public class Peptide extends ExperimentObject
Modifier and Type | Field and Description |
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static String |
MODIFICATION_LOCALIZATION_SEPARATOR
Separator preceding confident localization of the confident localization
of a modification
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static String |
MODIFICATION_SEPARATOR
Separator used to separate modifications in peptide keys
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Constructor and Description |
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Peptide()
Constructor for the peptide.
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Peptide(String aSequence,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide.
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Peptide(String aSequence,
Double mass,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Deprecated.
use the constructor without mass. The mass will be
recalculated.
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Modifier and Type | Method and Description |
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void |
addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match.
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void |
clearModificationMatches()
Clears the list of imported modification matches.
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void |
estimateTheoreticMass()
Estimates the theoretic mass of the peptide.
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String |
getCTerminal()
Returns the C-terminal of the peptide as a String.
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HashMap<Integer,ArrayList<String>> |
getIndexedFixedModifications()
Returns an indexed map of all fixed modifications amino acid, (1 is the
first) -> list of modification names.
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String |
getKey()
Returns the index of a peptide.
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Double |
getMass()
Getter for the mass.
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static int |
getModificationCount(String peptideKey,
String modification)
Returns how many of the given modification was found in the given
peptide.
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static ArrayList<String> |
getModificationFamily(String peptideKey)
Returns a list of names of the variable modifications found in the key of
a peptide.
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ArrayList<ModificationMatch> |
getModificationMatches()
Getter for the modifications carried by this peptide.
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ArrayList<Integer> |
getModifiedIndexes()
Returns the indexes of the residues in the peptide that contain at least
one modification.
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int |
getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
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static int |
getNMissedCleavages(String sequence,
Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
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static ArrayList<Integer> |
getNModificationLocalized(String peptideKey,
String modification)
Returns the list of modifications confidently localized or inferred for
the peptide indexed by the given key.
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String |
getNTerminal()
Returns the N-terminal of the peptide as a String.
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ArrayList<String> |
getParentProteins()
Getter for the parent proteins.
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ArrayList<Integer> |
getPotentialModificationSites(PTM ptm)
Returns the potential modification sites as an ordered list of string.
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static ArrayList<Integer> |
getPotentialModificationSites(String sequence,
PTM ptm)
Returns the potential modification sites as an ordered list of string.
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String |
getSequence()
Getter for the sequence.
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static String |
getSequence(String peptideKey)
Returns the sequence of the peptide indexed by the given key.
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String |
getTaggedModifiedSequence(ModificationProfile modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
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static String |
getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
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ArrayList<String> |
isCterm()
Returns a list of proteins where this peptide can be found in the
C-terminus.
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boolean |
isModifiable(PTM ptm)
Indicates whether the given modification can be found on the peptide.
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static boolean |
isModified(String peptideKey)
Returns a boolean indicating whether the peptide has variable
modifications based on its key.
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static boolean |
isModified(String peptideKey,
String modification)
Returns a boolean indicating whether the peptide has the given variable
modification based on its key.
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ArrayList<String> |
isNterm()
Returns a list of proteins where this peptide can be found in the
N-terminus.
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boolean |
isSameAs(Peptide anotherPeptide)
A method which compares two peptides.
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boolean |
sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
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void |
setParentProteins(ArrayList<String> parentProteins)
Sets the parent proteins.
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addUrParam, getParameterKey, getUrParam
public static String MODIFICATION_LOCALIZATION_SEPARATOR
public static String MODIFICATION_SEPARATOR
public Peptide()
public Peptide(String aSequence, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications) throws IllegalArgumentException
aSequence
- The peptide sequenceparentProteins
- The parent proteins, cannot be null or emptymodifications
- The PTM of this peptideIllegalArgumentException
- Thrown if the peptide sequence contains
unknown amino acidspublic Peptide(String aSequence, Double mass, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications)
aSequence
- The peptide sequencemass
- The peptide massparentProteins
- The parent proteins, cannot be null or emptymodifications
- The PTM of this peptidepublic Double getMass()
public ArrayList<ModificationMatch> getModificationMatches()
public void clearModificationMatches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic String getSequence()
public int getNMissedCleavages(Enzyme enzyme)
enzyme
- the enzyme usedpublic static int getNMissedCleavages(String sequence, Enzyme enzyme)
sequence
- the peptide sequenceenzyme
- the enzyme usedpublic ArrayList<String> getParentProteins()
public void setParentProteins(ArrayList<String> parentProteins)
parentProteins
- the parent proteins as list, cannot be null or
emptypublic String getKey()
public static boolean isModified(String peptideKey)
peptideKey
- the peptide keypublic static boolean isModified(String peptideKey, String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static int getModificationCount(String peptideKey, String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static ArrayList<Integer> getNModificationLocalized(String peptideKey, String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static String getSequence(String peptideKey)
peptideKey
- the peptide keypublic static ArrayList<String> getModificationFamily(String peptideKey)
peptideKey
- the key of a peptidepublic boolean isModifiable(PTM ptm) throws IOException, IllegalArgumentException, InterruptedException
ptm
- the PTM of interestIOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic ArrayList<Integer> getPotentialModificationSites(PTM ptm) throws IOException, IllegalArgumentException, InterruptedException
ptm
- the PTM consideredIOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic static ArrayList<Integer> getPotentialModificationSites(String sequence, PTM ptm) throws IllegalArgumentException
sequence
- the sequence of the peptide of interestptm
- the PTM consideredIllegalArgumentException
public boolean isSameAs(Peptide anotherPeptide)
anotherPeptide
- another peptidepublic boolean sameModificationsAs(Peptide anotherPeptide)
anotherPeptide
- another peptidepublic String getNTerminal()
public String getCTerminal()
public String getTaggedModifiedSequence(ModificationProfile modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
modificationProfile
- the modification profile of the searchuseHtmlColorCoding
- if true, color coded HTML is used, otherwise
PTM tags, e.g, <mox>, are usedincludeHtmlStartEndTags
- if true, start and end HTML tags are addeduseShortName
- if true the short names are used in the tagspublic static String getTaggedModifiedSequence(ModificationProfile modificationProfile, Peptide peptide, HashMap<Integer,ArrayList<String>> mainModificationSites, HashMap<Integer,ArrayList<String>> secondaryModificationSites, HashMap<Integer,ArrayList<String>> fixedModificationSites, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
modificationProfile
- the modification profile of the searchincludeHtmlStartEndTags
- if true, start and end HTML tags are addedpeptide
- the peptide to annotatemainModificationSites
- the main variable modification sites in a
map: aa number -> list of modifications (1 is the first AA) (can be null)secondaryModificationSites
- the secondary variable modification
sites in a map: aa number -> list of modifications (1 is the first AA)
(can be null)fixedModificationSites
- the fixed modification sites in a map: aa
number -> list of modifications (1 is the first AA) (can be null)useHtmlColorCoding
- if true, color coded HTML is used, otherwise
PTM tags, e.g, <mox>, are useduseShortName
- if true the short names are used in the tagspublic ArrayList<Integer> getModifiedIndexes()
public HashMap<Integer,ArrayList<String>> getIndexedFixedModifications()
public void estimateTheoreticMass() throws IllegalArgumentException
IllegalArgumentException
- if the peptide sequence contains unknown
amino acidspublic ArrayList<String> isNterm() throws IOException, IllegalArgumentException, InterruptedException
IOException
- exception thrown whenever an error occurred while
reading the protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading the protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading the protein sequencepublic ArrayList<String> isCterm() throws IOException, IllegalArgumentException, InterruptedException
IOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceCopyright © 2013. All Rights Reserved.