public class TagMatcher extends Object
Constructor and Description |
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TagMatcher() |
Modifier and Type | Method and Description |
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static HashMap<Integer,ArrayList<Peptide>> |
getPeptideMatches(Tag tag,
String sequence,
int tagIndex,
int componentIndex,
SequenceMatchingPreferences sequenceMatchingPreferences,
double massTolerance,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean reportFixedPtms)
Returns the possible peptides which can be created on this sequence
indexed by their start index.
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public static HashMap<Integer,ArrayList<Peptide>> getPeptideMatches(Tag tag, String sequence, int tagIndex, int componentIndex, SequenceMatchingPreferences sequenceMatchingPreferences, double massTolerance, ArrayList<String> fixedModifications, ArrayList<String> variableModifications, boolean reportFixedPtms)
tag
- the tag to look forsequence
- the sequence where to look for the tagtagIndex
- the index where the tag is locatedcomponentIndex
- the index of the component of the tag indexed by
tagIndex in the content listsequenceMatchingPreferences
- the sequence matching preferencesmassTolerance
- the ms2 tolerancefixedModifications
- the fixed modifications to considervariableModifications
- the variable modifications to considerreportFixedPtms
- a boolean indicating whether fixed PTMs should be
reported in the Peptide objectCopyright © 2014. All rights reserved.