Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
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com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
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Modifier and Type | Method and Description |
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AminoAcidSequence |
Peptide.getSequenceAsAminoAcidSequence()
Returns the sequence of this peptide as AminoAcidSequence.
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static AminoAcidSequence |
Peptide.getSequenceAsAminoAcidSequence(String sequence)
Returns the given sequence as AminoAcidSequence.
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AminoAcidSequence |
AminoAcidSequence.reverse()
Returns an amino acid sequence which is a reversed version of the current
pattern.
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Modifier and Type | Method and Description |
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void |
AminoAcidSequence.appendCTerm(AminoAcidSequence otherSequence)
Appends another sequence at the end of this sequence.
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void |
AminoAcidSequence.appendNTerm(AminoAcidSequence otherSequence)
Appends another sequence at the beginning of this sequence keeping the
original order.
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int |
AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
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void |
AminoAcidSequence.insert(int offset,
AminoAcidSequence otherSequence)
Inserts another sequence in this sequence.
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boolean |
AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence has a matching sequence.
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boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence targets the same sequence without
accounting for PTM localization.
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boolean |
AminoAcidSequence.matches(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence matches the given amino acid sequence in
size and according to the given matching preferences.
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boolean |
AminoAcidSequence.matchesIn(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence is found in the given amino acid sequence.
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Constructor and Description |
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AminoAcidPattern(AminoAcidSequence aminoAcidSequence)
Creates an amino acid pattern based on the given amino acid sequence.
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AminoAcidSequence(AminoAcidSequence sequence)
Creates a sequence from another sequence.
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Modifier and Type | Method and Description |
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void |
Tag.addAminoAcidSequence(AminoAcidSequence aminoAcidSequence)
Adds a sequence of amino acids to the tag.
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void |
SequenceSegment.appendTerminus(AminoAcidSequence aminoAcidSequence)
Appends an amino acid sequence to the terminus of sequencing.
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Constructor and Description |
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Tag(double nTermGap,
AminoAcidSequence sequenceTag,
double cTermGap)
Constructor for a tag consisting of a sequence tag between two mass tags.
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Modifier and Type | Method and Description |
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HashMap<String,HashMap<String,ArrayList<Integer>>> |
Node.getProteinMapping(AminoAcidSequence query,
String currentSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
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