Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.experiment.identification.tags |
Modifier and Type | Method and Description |
---|---|
AminoAcidSequence |
Peptide.getSequenceAsAminoAcidSequence()
Returns the sequence of this peptide as AminoAcidSequence.
|
static AminoAcidSequence |
Peptide.getSequenceAsAminoAcidSequence(String sequence)
Returns the given sequence as AminoAcidSequence.
|
AminoAcidSequence |
AminoAcidSequence.reverse()
Returns an amino acid sequence which is a reversed version of the current
pattern.
|
Modifier and Type | Method and Description |
---|---|
void |
AminoAcidSequence.append(AminoAcidSequence otherSequence)
Appends another sequence at the end of this sequence.
|
int |
AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
boolean |
AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence has a matching sequence.
|
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence targets the same sequence without
accounting for PTM localization.
|
boolean |
AminoAcidSequence.matches(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence is found in the given amino acid sequence.
|
Constructor and Description |
---|
AminoAcidPattern(AminoAcidSequence aminoAcidSequence)
Creates an amino acid pattern based on the given amino acid sequence.
|
AminoAcidSequence(AminoAcidSequence sequence)
Creates a sequence from another sequence.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,HashMap<String,ArrayList<Integer>>> |
Node.getProteinMapping(AminoAcidSequence query,
String currentSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
void |
Tag.addAminoAcidSequence(AminoAcidSequence aminoAcidSequence)
Adds a sequence of amino acids to the tag.
|
Constructor and Description |
---|
Tag(double nTermGap,
AminoAcidSequence sequenceTag,
double cTermGap)
Constructor for a tag consisting of a sequence tag between two mass tags.
|
Copyright © 2014. All rights reserved.