFeatTagval (
AjIList iter,
AjPStr* Ptagnam,
AjPStr* Ptagval
);
| Type | Name | Read/Write | Description |
|---|
| AjIList | iter | Modify | List iterator from ajFeatTagIter |
| AjPStr* | Ptagnam | Output | Tag name |
| AjPStr* | Ptagval | Output | Tag val |
| AjBool | | RETURN | ajTrue if another tag-value pair was returned |
Output
| Ptagnam: | (Output) | Tag name |
| Ptagval: | (Output) | Tag val |
Input & Output
| iter: | (Modify) | List iterator from ajFeatTagIter |
Returns
| AjBool: | ajTrue if another tag-value pair was returned |
Description
Returns the tag-value pairs of a feature object
See Also
See other functions in this section
Availability
In release 6.4.0
Traces (to the debug file) a complete feature table
Synopsis
Prototype
void ajFeattableTrace (
const AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Feature table |
| void | | RETURN | |
Input
| thys: | (Input) | Feature table |
Returns
Description
Traces (to the debug file) a complete feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for the internal DNA feature table
Synopsis
Prototype
const AjPStr ajFeatTypeNuc (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for the internal DNA feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for the internal protein feature table
Synopsis
Prototype
const AjPStr ajFeatTypeProt (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for the internal protein feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for a feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetExternal (
const AjPStr type,
const AjPTable table
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPTable | table | Input | Feature table |
| const AjPStr | | RETURN | Valid feature type |
Input
| type: | (Input) | Type name |
| table: | (Input) | Feature table |
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for an internal feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternal (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for an internal feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for an EMBL format feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternalEmbl (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for an EMBL format feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for an internal feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternalNuc (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for an internal feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for an internal feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternalPir (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for an internal feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for an internal feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternalProt (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for an internal feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature type name,
returns the valid feature type for a REFSEQP format feature table
Synopsis
Prototype
const AjPStr ajFeattypeGetInternalRefseqp (
const AjPStr type
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | type | Input | Type name |
| const AjPStr | | RETURN | Valid feature type |
Input
Returns
| const AjPStr: | Valid feature type |
Description
Given a feature type name,
returns the valid feature type for a REFSEQP format feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature tag name,
returns the valid feature tag name for a feature table
Synopsis
Prototype
const AjPStr ajFeattagGetNameC (
const char* tag,
const AjPTable table,
AjBool* knowntag
);
| Type | Name | Read/Write | Description |
|---|
| const char* | tag | Input | Type name |
| const AjPTable | table | Input | Feature table |
| AjBool* | knowntag | Output | ajTrue if the tag name is known
ajFalse if the default name was substituted |
| const AjPStr | | RETURN | Valid feature tag name |
Input
| tag: | (Input) | Type name |
| table: | (Input) | Feature table |
Output
| knowntag: | (Output) | ajTrue if the tag name is known
ajFalse if the default name was substituted |
Returns
| const AjPStr: | Valid feature tag name |
Description
Given a feature tag name,
returns the valid feature tag name for a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Given a feature tag name,
returns the valid feature tag name for a feature table
Synopsis
Prototype
const AjPStr ajFeattagGetNameS (
const AjPStr tag,
const AjPTable table,
AjBool* knowntag
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | tag | Input | Type name |
| const AjPTable | table | Input | Feature table |
| AjBool* | knowntag | Output | ajTrue if the tag was found in the
list of known tags |
| const AjPStr | | RETURN | Valid feature tag name |
Input
| tag: | (Input) | Type name |
| table: | (Input) | Feature table |
Output
| knowntag: | (Output) | ajTrue if the tag was found in the
list of known tags |
Returns
| const AjPStr: | Valid feature tag name |
Description
Given a feature tag name,
returns the valid feature tag name for a feature table
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a feature tag value into the correct format, after
checking it is an acceptable value
Synopsis
Prototype
void ajFeattagFormat (
const AjPStr name,
const AjPTable table,
AjPStr* retstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | name | Input | Tag name |
| const AjPTable | table | Input | Tag table |
| AjPStr* | retstr | Output | string with formatted value. |
| void | | RETURN | |
Input
| name: | (Input) | Tag name |
| table: | (Input) | Tag table |
Output
| retstr: | (Output) | string with formatted value. |
Returns
Description
Converts a feature tag value into the correct format, after
checking it is an acceptable value
See Also
See other functions in this section
Availability
In release 6.4.0
Returns the controlled vocabulary list for a limited value.
Synopsis
Prototype
void ajFeattagGetLimit (
const AjPStr name,
const AjPTable table,
AjPStr* retstr
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | name | Input | Tag name |
| const AjPTable | table | Input | Tag table |
| AjPStr* | retstr | Output | string with formatted value. |
| void | | RETURN | |
Input
| name: | (Input) | Tag name |
| table: | (Input) | Tag table |
Output
| retstr: | (Output) | string with formatted value. |
Returns
Description
Returns the controlled vocabulary list for a limited value.
See Also
See other functions in this section
Availability
In release 6.4.0
Dummy function to prevent compiler warnings
Synopsis
Prototype
void ajFeatUnused (
void
);
| Type | Name | Read/Write | Description |
|---|
| void | | RETURN | |
Returns
Description
Dummy function to prevent compiler warnings
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is a CDS feature
Synopsis
Prototype
AjBool ajFeatTypeIsCds (
const AjPFeature gf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| AjBool | | RETURN | ajTrue on success |
Input
Returns
Description
Tests whether the feature is a CDS feature
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature type matches a given string
including testing for alternative names
Synopsis
Prototype
AjBool ajFeatTypeMatchC (
const AjPFeature gf,
const char* txt
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| const char* | txt | Input | Feature type name to test |
| AjBool | | RETURN | ajTrue on success |
Input
| gf: | (Input) | Feature |
| txt: | (Input) | Feature type name to test |
Returns
Description
Tests whether the feature type matches a given string
including testing for alternative names
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature type matches a given string
including testing for alternative names
Synopsis
Prototype
AjBool ajFeatTypeMatchS (
const AjPFeature gf,
const AjPStr str
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| const AjPStr | str | Input | Feature type name to test |
| AjBool | | RETURN | ajTrue on success |
Input
| gf: | (Input) | Feature |
| str: | (Input) | Feature type name to test |
Returns
Description
Tests whether the feature type matches a given string
including testing for alternative names
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature type matches a given wildcard string
including testing for alternative names
Synopsis
Prototype
AjBool ajFeatTypeMatchWildS (
const AjPFeature gf,
const AjPStr str
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| const AjPStr | str | Input | Feature type name to test |
| AjBool | | RETURN | ajTrue on success |
Input
| gf: | (Input) | Feature |
| str: | (Input) | Feature type name to test |
Returns
Description
Tests whether the feature type matches a given wildcard string
including testing for alternative names
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is local to the sequence.
Returns AJTRUE if it is local, AJFALSE if remote.
Synopsis
Prototype
AjBool ajFeatIsLocal (
const AjPFeature gf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| AjBool | | RETURN | ajTrue on success |
Input
Returns
Description
Tests whether the feature is local to the sequence.
Returns AJTRUE if it is local, AJFALSE if remote.
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is local and in the specified range of the
sequence.
Returns AJTRUE if it is local and within the range.
(Any label location is assumed to be outside the range.)
Synopsis
Prototype
AjBool ajFeatIsLocalRange (
const AjPFeature gf,
ajuint start,
ajuint end
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| ajuint | start | Input | start of range |
| ajuint | end | Input | end of range |
| AjBool | | RETURN | ajTrue on success |
Input
| gf: | (Input) | Feature |
| start: | (Input) | start of range |
| end: | (Input) | end of range |
Returns
Description
Tests whether the feature is local and in the specified range of the
sequence.
Returns AJTRUE if it is local and within the range.
(Any label location is assumed to be outside the range.)
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is a child member of a join
The parent (first) feature of a join gives:
ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue
Synopsis
Prototype
AjBool ajFeatIsChild (
const AjPFeature gf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| AjBool | | RETURN | Returns AJTRUE if it is a child,
AJFALSE if it is not a child |
Input
Returns
| AjBool: | Returns AJTRUE if it is a child,
AJFALSE if it is not a child |
Description
Tests whether the feature is a child member of a join
The parent (first) feature of a join gives:
ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is a member of a join, group order or one_of
Synopsis
Prototype
AjBool ajFeatIsMultiple (
const AjPFeature gf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| AjBool | | RETURN | Returns AJTRUE if it is a member |
Input
Returns
| AjBool: | Returns AJTRUE if it is a member |
Description
Tests whether the feature is a member of a join, group order or one_of
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature is a member of a complement around a
multiple (join, etc.)
Synopsis
Prototype
AjBool ajFeatIsCompMult (
const AjPFeature gf
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeature | gf | Input | Feature |
| AjBool | | RETURN | Returns AJTRUE if it is a complemented multiple |
Input
Returns
| AjBool: | Returns AJTRUE if it is a complemented multiple |
Description
Tests whether the feature is a member of a complement around a
multiple (join, etc.)
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a string position into a true position. If ipos is negative,
it is counted from the end of the string rather than the beginning.
For strings, the result can go off the end to the terminating NULL.
For sequences the maximum is the last base.
Synopsis
Prototype
ajuint ajFeattablePos (
const AjPFeattable thys,
ajint ipos
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Target feature table. |
| ajint | ipos | Input | Position. |
| ajuint | | RETURN | string position between 1 and length. |
Input
| thys: | (Input) | Target feature table. |
| ipos: | (Input) | Position. |
Returns
| ajuint: | string position between 1 and length. |
Description
Converts a string position into a true position. If ipos is negative,
it is counted from the end of the string rather than the beginning.
For strings, the result can go off the end to the terminating NULL.
For sequences the maximum is the last base.
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a string position into a true position. If ipos is negative,
it is counted from the end of the string rather than the beginning.
imin is a minimum relative position, also counted from the end
if negative. Usually this is the start position when the end of a range
is being tested.
Synopsis
Prototype
ajuint ajFeattablePosI (
const AjPFeattable thys,
ajuint imin,
ajint ipos
);
| Type | Name | Read/Write | Description |
|---|
| const AjPFeattable | thys | Input | Target feature table. |
| ajuint | imin | Input | Start position. |
| ajint | ipos | Input | Position. |
| ajuint | | RETURN | string position between 1 and length. |
Input
| thys: | (Input) | Target feature table. |
| imin: | (Input) | Start position. |
| ipos: | (Input) | Position. |
Returns
| ajuint: | string position between 1 and length. |
Description
Converts a string position into a true position. If ipos is negative,
it is counted from the end of the string rather than the beginning.
imin is a minimum relative position, also counted from the end
if negative. Usually this is the start position when the end of a range
is being tested.
See Also
See other functions in this section
Availability
In release 6.4.0
Converts a position into a true position. If ipos is negative,
it is counted from the end of the sequence rather than the beginning.
imin is a minimum relative position, also counted from the end
if negative. Usually this is the start position when the end of a range
is being tested.
For strings, the result can go off the end to the terminating NULL.
For sequences the maximum is the last base.
Synopsis
Prototype
ajuint ajFeattablePosII (
ajuint ilen,
ajuint imin,
ajint ipos
);
| Type | Name | Read/Write | Description |
|---|
| ajuint | ilen | Input | maximum length. |
| ajuint | imin | Input | Start position. |
| ajint | ipos | Input | Position. |
| ajuint | | RETURN | string position between 1 and length. |
Input
| ilen: | (Input) | maximum length. |
| imin: | (Input) | Start position. |
| ipos: | (Input) | Position. |
Returns
| ajuint: | string position between 1 and length. |
Description
Converts a position into a true position. If ipos is negative,
it is counted from the end of the sequence rather than the beginning.
imin is a minimum relative position, also counted from the end
if negative. Usually this is the start position when the end of a range
is being tested.
For strings, the result can go off the end to the terminating NULL.
For sequences the maximum is the last base.
See Also
See other functions in this section
Availability
In release 6.4.0
Trim a feature table using the Begin and Ends.
Called where a sequence has been trimmed, so we have to allow for
missing sequence positions at the start (ioffset) or at the end (ilen).
Synopsis
Prototype
AjBool ajFeattableTrimOff (
AjPFeattable thys,
ajuint ioffset,
ajuint ilen
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Target feature table. |
| ajuint | ioffset | Input | Offset from start of sequence |
| ajuint | ilen | Input | Length of sequence |
| AjBool | | RETURN | AjTrue returned if successful. |
Input
| ioffset: | (Input) | Offset from start of sequence |
| ilen: | (Input) | Length of sequence |
Input & Output
| thys: | (Modify) | Target feature table. |
Returns
| AjBool: | AjTrue returned if successful. |
Description
Trim a feature table using the Begin and Ends.
Called where a sequence has been trimmed, so we have to allow for
missing sequence positions at the start (ioffset) or at the end (ilen).
See Also
See other functions in this section
Availability
In release 6.4.0
Trim a feature table using the Begin and Ends.
Synopsis
Prototype
AjBool ajFeattableTrim (
AjPFeattable thys
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeattable | thys | Modify | Target feature table. |
| AjBool | | RETURN | AjTrue returned if successful. |
Input & Output
| thys: | (Modify) | Target feature table. |
Returns
| AjBool: | AjTrue returned if successful. |
Description
Trim a feature table using the Begin and Ends.
See Also
See other functions in this section
Availability
In release 6.4.0
Trim a feature table using the Begin and Ends.
Called where a sequence has been trimmed, so we have to allow for
missing sequence positions at the start (ioffset)
Synopsis
Prototype
AjBool ajFeatTrimOffRange (
AjPFeature ft,
ajuint ioffset,
ajuint begin,
ajuint end,
AjBool dobegin,
AjBool doend
);
| Type | Name | Read/Write | Description |
|---|
| AjPFeature | ft | Modify | Target feature |
| ajuint | ioffset | Input | Offset from start of sequence |
| ajuint | begin | Input | Range start of sequence |
| ajuint | end | Input | Range end of sequence |
| AjBool | dobegin | Input | Reset begin |
| AjBool | doend | Input | Reset end |
| AjBool | | RETURN | AjTrue returned if successful. |
Input
| ioffset: | (Input) | Offset from start of sequence |
| begin: | (Input) | Range start of sequence |
| end: | (Input) | Range end of sequence |
| dobegin: | (Input) | Reset begin |
| doend: | (Input) | Reset end |
Input & Output
| ft: | (Modify) | Target feature |
Returns
| AjBool: | AjTrue returned if successful. |
Description
Trim a feature table using the Begin and Ends.
Called where a sequence has been trimmed, so we have to allow for
missing sequence positions at the start (ioffset)
See Also
See other functions in this section
Availability
In release 6.4.0
Tests whether the feature tag is a note (the default feature tag)
Synopsis
Prototype
AjBool ajFeattagIsNote (
const AjPStr tag
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | tag | Input | Feature tag |
| AjBool | | RETURN | ajTrue on success |
Input
Returns
Description
Tests whether the feature tag is a note (the default feature tag)
See Also
See other functions in this section
Availability
In release 6.4.0
Cleans up feature table internal memory
Synopsis
Prototype
void ajFeatExit (
void
);
| Type | Name | Read/Write | Description |
|---|
| void | | RETURN | |
Returns
Description
Cleans up feature table internal memory
See Also
See other functions in this section
Availability
In release 6.4.0
Formatted write as a warning message.
Synopsis
Prototype
void ajFeatWarn (
const char* fmt,
...
);
| Type | Name | Read/Write | Description |
|---|
| const char* | fmt | Input | Format string |
| ... | vararg | Vararg | Format arguments. |
| void | | RETURN | |
Input
| fmt: | (Input) | Format string |
| : | (Vararg) | Format arguments. |
Returns
Description
Formatted write as a warning message.
See Also
See other functions in this section
Availability
In release 6.4.0