com.compomics.util.experiment.biology
Class Peptide

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Peptide
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class Peptide
extends ExperimentObject

This class models a peptide.

Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:56:40 AM

See Also:
Serialized Form

Constructor Summary
Peptide()
          Constructor for the peptide
Peptide(java.lang.String aSequence, java.lang.Double mass, java.util.ArrayList<java.lang.String> parentProteins, java.util.ArrayList<ModificationMatch> modifications)
          Constructor for the peptide
 
Method Summary
 void addModificationMatch(ModificationMatch modificationMatch)
          Adds a modification match
 void clearModificationMAtches()
          Clears the list of imported modification matches
 java.lang.String getCTerminal()
          Returns the C-terminal of the peptide as a String.
 java.lang.String getKey()
          Returns the index of a peptide. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically.
 java.lang.Double getMass()
          getter for the mass
static java.util.ArrayList<java.lang.String> getModificationFamily(java.lang.String peptideKey)
          Returns a list of names of the variable modifications found in the key of a peptide
 java.util.ArrayList<ModificationMatch> getModificationMatches()
          getter for the modifications carried by this peptide
 int getNMissedCleavages(Enzyme enzyme)
          Returns the amount of missed cleavages using the specified enzyme
static int getNMissedCleavages(java.lang.String sequence, Enzyme enzyme)
          Returns the amount of missed cleavages using the specified enzyme for the given sequence
 java.lang.String getNTerminal()
          Returns the N-terminal of the peptide as a String.
 java.util.ArrayList<java.lang.String> getParentProteins()
          Getter for the parent proteins
 java.lang.String getSequence()
          getter for the sequence
static java.lang.String getSequence(java.lang.String peptideKey)
          Returns the sequence of the peptide indexed by the given key
static boolean isModified(java.lang.String peptideKey)
          Returns a boolean indicating whether the peptide has variable modifications based on its key
 boolean isSameAs(Peptide anotherPeptide)
          a method which compares to peptides.
 boolean sameModificationsAs(Peptide anotherPeptide)
          Indicates whether another peptide has the same modifications at the same localization as this peptide.
 void setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
          Sets the parent proteins
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Peptide

public Peptide()
Constructor for the peptide


Peptide

public Peptide(java.lang.String aSequence,
               java.lang.Double mass,
               java.util.ArrayList<java.lang.String> parentProteins,
               java.util.ArrayList<ModificationMatch> modifications)
Constructor for the peptide

Parameters:
aSequence - The peptide sequence
mass - The peptide mass
parentProteins - The parent proteins
modifications - The PTM of this peptide
Method Detail

getMass

public java.lang.Double getMass()
getter for the mass

Returns:
the peptide mass

getModificationMatches

public java.util.ArrayList<ModificationMatch> getModificationMatches()
getter for the modifications carried by this peptide

Returns:
the modifications matches as found by the search engine

clearModificationMAtches

public void clearModificationMAtches()
Clears the list of imported modification matches


addModificationMatch

public void addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match

Parameters:
modificationMatch - the modification match to add

getSequence

public java.lang.String getSequence()
getter for the sequence

Returns:
the peptide sequence

getNMissedCleavages

public int getNMissedCleavages(Enzyme enzyme)
Returns the amount of missed cleavages using the specified enzyme

Parameters:
enzyme - the enzyme used
Returns:
the amount of missed cleavages

getNMissedCleavages

public static int getNMissedCleavages(java.lang.String sequence,
                                      Enzyme enzyme)
Returns the amount of missed cleavages using the specified enzyme for the given sequence

Parameters:
enzyme - the enzyme used
Returns:
the amount of missed cleavages

getParentProteins

public java.util.ArrayList<java.lang.String> getParentProteins()
Getter for the parent proteins

Returns:
the parent proteins

setParentProteins

public void setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
Sets the parent proteins

Parameters:
parentProteins - the parent proteins as list

getKey

public java.lang.String getKey()
Returns the index of a peptide. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically.

Returns:
the index of a peptide

isModified

public static boolean isModified(java.lang.String peptideKey)
Returns a boolean indicating whether the peptide has variable modifications based on its key

Parameters:
peptideKey - the peptide key
Returns:
a boolean indicating whether the peptide has variable modifications

getSequence

public static java.lang.String getSequence(java.lang.String peptideKey)
Returns the sequence of the peptide indexed by the given key

Parameters:
peptideKey - the peptide key
Returns:
the corresponding sequence

getModificationFamily

public static java.util.ArrayList<java.lang.String> getModificationFamily(java.lang.String peptideKey)
Returns a list of names of the variable modifications found in the key of a peptide

Parameters:
peptideKey - the key of a peptide
Returns:
a list of names of the variable modifications found in the key

isSameAs

public boolean isSameAs(Peptide anotherPeptide)
a method which compares to peptides. Two same peptides present the same sequence and same modifications at the same place.

Parameters:
anOtherPeptide - another peptide
Returns:
a boolean indicating if the other peptide is the same.

sameModificationsAs

public boolean sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same localization as this peptide. This method comes as a complement of isSameAs which does not account for PTM location.

Parameters:
anotherPeptide - another peptide
Returns:
true if the other peptide has the same positions at the same location as the considered peptide

getNTerminal

public java.lang.String getNTerminal()
Returns the N-terminal of the peptide as a String. Returns "NH3" if the terminal is not modified, otherwise returns the name of the modification.

Returns:
the N-terminal of the peptide as a String, e.g., "NH3"

getCTerminal

public java.lang.String getCTerminal()
Returns the C-terminal of the peptide as a String. Returns "COOH" if the terminal is not modified, otherwise returns the name of the modification.

Returns:
the C-terminal of the peptide as a String, e.g., "COOH"


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