Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
Modifier and Type | Method and Description |
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ArrayList<ModificationMatch> |
Peptide.getModificationMatches()
Getter for the modifications carried by this peptide.
|
HashMap<Integer,ArrayList<ModificationMatch>> |
AminoAcidSequence.getModificationMatches()
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
|
HashMap<Integer,ArrayList<ModificationMatch>> |
AminoAcidPattern.getModificationMatches()
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
|
ArrayList<ModificationMatch> |
AminoAcidSequence.getModificationsAt(int localization)
Returns the modifications found at a given localization.
|
ArrayList<ModificationMatch> |
AminoAcidPattern.getModificationsAt(int localization)
Returns the modifications found at a given localization.
|
Modifier and Type | Method and Description |
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void |
AminoAcidSequence.addModificationMatch(int localization,
ModificationMatch modificationMatch)
Adds a modification to one of the amino acid sequence.
|
void |
AminoAcidPattern.addModificationMatch(int localization,
ModificationMatch modificationMatch)
Adds a modification to one of the amino acid pattern.
|
void |
Peptide.addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match.
|
void |
AminoAcidSequence.changeModificationSite(ModificationMatch modificationMatch,
int oldLocalization,
int newLocalization)
Changes the localization of a modification match.
|
void |
AminoAcidPattern.changeModificationSite(ModificationMatch modificationMatch,
int oldLocalization,
int newLocalization)
Changes the localization of a modification match.
|
void |
AminoAcidSequence.removeModificationMatch(int localisation,
ModificationMatch modificationMatch)
Removes a modification match in the given sequence.
|
void |
AminoAcidPattern.removeModificationMatch(int localisation,
ModificationMatch modificationMatch)
Removes a modification match in the given pattern.
|
Modifier and Type | Method and Description |
---|---|
void |
AminoAcidSequence.addModificationMatches(int localization,
ArrayList<ModificationMatch> modificationMatches)
Adds a list of modifications to one of the amino acid sequence.
|
void |
AminoAcidPattern.addModificationMatches(int localization,
ArrayList<ModificationMatch> modificationMatches)
Adds a list of modifications to one of the amino acid pattern.
|
static String |
Peptide.getKey(String sequence,
ArrayList<ModificationMatch> modificationMatches)
Returns the reference key of a peptide.
|
void |
Peptide.setModificationMatches(ArrayList<ModificationMatch> modificationMatches)
Sets new modification matches for the peptide.
|
Constructor and Description |
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AminoAcidSequence(String sequence,
HashMap<Integer,ArrayList<ModificationMatch>> modifications)
Constructor taking a sequence of amino acids as input.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<Peptide>> |
TagMatcher.buildPeptides(String sequence,
ArrayList<SequenceSegment> nTermPossibleSequences,
String seedSequence,
ArrayList<SequenceSegment> cTermPossibleSequences,
HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex,
int mutationsAtIndex)
Builds the possible peptides based on the given terminal segments and the
seed sequence.
|
Modifier and Type | Method and Description |
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ModificationMatch |
ModificationMatch.clone()
Clones the modification match into a new match with the same attributes.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ModificationMatch.isSameAs(ModificationMatch anotherModificationMatch)
Indicates whether this modification match is the same of another one.
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