public class Peptide extends ExperimentObject
Modifier and Type | Field and Description |
---|---|
static String |
MODIFICATION_LOCALIZATION_SEPARATOR
Separator preceding confident localization of the confident localization
of a modification
|
static String |
MODIFICATION_SEPARATOR
Separator used to separate modifications in peptide keys
|
Constructor and Description |
---|
Peptide()
Constructor for the peptide.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide.
|
Peptide(String aSequence,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Deprecated.
use peptide without proteins and remap the peptide to the
proteins a posteriori instead
|
Peptide(String aSequence,
Double mass,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Deprecated.
use the constructor without mass. The mass will be
recalculated.
|
Modifier and Type | Method and Description |
---|---|
void |
addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match.
|
void |
clearModificationMatches()
Clears the list of imported modification matches.
|
void |
estimateTheoreticMass()
Estimates the theoretic mass of the peptide.
|
String |
getCTerminal()
Returns the C-terminal of the peptide as a String.
|
HashMap<Integer,ArrayList<String>> |
getIndexedFixedModifications()
Returns an indexed map of all fixed modifications amino acid, (1 is the
first) > list of modification names.
|
String |
getKey()
Returns the reference key of a peptide.
|
static String |
getKey(String sequence,
ArrayList<ModificationMatch> modificationMatches)
Returns the reference key of a peptide.
|
Double |
getMass()
Getter for the mass.
|
String |
getMatchingKey(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a unique key for the peptide when considering the given matching
preferences.
|
static int |
getModificationCount(String peptideKey,
Double modificationMass)
Returns how many of the given modification was found in the given
peptide.
|
static ArrayList<String> |
getModificationFamily(String peptideKey)
Returns a list of masses of the variable modifications found in the key
of a peptide.
|
ArrayList<ModificationMatch> |
getModificationMatches()
Getter for the modifications carried by this peptide.
|
ArrayList<Integer> |
getModifiedIndexes()
Returns the indexes of the residues in the peptide that contain at least
one variable modification.
|
ArrayList<Integer> |
getModifiedIndexes(boolean excludeFixed)
Returns the indexes of the residues in the peptide that contain at least
one modification.
|
int |
getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
|
static int |
getNMissedCleavages(String sequence,
Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
|
static ArrayList<Integer> |
getNModificationLocalized(String peptideKey,
Double ptmMass)
Returns the list of modifications confidently localized or inferred for
the peptide indexed by the given key.
|
static Peptide |
getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
String |
getNTerminal()
Returns the N-terminal of the peptide as a String.
|
int |
getNVariableModifications(double modificationMass)
Returns the number of variable modifications found with the given mass.
|
ArrayList<String> |
getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
|
ArrayList<String> |
getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein.
|
ArrayList<String> |
getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set using the default protein tree of the sequence
factory.
|
ArrayList<String> |
getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
|
ArrayList<String> |
getParentProteinsNoRemapping()
Returns the parent proteins without remapping them.
|
ArrayList<Integer> |
getPotentialModificationSites(Double ptmMass,
SequenceMatchingPreferences sequenceMatchingPreferences,
ModificationProfile modificationProfile)
Returns the potential modification sites as an ordered list of string.
|
ArrayList<Integer> |
getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
String |
getSequence()
Getter for the sequence.
|
static String |
getSequence(String peptideKey)
Returns the sequence of the peptide indexed by the given key.
|
AminoAcidSequence |
getSequenceAsAminoAcidSequence()
Returns the sequence of this peptide as AminoAcidSequence.
|
static AminoAcidSequence |
getSequenceAsAminoAcidSequence(String sequence)
Returns the given sequence as AminoAcidSequence.
|
AminoAcidPattern |
getSequenceAsPattern()
Returns the sequence of this peptide as AminoAcidPattern.
|
static AminoAcidPattern |
getSequenceAsPattern(String sequence)
Returns the given sequence as AminoAcidPattern.
|
String |
getSequenceWithLowerCasePtms()
Returns the peptide sequence as a String where the modified residues are
in lower case.
|
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>.
|
String |
getTaggedModifiedSequence(ModificationProfile modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
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>.
|
ArrayList<String> |
isCterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
C-terminus.
|
boolean |
isDecoy(SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether a peptide can be derived from a decoy protein.
|
boolean |
isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
|
static boolean |
isModified(String peptideKey)
Returns a boolean indicating whether the peptide has variable
modifications based on its key.
|
static boolean |
isModified(String peptideKey,
String modification)
Returns a boolean indicating whether the peptide has the given variable
modification based on its key.
|
ArrayList<String> |
isNterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
N-terminus.
|
boolean |
isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
|
boolean |
isSameSequence(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
boolean |
sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
boolean |
sameModificationsAs(Peptide anotherPeptide,
ArrayList<String> ptms)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
void |
setModificationMatches(ArrayList<ModificationMatch> modificationMatches)
Sets new modification matches for the peptide.
|
void |
setParentProteins(ArrayList<String> parentProteins)
Sets the parent proteins.
