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<ModificationMatch> modifications)
Constructor for the peptide.
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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 reference key of a peptide.
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static String |
getKey(String sequence,
ArrayList<ModificationMatch> modificationMatches)
Returns the reference key of a peptide.
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Double |
getMass()
Getter for the mass.
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String |
getMatchingKey(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a unique key for the peptide when considering the given matching
preferences.
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static int |
getModificationCount(String peptideKey,
Double modificationMass)
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 masses 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 variable modification.
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ArrayList<Integer> |
getModifiedIndexes(boolean excludeFixed)
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,
Double ptmMass)
Returns the list of modifications confidently localized or inferred for
the peptide indexed by the given key.
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int |
getNModifications()
Returns the number of modifications carried by this peptide.
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static Peptide |
getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
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String |
getNTerminal()
Returns the N-terminal of the peptide as a String.
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int |
getNVariableModifications(double modificationMass)
Returns the number of variable modifications found with the given mass.
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ArrayList<String> |
getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
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ArrayList<String> |
getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein.
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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.
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ArrayList<String> |
getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
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ArrayList<String> |
getParentProteinsCreateTree(SequenceMatchingPreferences sequenceMatchingPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
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.
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ArrayList<String> |
getParentProteinsNoRemapping()
Returns the parent proteins without remapping them.
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static String |
getPeptideModificationsAsString(Peptide peptide,
boolean variablePtms)
Returns the peptide modifications as a string.
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ArrayList<Integer> |
getPotentialModificationSites(Double ptmMass,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Returns the potential modification sites as an ordered list of string.
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ArrayList<Integer> |
getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
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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AminoAcidSequence |
getSequenceAsAminoAcidSequence()
Returns the sequence of this peptide as AminoAcidSequence.
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static AminoAcidSequence |
getSequenceAsAminoAcidSequence(String sequence)
Returns the given sequence as AminoAcidSequence.
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AminoAcidPattern |
getSequenceAsPattern()
Returns the sequence of this peptide as AminoAcidPattern.
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static AminoAcidPattern |
getSequenceAsPattern(String sequence)
Returns the given sequence as AminoAcidPattern.
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String |
getSequenceWithLowerCasePtms()
Returns the peptide sequence as a String where the modified residues are
in lower case.
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String |
getTaggedModifiedSequence(PtmSettings 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(PtmSettings 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>.
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static String |
getTaggedModifiedSequence(PtmSettings 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>.
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ArrayList<String> |
isCterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
C-terminus.
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boolean |
isDecoy(SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether a peptide can be derived from a decoy protein.
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boolean |
isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
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boolean |
isModified()
Indicates whether a peptide carries modifications.
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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,
Double modificationMass)
Returns a boolean indicating whether the peptide has the given variable
modification based on its key.
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ArrayList<String> |
isNterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
N-terminus.
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boolean |
isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
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boolean |
isSameSequence(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
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boolean |
isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
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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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boolean |
sameModificationsAs(Peptide anotherPeptide,
ArrayList<String> ptms)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
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void |
setModificationMatches(ArrayList<ModificationMatch> modificationMatches)
Sets new modification matches for the peptide.
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void |
setParentProteins(ArrayList<String> parentProteins)
Sets the parent proteins.
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addUrParam, getParameterKey, getUrParam
public static final String MODIFICATION_LOCALIZATION_SEPARATOR
public static final String MODIFICATION_SEPARATOR
public Peptide()
public Peptide(String aSequence, ArrayList<ModificationMatch> modifications) throws IllegalArgumentException
aSequence
- the peptide sequence, assumed to be in upper case onlymodifications
- the PTM of this peptideIllegalArgumentException
- if the peptide sequence contains unknown
amino acidspublic 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
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.public 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
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.public ArrayList<String> getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, SQLException, ClassNotFoundException
sequenceMatchingPreferences
- the sequence matching preferencesIOException
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.public ArrayList<String> getParentProteinsCreateTree(SequenceMatchingPreferences sequenceMatchingPreferences, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) throws IOException, InterruptedException, SQLException, ClassNotFoundException
sequenceMatchingPreferences
- the sequence matching preferenceswaitingHandler
- the waiting handler used to display progress to the
user and cancel the process. Can be null but strongly recommended.exceptionHandler
- handler for the exceptions encountered while
creating the treeIOException
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.public 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
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.public 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 boolean isModified()
public static boolean isModified(String peptideKey)
peptideKey
- the peptide keypublic static boolean isModified(String peptideKey, Double modificationMass)
peptideKey
- the peptide keymodificationMass
- the mass 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 int getNModifications()
public 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, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PtmSettings modificationProfile) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
ptmMass
- the mass of the potential PTMsequenceMatchingPreferences
- the sequence matching preferences for
peptide to protein mappingptmSequenceMatchingPreferences
- the sequence matching preferences
for PTM to peptide mappingmodificationProfile
- 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, SequenceMatchingPreferences ptmSequenceMatchingPreferences) throws IOException, InterruptedException, ClassNotFoundException, SQLException
ptm
- the PTM consideredsequenceMatchingPreferences
- the sequence matching preferences for
peptide to protein mappingptmSequenceMatchingPreferences
- the sequence matching preferences
for PTM to peptide mappingIOException
- exception thrown whenever an error occurred while
interacting with a file while mapping potential modification sitesInterruptedException
- exception thrown whenever a threading issue
occurred while mapping potential modification sitesClassNotFoundException
- exception thrown whenever an error
occurred while deserializing an object from the ProteinTreeSQLException
- exception thrown whenever an error occurred while
interacting with the ProteinTreepublic 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(PtmSettings 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(PtmSettings 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(PtmSettings 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 static String getPeptideModificationsAsString(Peptide peptide, boolean variablePtms)
peptide
- the peptidevariablePtms
- if true, only variable PTMs are shown, false return
only the fixed PTMspublic 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 © 2016. All rights reserved.