Class IteratorFactory
java.lang.Object
com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
public class IteratorFactory extends Object
The iterator goes through a sequence and lists possible peptides with their
fixed modifications.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description IteratorFactory()
Empty default constructorIteratorFactory(ArrayList<String> fixedModifications)
Constructor with 2 Xs allowed.IteratorFactory(ArrayList<String> fixedModifications, Integer maxX)
Constructor. -
Method Summary
Modifier and Type Method Description SequenceIterator
getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax)
Returns a sequence iterator for the given protein sequence and digestion preferences.
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Constructor Details
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IteratorFactory
public IteratorFactory()Empty default constructor -
IteratorFactory
Constructor.- Parameters:
fixedModifications
- a list of fixed modifications to consider when iterating the protein sequences.maxX
- The maximal number of Xs allowed in a sequence to derive the possible peptides
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IteratorFactory
Constructor with 2 Xs allowed.- Parameters:
fixedModifications
- a list of fixed modifications to consider when iterating the protein sequences.
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Method Details
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getSequenceIterator
public SequenceIterator getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax) throws InterruptedExceptionReturns a sequence iterator for the given protein sequence and digestion preferences.- Parameters:
sequence
- the sequence to iteratedigestionPreferences
- the digestion preferences to usemassMin
- the minimal mass of a peptidemassMax
- the maximal mass of a peptide- Returns:
- a sequence iterator
- Throws:
InterruptedException
- exception thrown if a thread is interrupted
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