pgb_liv\php_ms\Core\Modification
A modification object which may be applied to a peptide or protein
- Author: Andrew Collins
Synopsis
- // constants
- const TYPE_FIXED = 0;
- const TYPE_VARIABLE = 1;
- const POSITION_ANY = 'any';
- const POSITION_NTERM = 'N-term';
- const POSITION_CTERM = 'C-term';
- const POSITION_PROTEIN_NTERM = 'Prot-N-term';
- const POSITION_PROTEIN_CTERM = 'Prot-C-term';
- // members
- private $location;
- private $monoisotopicMass;
- private $averageMass;
- private $name;
- private $residues;
- private $type = Modification::TYPE_VARIABLE;
- private $position = Modification::POSITION_ANY;
- private $accession;
- // methods
- public void setLocation()
- public int getLocation()
- public void setMonoisotopicMass()
- public float getMonoisotopicMass()
- public void setAverageMass()
- public void getAverageMass()
- public void setName()
- public string getName()
- public void setResidues()
- public array getResidues()
- public void setType()
- public void getType()
- public void isFixed()
- public void isVariable()
- public void setPosition()
- public void getPosition()
- public void setAccession()
- public string getAccession()
Coverage
| Methods | 100% | 18 / 18 |
| Lines | 100% | 53 / 53 |
Violations
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 73 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 73 | 98 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
| 100 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 100 | 106 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
| 120 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 120 | 106 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
| 161 | 140 | warning | Line exceeds 120 characters; contains 140 characters |
Constants
| Name | Value |
|---|---|
| TYPE_FIXED | 0 |
| TYPE_VARIABLE | 1 |
| POSITION_ANY | 'any' |
| POSITION_NTERM | 'N-term' |
| POSITION_CTERM | 'C-term' |
| POSITION_PROTEIN_NTERM | 'Prot-N-term' |
| POSITION_PROTEIN_CTERM | 'Prot-C-term' |
Members
private
- $accession
—
string
Accession (HUPO-PSI format) for this modification - $averageMass
- $location
- $monoisotopicMass
- $name
- $position
- $residues
- $type
Methods
public
- getAccession() — Gets the accession for this modification if present
- getAverageMass()
- getLocation() — Gets the location of this modification
- getMonoisotopicMass() — Gets the monoisotopic mass
- getName() — Gets this name of this instance
- getPosition()
- getResidues() — Gets the residues the modification is assosciated with
- getType()
- isFixed()
- isVariable()
- setAccession() — Sets the accession for this modification.
- setAverageMass()
- setLocation() — Sets the location for this modification
- setMonoisotopicMass() — Sets the monoisotopic mass for this modification
- setName()
- setPosition() — Sets the position this modification can occur on within the peptide or protein.
- setResidues() — Set residues for this modification
- setType()
History
-
2019-04-01T14:53:41+01:00 (commit #cc91234)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats. Should be better suited for PEFF
-
2018-09-25T17:46:03+01:00 (commit #291246d)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed modification residues allowing [ and ] Added support for protein decoys in mzidentml
-
2017-10-24T16:05:10+01:00 (commit #b2240f0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked PHPMD rules
-
2017-10-12T10:12:32+01:00 (commit #df688f9)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
* Added support for modification accession value
-
2017-09-28T13:18:16+01:00 (commit #3acafbc)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed modification not allowing integer masses Fixed MS-GF+ Search not encapsulating file paths with quotes
-
2017-08-08T18:42:00+01:00 (commit #2b783b9)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added modification support to fragmenters Fixed null pointer if residues was not set before a get residues call
-
2017-07-13T11:22:57+01:00 (commit #59351c4)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Removed deprecated methods Fixed comments Added further method validation
-
2017-07-03T17:46:48+01:00 (commit #58326dd)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional unit tests
-
2017-04-19T18:15:41+01:00 (commit #856a8a6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated Peptide/Modification to use methods from CrowdSourcing
-
2017-04-19T17:02:35+01:00 (commit #81c98fa)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
2017-04-19T16:43:03+01:00 (commit #ba22061)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed unit tests
-
2017-04-18T17:01:19+01:00 (commit #6727a89)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional MzIdentML parser support Partitioned code to allow branching between 1.1/1.2
-
2017-04-13T15:55:22+01:00 (commit #02f8b48)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Addded adapter code to translate between MzIdentML and MSGF params
-
2017-04-12T18:00:04+01:00 (commit #7965bf5)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added first pass of MzIdentML reader