SequenceImpl Class Reference
#include <sequence_impl.hh>
Inherits ost::GenericPropContainerImpl.
Data Structures |
struct | Shift |
Public Member Functions |
int | GetResidueIndex (int pos) const |
int | GetPos (int residue_index) const |
int | GetFirstNonGap () const |
int | GetLastNonGap () const |
const String & | GetName () const |
void | SetName (const String &name) |
void | Cut (int start, int n) |
void | ShiftRegion (int start, int end, int amount) |
const String & | GetString () const |
void | SetString (const String &seq) |
void | Normalise () |
void | Replace (const String &str, int start, int end) |
String | GetGaplessString () const |
int | GetOffset () const |
int | GetIndex (const String &substr) const |
void | SetOffset (int offset) |
int | GetLength () const |
| SequenceImpl (const String &seq_name, const String &sequence_string, const String &role) |
char | GetOneLetterCode (int position) const |
void | SetOneLetterCode (int position, char new_char) |
mol::ResidueView | GetResidue (int position) const |
mol::EntityView | GetAttachedView () const |
void | AttachView (const mol::EntityView &view) |
SequenceImplPtr | Copy () const |
void | AttachView (const mol::EntityView &view, const String &chain_name) |
bool | HasAttachedView () const |
void | Append (char olc) |
char & | operator[] (size_t index) |
char | operator[] (size_t index) const |
const String & | GetRole () const |
void | SetRole (const String &role) |
Static Public Member Functions |
static SequenceImplPtr | FromString (const String &seq_name, const String &sequence_string, const String &role="UNKNOWN") |
Detailed Description
Definition at line 49 of file sequence_impl.hh.
Constructor & Destructor Documentation
Construct new sequence object from sequence_string.
If you want to check whether the sequence String does only contain valid characters use CreateSequence
instead.
Member Function Documentation
attach entity view to sequence
The sequence is mapped onto the chain with given name
attach entity view to sequence
- Exceptions:
-
create copy sequence
The newly created sequence has the same attached view.
void Cut |
( |
int |
start, |
|
|
int |
n | |
|
) |
| | |
Construct new sequence object from sequence_string.
get attached view. may be an invalid entity view
int GetFirstNonGap |
( |
|
) |
const |
Get position of first non-gap character in sequence.
String GetGaplessString |
( |
|
) |
const |
Get sequence as String ignoring gaps.
int GetIndex |
( |
const String & |
substr |
) |
const |
int GetLastNonGap |
( |
|
) |
const |
Get position of last non-gap character in sequence.
Get lenght of sequence, including gaps.
const String& GetName |
( |
|
) |
const |
Get sequence offset from N-terminus.
- See also:
- SetOffset
char GetOneLetterCode |
( |
int |
position |
) |
const |
get one letter code of residue at position
int GetPos |
( |
int |
residue_index |
) |
const |
Get zero-based index for given residue number.
- Exceptions:
-
| out_of_range,if | number is not included in sequence. |
get residue at position
will return the residue view at the given sequence position or an invalid residue view when no view is attached, the index is out of bounds or the position contains a gap.
int GetResidueIndex |
( |
int |
pos |
) |
const |
Get residue index corresponding to given sequence position.
- Parameters:
-
- Exceptions:
-
| out_of_range | if pos is not in [0, length-1]. |
const String& GetRole |
( |
|
) |
const [inline] |
const String& GetString |
( |
|
) |
const [inline] |
bool HasAttachedView |
( |
|
) |
const |
whether the sequence has an attached view
Remove everything 'unusual' from sequence.
char operator[] |
( |
size_t |
index |
) |
const [inline] |
char& operator[] |
( |
size_t |
index |
) |
[inline] |
void Replace |
( |
const String & |
str, |
|
|
int |
start, |
|
|
int |
end | |
|
) |
| | |
replace substring starting from start to end
void SetName |
( |
const String & |
name |
) |
|
void SetOffset |
( |
int |
offset |
) |
|
Set sequence offset.
By default the sequence offset is zero, i.e. the beginning of the sequence lies exactly at the N-terminus. Setting the sequence offset to a positive number will shift the sequence towards the C-terminus.
void SetOneLetterCode |
( |
int |
position, |
|
|
char |
new_char | |
|
) |
| | |
void SetRole |
( |
const String & |
role |
) |
[inline] |
void SetString |
( |
const String & |
seq |
) |
|
void ShiftRegion |
( |
int |
start, |
|
|
int |
end, |
|
|
int |
amount | |
|
) |
| | |
The documentation for this class was generated from the following file: