Representation of a MzIdentML PeptideEvidence. More...
#include <OpenMS/METADATA/PeptideEvidence.h>
Public Member Functions | |
| PeptideEvidence & | operator= (const PeptideEvidence &source) |
| assignment operator | |
| bool | operator== (const PeptideEvidence &rhs) const |
| Equality operator. | |
| bool | operator!= (const PeptideEvidence &rhs) const |
| Inequality operator. | |
Constructors and Destructor | |
| PeptideEvidence () | |
| default constructor | |
| PeptideEvidence (DoubleReal score, UInt rank, Int charge, const AASequence &sequence) | |
| values constructor | |
| PeptideEvidence (const PeptideEvidence &source) | |
| copy constructor | |
| virtual | ~PeptideEvidence () |
| destructor | |
Accessors | |
| const String & | getDBSequenceRef () const |
| returns the corresponding protein db sequence ref | |
| void | setDBSequenceRef (const String &rhs) |
| sets the corresponding protein db sequence ref | |
| const String & | getTranslationTableRef () const |
| returns the translation table reference | |
| void | setTranslationTableRef (const String &rhs) |
| sets the translation table reference | |
| void | setStart (Int start) |
| start position in the sequence (xsd:int) | |
| Int | getStart () const |
| returns the start position in the sequence (xsd:int) | |
| void | setEnd (Int end) |
| sets the end position in the sequence | |
| Int | getEnd () const |
| returns the end position in the sequence | |
| void | setPre (char rhs) |
| sets the amino acid before the sequence, "-" if N-terminal, "?" if not applicable (e.g. de novo) | |
| char | getPre () const |
| returns the amino acid before the sequence | |
| void | setPost (char rhs) |
| sets the amino acid after the sequence, "-" if C-terminal, "?" if not applicable (e.g. de novo) | |
| char | getPost () const |
| returns the amino acid after the sequence | |
| void | setId (const String &id) |
| unique id of the file, set of files or repository | |
| const String & | getId () const |
| returns the unqiue id of the instance | |
| void | setName (const String &name) |
| sets the potentially ambigous but human readable name | |
| const String & | getName () const |
| returns the human readable name | |
| void | setMissedCleavages (Int rhs) |
| sets the number of missed cleavages | |
| Int | getMissedCleavages () const |
| returns the number of missed cleavages | |
| void | setIsDecoy (bool is_decoy) |
| sets whether the hit is a decoy hit | |
| bool | getIsDecoy () const |
| returns the whether the hit is decoy | |
| void | setFrame (Int frame) |
| Frame of the DB, e.g. from nucleic acids. | |
| Int | getFrame () const |
| returns the frame of the peptide evidence | |
Protected Attributes | |
| String | db_sequence_ref_ |
| String | translation_table_ref_ |
| Int | start_ |
| Int | end_ |
| char | pre_ |
| char | post_ |
| String | id_ |
| String | name_ |
| Int | missed_cleavages_ |
| bool | is_decoy_ |
| Int | frame_ |
Detailed Description
Representation of a MzIdentML PeptideEvidence.
It contains information about the protein the peptide comes from and additional information were it is located in the protein.
- Todo:
- implement CVParam
Constructor & Destructor Documentation
| PeptideEvidence | ( | ) |
default constructor
| PeptideEvidence | ( | DoubleReal | score, | |
| UInt | rank, | |||
| Int | charge, | |||
| const AASequence & | sequence | |||
| ) |
values constructor
| PeptideEvidence | ( | const PeptideEvidence & | source | ) |
copy constructor
| virtual ~PeptideEvidence | ( | ) | [virtual] |
destructor
Member Function Documentation
| const String& getDBSequenceRef | ( | ) | const |
returns the corresponding protein db sequence ref
| Int getEnd | ( | ) | const |
returns the end position in the sequence
| Int getFrame | ( | ) | const |
returns the frame of the peptide evidence
| const String& getId | ( | ) | const |
returns the unqiue id of the instance
| bool getIsDecoy | ( | ) | const |
returns the whether the hit is decoy
| Int getMissedCleavages | ( | ) | const |
returns the number of missed cleavages
| const String& getName | ( | ) | const |
returns the human readable name
| char getPost | ( | ) | const |
returns the amino acid after the sequence
| char getPre | ( | ) | const |
returns the amino acid before the sequence
| Int getStart | ( | ) | const |
returns the start position in the sequence (xsd:int)
| const String& getTranslationTableRef | ( | ) | const |
returns the translation table reference
| bool operator!= | ( | const PeptideEvidence & | rhs | ) | const |
Inequality operator.
| PeptideEvidence& operator= | ( | const PeptideEvidence & | source | ) |
assignment operator
| bool operator== | ( | const PeptideEvidence & | rhs | ) | const |
Equality operator.
| void setDBSequenceRef | ( | const String & | rhs | ) |
sets the corresponding protein db sequence ref
| void setEnd | ( | Int | end | ) |
sets the end position in the sequence
| void setFrame | ( | Int | frame | ) |
Frame of the DB, e.g. from nucleic acids.
| void setId | ( | const String & | id | ) |
unique id of the file, set of files or repository
| void setIsDecoy | ( | bool | is_decoy | ) |
sets whether the hit is a decoy hit
| void setMissedCleavages | ( | Int | rhs | ) |
sets the number of missed cleavages
| void setName | ( | const String & | name | ) |
sets the potentially ambigous but human readable name
| void setPost | ( | char | rhs | ) |
sets the amino acid after the sequence, "-" if C-terminal, "?" if not applicable (e.g. de novo)
| void setPre | ( | char | rhs | ) |
sets the amino acid before the sequence, "-" if N-terminal, "?" if not applicable (e.g. de novo)
| void setStart | ( | Int | start | ) |
start position in the sequence (xsd:int)
| void setTranslationTableRef | ( | const String & | rhs | ) |
sets the translation table reference
Member Data Documentation
String db_sequence_ref_ [protected] |
bool is_decoy_ [protected] |
Int missed_cleavages_ [protected] |
char post_ [protected] |
char pre_ [protected] |
String translation_table_ref_ [protected] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |