Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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Modifier and Type | Method and Description |
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ArrayList<ModificationMatch> |
Peptide.getModificationMatches()
Getter for the modifications carried by this peptide.
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HashMap<Integer,ArrayList<ModificationMatch>> |
AminoAcidPattern.getModificationMatches()
Getter for the modifications carried by this sequence.
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ArrayList<ModificationMatch> |
AminoAcidPattern.getModificationsAt(int localization)
Returns the modifications found at a given localization.
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Modifier and Type | Method and Description |
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void |
AminoAcidPattern.addModificationMatch(int localization,
ModificationMatch modificationMatch)
Adds a modification to one of the amino acid pattern.
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void |
Peptide.addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match.
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void |
AminoAcidPattern.changeModificationSite(ModificationMatch modificationMatch,
int oldLocalization,
int newLocalization)
Changes the localization of a modification match.
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Modifier and Type | Method and Description |
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void |
AminoAcidPattern.addModificationMatches(int localization,
ArrayList<ModificationMatch> modificationMatches)
Adds a list of modifications to one of the amino acid pattern.
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static String |
Peptide.getKey(String sequence,
ArrayList<ModificationMatch> modificationMatches)
Returns the reference key of a peptide.
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Constructor and Description |
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Peptide(String aSequence,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide.
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Peptide(String aSequence,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Deprecated.
use peptide without proteins and remap the peptide to the
proteins a posteriori instead
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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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boolean |
ModificationMatch.isSameAs(ModificationMatch anotherModificationMatch)
Indicates whether this modification match is the same of another one.
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