pgb_liv\php_ms\Core\Protein
A protein object that encapsulates a modifiable sequence and provides additional properties
- Author: Andrew Collins
Synopsis
- // members
- private $identifier;
- private $description;
- private Gene $gene;
- private Transcript $transcript;
- private Organism $organism;
- private Chromosome $chromosome;
- // methods
- public void setDescription()
- public void getDescription()
- public void setGene()
- public Gene getGene()
- public void setTranscript()
- public Transcript getTranscript()
- public void setOrganism()
- public Organism getOrganism()
- public void setChromosome()
- public Chromosome getChromosome()
- public string setIdentifier()
- public string getIdentifier()
- // Inherited methods from ModifiableSequenceTrait
- public void setSequence()
- public string getSequence()
- public void addModification()
- public void addModifications()
- public array getModifications()
- public void clearModifications()
- public void removeModification()
- public boolean isModified()
- public void setIsDecoy()
- public boolean isDecoy()
- public int getLength()
- public float getMass()
- public float getMonoisotopicMass()
- public void getMonoisotopicMassCharge()
- public void reverseSequence()
- // Inherited methods from DatabaseEntryTrait
- public void setDatabaseEntry()
- public DatabaseEntry getDatabaseEntry()
Hierarchy
Uses
Implements
Coverage
| Methods | 50% | 6 / 12 |
| Lines | 50% | 9 / 18 |
Tasks
| Line | Task |
|---|---|
| 276+ | This method does not yet respect modification absolute location data |
Members
private
- $chromosome — pgb_liv\php_ms\Core\Chromosome
- $description
—
string
The description or name of this sequence. - $gene — pgb_liv\php_ms\Core\Gene
- $identifier
—
string
The unique identifier for this sequence. - $organism — pgb_liv\php_ms\Core\Organism
- $transcript — pgb_liv\php_ms\Core\Transcript
Methods
public
- getChromosome()
- getDescription()
- getGene() — Gets the parent gene of this protein
- getIdentifier() — This will get the unique identifier for this sequence.
- getOrganism()
- getTranscript() — Gets the parent transcript of this protein
- setChromosome()
- setDescription()
- setGene() — Sets the parent gene of this protein
- setIdentifier() — This will get the unique identifier for this sequence.
- setOrganism()
- setTranscript() — Sets the parent transcript of this protein
Inherited from pgb_liv\php_ms\Core\ModifiableSequenceTrait
public
- addModification() — Adds the specified modification to this protein
- addModifications() — Adds the specified modifications to this protein
- clearModifications() — Clears the modifications
- getLength() — Gets the length of the sequence in this object
- getMass() — Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications
- getModifications() — Gets the modifications
- getMonoisotopicMass() — Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications
- getMonoisotopicMassCharge() — Calculates the theoretical mass/charge value for this sequence.
- getSequence() — Gets the sequence for this object
- isDecoy() — Gets whether this sequence is a decoy sequence
- isModified() — Returns whether this protein contains modifications or not
- removeModification() — Remove a modification
- reverseSequence() — Reverses the current sequence.
- setIsDecoy() — Sets whether this sequence is a decoy sequence
- setSequence() — Sets the sequence for this object
Inherited from pgb_liv\php_ms\Core\DatabaseEntryTrait
public
- getDatabaseEntry() — Gets the database entry for this instance
- setDatabaseEntry()
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
-
2018-03-02T11:23:12+00:00 (commit #18615e6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for fragmenting protein sequences Added support for reading/writing MGF precursor intensities
-
2017-10-25T14:16:01+01:00 (commit #d497193)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-10-12T11:54:29+01:00 (commit #c1a6d58)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for multiple proteins on peptide identifications Added support for Chromosome objects on proteins Added support for writing proBedFiles
-
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
-
2017-07-03T18:29:34+01:00 (commit #7a6d197)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional unit tests Fixed database name not returning the correct value
-
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
-
2017-06-30T12:56:00+01:00 (commit #60f1a8b)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed protein name not returning a value Allowed peptide sequence to be set in constructor Moved fragmentation code to separate classes
-
2017-05-31T14:38:50+01:00 (commit #68bb326)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MzML merge not updating precursor references Fixed FastaReader failing if protein did not have a description text after the identifier
-
2017-05-09T17:19:06+01:00 (commit #cfe67d8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Unimod fasta regex Added Fasta/PEFF writer support
-
2017-05-09T15:17:48+01:00 (commit #b5944dd)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated to require PHP 5.4 / added traits
-
2017-05-08T17:36:37+01:00 (commit #7de6913)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added PEFF support Added support for modifications on proteins
-
2017-02-09T16:03:57+00:00 (commit #5484745)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional coverage tests
-
2017-02-01T16:00:55+00:00 (commit #1e9884c)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Protein sequence reverse method
-
2017-01-10T17:51:30+00:00 (commit #b3dacff)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added initial Protein code Added initial Peptide code Added initial digestion code Improved Fasta and MGF tests