Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
|
com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.experiment.identification.protein_inference.proteintree.kenneth | |
com.compomics.util.gui.searchsettings | |
com.compomics.util.protein |
The classes in this package concern useful Objects and their
operations for modelling and handling proteins.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeFactory.getEnzyme(java.lang.String enzymeName)
Returns the enzyme corresponding to the given name.
|
Enzyme |
EnzymeFactory.getUtilitiesEnzyme(java.lang.String prideEnzymeName)
Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA
enzyme.
|
Modifier and Type | Method and Description |
---|---|
java.util.ArrayList<Enzyme> |
EnzymeFactory.getEnzymes()
Get the imported enzymes.
|
Modifier and Type | Method and Description |
---|---|
void |
EnzymeFactory.addEnzyme(Enzyme enzyme)
Adds an enzyme in the factory.
|
boolean |
Enzyme.equals(Enzyme otherEnzyme)
Returns true of the two enzymes are identical.
|
int |
Protein.getNCleavageSites(Enzyme enzyme)
Returns the number of cleavage sites.
|
int |
Peptide.getNMissedCleavages(Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme.
|
static int |
Peptide.getNMissedCleavages(java.lang.String sequence,
Enzyme enzyme)
Returns the number of missed cleavages using the specified enzyme for the
given sequence.
|
int |
Protein.getObservableLength(Enzyme enzyme,
int pepMaxLength)
Returns the number of observable amino acids in the sequence.
|
boolean |
Protein.isEnzymaticPeptide(java.lang.String peptideSequence,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
SearchParameters.getEnzyme()
Returns the enzyme used for digestion.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ProteinMatch.hasEnzymaticPeptide(java.lang.String accession,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Indicates whether the protein group has an enzymatic peptide when
considering the given accession as main accession.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
Modifier and Type | Field and Description |
---|---|
protected Enzyme |
ProteinTree.SequenceIndexer.enzyme
The enzyme to use.
|
Modifier and Type | Method and Description |
---|---|
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
ProteinTree.SequenceIndexer.getTagToIndexesMap(java.lang.String sequence,
java.util.ArrayList<java.lang.String> tags,
Enzyme enzyme)
Returns all the positions of the given tags on the given sequence in
a map: tag -> list of indexes in the sequence.
|
protected void |
ProteinTree.importDb(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Imports the db which is in the sequence factory into the tree and saves
it in the nodeFactory.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean printExpectedImportTime,
boolean displayProgress)
Initiates the tree.
|
protected void |
ProteinTree.loadTags(java.util.ArrayList<java.lang.String> tags,
java.util.ArrayList<java.lang.String> accessions,
WaitingHandler waitingHandler,
int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
java.util.ArrayList<java.lang.String> loadedAccessions,
boolean displayProgress)
Loads the tags found in the given proteins in the tree and saves the end
nodes in the NodeFactory if not null.
|
Constructor and Description |
---|
ProteinTree.SequenceIndexer(java.util.concurrent.BlockingQueue<Protein> proteinQueue,
java.util.ArrayList<java.lang.String> tags,
int initialTagSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Enzyme |
EnzymeSelectionDialog.getEnzyme()
Returns the selected enzyme.
|
Constructor and Description |
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Enzyme(Enzyme enzyme,
int maxMissedCleavages)
Creates a new Enzyme from a com.compomics.util.experiment.biology.Enzyme
enzyme and the maximum number of missed cleavages.
|
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