public class Peptide extends ExperimentObject
Modifier and Type | Field and Description |
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static java.lang.String |
MODIFICATION_LOCALIZATION_SEPARATOR
Separator preceding confident localization of the confident localization
of a modification
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static java.lang.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(java.lang.String aSequence,
java.util.ArrayList<java.lang.String> parentProteins,
java.util.ArrayList<ModificationMatch> modifications)
Constructor for the peptide.
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Peptide(java.lang.String aSequence,
java.lang.Double mass,
java.util.ArrayList<java.lang.String> parentProteins,
java.util.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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java.lang.String |
getCTerminal()
Returns the C-terminal of the peptide as a String.
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java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> |
getIndexedFixedModifications()
Returns an indexed map of all fixed modifications amino acid, (1 is the
first) -> list of modification names.
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java.lang.String |
getKey()
Returns the index of a peptide.
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java.lang.Double |
getMass()
Getter for the mass.
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static int |
getModificationCount(java.lang.String peptideKey,
java.lang.String modification)
Returns how many of the given modification was found in the given
peptide.
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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.
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java.util.ArrayList<ModificationMatch> |
getModificationMatches()
Getter for the modifications carried by this peptide.
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java.util.ArrayList<java.lang.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(java.lang.String sequence,
Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
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static java.util.ArrayList<java.lang.Integer> |
getNModificationLocalized(java.lang.String peptideKey,
java.lang.String modification)
Returns the list of modifications confidently localized or inferred for
the peptide indexed by the given key.
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java.lang.String |
getNTerminal()
Returns the N-terminal of the peptide as a String.
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java.util.ArrayList<java.lang.String> |
getParentProteins()
Getter for the parent proteins.
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java.util.ArrayList<java.lang.Integer> |
getPotentialModificationSites(PTM ptm)
Returns the potential modification sites as an ordered list of string.
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static java.util.ArrayList<java.lang.Integer> |
getPotentialModificationSites(java.lang.String sequence,
PTM ptm)
Returns the potential modification sites as an ordered list of string.
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java.lang.String |
getSequence()
Getter for the sequence.
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static java.lang.String |
getSequence(java.lang.String peptideKey)
Returns the sequence of the peptide indexed by the given key.
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AminoAcidPattern |
getSequenceAsPattern()
Returns the sequence of this peptide as AminoAcidPattern.
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static AminoAcidPattern |
getSequenceAsPattern(java.lang.String sequence)
Returns the given sequence as AminoAcidPattern.
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java.lang.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 java.lang.String |
getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.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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java.util.ArrayList<java.lang.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(java.lang.String peptideKey)
Returns a boolean indicating whether the peptide has variable
modifications based on its key.
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static boolean |
isModified(java.lang.String peptideKey,
java.lang.String modification)
Returns a boolean indicating whether the peptide has the given variable
modification based on its key.
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java.util.ArrayList<java.lang.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 |
isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
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boolean |
isSameSequence(Peptide anotherPeptide)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
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boolean |
isSameSequenceAndModificationStatus(Peptide anotherPeptide)
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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void |
setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
Sets the parent proteins.
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addUrParam, getParameterKey, getUrParam
public static final java.lang.String MODIFICATION_LOCALIZATION_SEPARATOR
public static final java.lang.String MODIFICATION_SEPARATOR
public Peptide()
public Peptide(java.lang.String aSequence, java.util.ArrayList<java.lang.String> parentProteins, java.util.ArrayList<ModificationMatch> modifications) throws java.lang.IllegalArgumentException
aSequence
- The peptide sequenceparentProteins
- The parent proteins, cannot be null or emptymodifications
- The PTM of this peptidejava.lang.IllegalArgumentException
- Thrown if the peptide sequence contains
unknown amino acidspublic Peptide(java.lang.String aSequence, java.lang.Double mass, java.util.ArrayList<java.lang.String> parentProteins, java.util.ArrayList<ModificationMatch> modifications)
aSequence
- The peptide sequencemass
- The peptide massparentProteins
- The parent proteins, cannot be null or emptymodifications
- The PTM of this peptidepublic java.lang.Double getMass()
public java.util.ArrayList<ModificationMatch> getModificationMatches()
public void clearModificationMatches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic java.lang.String getSequence()
public int getNMissedCleavages(Enzyme enzyme)
enzyme
- the enzyme usedpublic static int getNMissedCleavages(java.lang.String sequence, Enzyme enzyme)
sequence
- the peptide sequenceenzyme
- the enzyme usedpublic java.util.ArrayList<java.lang.String> getParentProteins()
public void setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
parentProteins
- the parent proteins as list, cannot be null or
emptypublic java.lang.String getKey()
public static boolean isModified(java.lang.String peptideKey)
peptideKey
- the peptide keypublic static boolean isModified(java.lang.String peptideKey, java.lang.String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static int getModificationCount(java.lang.String peptideKey, java.lang.String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static java.util.ArrayList<java.lang.Integer> getNModificationLocalized(java.lang.String peptideKey, java.lang.String modification)
peptideKey
- the peptide keymodification
- the name of the modificationpublic static java.lang.String getSequence(java.lang.String peptideKey)
peptideKey
- the peptide keypublic static java.util.ArrayList<java.lang.String> getModificationFamily(java.lang.String peptideKey)
peptideKey
- the key of a peptidepublic boolean isModifiable(PTM ptm) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
ptm
- the PTM of interestjava.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic java.util.ArrayList<java.lang.Integer> getPotentialModificationSites(PTM ptm) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
ptm
- the PTM consideredjava.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic static java.util.ArrayList<java.lang.Integer> getPotentialModificationSites(java.lang.String sequence, PTM ptm) throws java.lang.IllegalArgumentException
sequence
- the sequence of the peptide of interestptm
- the PTM consideredjava.lang.IllegalArgumentException
public boolean isSameAs(Peptide anotherPeptide)
anotherPeptide
- another peptidepublic boolean isSameSequenceAndModificationStatus(Peptide anotherPeptide)
anotherPeptide
- the other peptide to compare to this instancepublic boolean isSameSequence(Peptide anotherPeptide)
anotherPeptide
- the other peptide to comparepublic boolean isSameModificationStatus(Peptide anotherPeptide)
anotherPeptide
- the other peptidepublic boolean sameModificationsAs(Peptide anotherPeptide)
anotherPeptide
- another peptidepublic java.lang.String getNTerminal()
public java.lang.String getCTerminal()
public java.lang.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 java.lang.String getTaggedModifiedSequence(ModificationProfile modificationProfile, Peptide peptide, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.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 java.util.ArrayList<java.lang.Integer> getModifiedIndexes()
public java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> getIndexedFixedModifications()
public void estimateTheoreticMass() throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
- if the peptide sequence contains unknown
amino acidspublic java.util.ArrayList<java.lang.String> isNterm() throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
java.io.IOException
- exception thrown whenever an error occurred while
reading the protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading the protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading the protein sequencepublic java.util.ArrayList<java.lang.String> isCterm() throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
java.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencepublic AminoAcidPattern getSequenceAsPattern()
public static AminoAcidPattern getSequenceAsPattern(java.lang.String sequence)
sequence
- the sequence of interestCopyright © 2013. All Rights Reserved.