pgb_liv\php_ms\Core\ModifiableSequenceInterface
Interface to common properties for a modifiable sequence object, such as peptide or protein sequence
- Author: Andrew Collins
Synopsis
interface ModifiableSequenceInterface
{
- // methods
- public void setSequence()
- public string getSequence()
- public void addModification()
- public void addModifications()
- public array getModifications()
- public void clearModifications()
- public boolean isModified()
- public void setIsDecoy()
- public boolean isDecoy()
- public int getLength()
- public double getMass()
- public double getMonoisotopicMass()
- public void getMonoisotopicMassCharge()
- public void reverseSequence()
Methods
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
- reverseSequence() — Reverses the current sequence.
- setIsDecoy() — Sets whether this sequence is a decoy sequence
- setSequence() — Sets the sequence for this object