|
addUrParam, getParameterKey, getUrParam
public static final String MODIFICATION_LOCALIZATION_SEPARATOR
public static final 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, ArrayList<ModificationMatch> modifications) throws IllegalArgumentException
aSequence
- The peptide sequencemodifications
- 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 setModificationMatches(ArrayList<ModificationMatch> modificationMatches)
modificationMatches
- the new modification matchespublic void clearModificationMatches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic String getSequence()
public String getSequenceWithLowerCasePtms()
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(boolean remap, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, ClassNotFoundException, InterruptedException, SQLException
remap
- boolean indicating whether the peptide sequence should be
remapped to the proteins if no protein is foundsequenceMatchingPreferences
- the sequence matching preferencesIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occursSQLException
- if an SQLException occurspublic ArrayList<String> getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences, ProteinTree proteinTree) throws IOException, InterruptedException, SQLException, ClassNotFoundException
proteinTree
- the protein tree to use for peptide to protein mappingsequenceMatchingPreferences
- the sequence matching preferencesIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occursSQLException
- if an SQLException occurspublic ArrayList<String> getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, SQLException, ClassNotFoundException
sequenceMatchingPreferences
- the sequence matching preferencesIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occursSQLException
- if an SQLException occurspublic ArrayList<String> getParentProteins(boolean remap, SequenceMatchingPreferences sequenceMatchingPreferences, ProteinTree proteinTree) throws IOException, InterruptedException, SQLException, ClassNotFoundException
remap
- boolean indicating whether the peptide sequence should be
remapped to the proteins if no protein is foundsequenceMatchingPreferences
- the sequence matching preferencesproteinTree
- the protein tree to use for peptide to protein mappingIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occursSQLException
- if an SQLException occurspublic ArrayList<String> getParentProteinsNoRemapping()
public void setParentProteins(ArrayList<String> parentProteins)
parentProteins
- the parent proteins as list, cannot be null or
emptypublic String getMatchingKey(SequenceMatchingPreferences sequenceMatchingPreferences)
sequenceMatchingPreferences
- the sequence matching preferencespublic String getKey()
public static String getKey(String sequence, ArrayList<ModificationMatch> modificationMatches)
sequence
- the sequence of the peptidemodificationMatches
- list of modification matchespublic 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, Double modificationMass)
peptideKey
- the peptide keymodificationMass
- the mass of the modificationpublic int getNVariableModifications(double modificationMass)
modificationMass
- the mass of the modificationpublic static ArrayList<Integer> getNModificationLocalized(String peptideKey, Double ptmMass)
peptideKey
- the peptide keyptmMass
- the mass of the modificationpublic static String getSequence(String peptideKey)
peptideKey
- the peptide keypublic static ArrayList<String> getModificationFamily(String peptideKey)
peptideKey
- the key of a peptidepublic ArrayList<String> isNterm(SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
sequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursFileNotFoundException
- if a FileNotFoundException occurspublic ArrayList<String> isCterm(SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
sequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursFileNotFoundException
- if a FileNotFoundException occurspublic boolean isModifiable(PTM ptm, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
ptm
- the PTM of interestsequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursFileNotFoundException
- if a FileNotFoundException occurspublic ArrayList<Integer> getPotentialModificationSites(Double ptmMass, SequenceMatchingPreferences sequenceMatchingPreferences, ModificationProfile modificationProfile) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
ptmMass
- the mass of the potential PTMsequenceMatchingPreferences
- the sequence matching preferencesmodificationProfile
- the modification profile of the identificationIOException
- 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 sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursFileNotFoundException
- if a FileNotFoundException occurspublic ArrayList<Integer> getPotentialModificationSites(PTM ptm, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
ptm
- the PTM consideredsequenceMatchingPreferences
- the sequence matching preferencesIOException
- 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 sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursFileNotFoundException
- if a FileNotFoundException occurspublic boolean isSameSequenceAndModificationStatus(Peptide anotherPeptide, SequenceMatchingPreferences sequenceMatchingPreferences)
anotherPeptide
- the other peptide to compare to this instancesequenceMatchingPreferences
- the sequence matching preferencespublic boolean isSameSequence(Peptide anotherPeptide, SequenceMatchingPreferences sequenceMatchingPreferences)
anotherPeptide
- the other peptide to comparesequenceMatchingPreferences
- the sequence matching preferencespublic boolean isSameModificationStatus(Peptide anotherPeptide)
anotherPeptide
- the other peptidepublic boolean sameModificationsAs(Peptide anotherPeptide, ArrayList<String> ptms)
anotherPeptide
- another peptideptms
- the PTMspublic boolean sameModificationsAs(Peptide anotherPeptide)
anotherPeptide
- another peptidepublic String getNTerminal()
public String getCTerminal()
public String getTaggedModifiedSequence(ModificationProfile modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean excludeAllFixedPtms)
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 tagsexcludeAllFixedPtms
- if true, all fixed PTMs are excludedpublic 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>> confidentModificationSites, HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites, HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites, 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 annotateconfidentModificationSites
- the confidently localized variable
modification sites in a map: aa number > list of modifications (1 is the
first AA) (can be null)representativeAmbiguousModificationSites
- the representative site
of the ambiguously localized variable modifications in a map: aa number
> list of modifications (1 is the first AA) (can be null)secondaryAmbiguousModificationSites
- the secondary sites of the
ambiguously localized variable modifications 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 ArrayList<Integer> getModifiedIndexes(boolean excludeFixed)
excludeFixed
- exclude fixed PTMspublic HashMap<Integer,ArrayList<String>> getIndexedFixedModifications()
public void estimateTheoreticMass() throws IllegalArgumentException
IllegalArgumentException
- if the peptide sequence contains unknown
amino acidspublic AminoAcidPattern getSequenceAsPattern()
public static AminoAcidPattern getSequenceAsPattern(String sequence)
sequence
- the sequence of interestpublic AminoAcidSequence getSequenceAsAminoAcidSequence()
public static AminoAcidSequence getSequenceAsAminoAcidSequence(String sequence)
sequence
- the sequence of interestpublic boolean isDecoy(SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, SQLException, ClassNotFoundException
sequenceMatchingPreferences
- the sequence matching preferencesIOException
- exception thrown whenever an error occurred while
reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occurspublic static Peptide getNoModPeptide(Peptide peptide, ArrayList<PTM> ptms) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the original peptideptms
- list of inspected PTMsIOException
- exception thrown whenever an error occurred while
reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursCopyright © 2015. All rights reserved.