public class IteratorFactory extends Object
Constructor and Description |
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IteratorFactory()
Empty default constructor
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IteratorFactory(ArrayList<String> fixedModifications)
Constructor with 2 Xs allowed.
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IteratorFactory(ArrayList<String> fixedModifications,
Integer maxX)
Constructor.
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Modifier and Type | Method and Description |
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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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public IteratorFactory()
public IteratorFactory(ArrayList<String> fixedModifications, Integer maxX)
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 peptidespublic SequenceIterator getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax) throws InterruptedException
sequence
- the sequence to iteratedigestionPreferences
- the digestion preferences to usemassMin
- the minimal mass of a peptidemassMax
- the maximal mass of a peptideInterruptedException
- exception thrown if a thread is
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