Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.gui |
This package contains basic GUI classes.
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Modifier and Type | Method and Description |
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AminoAcidPattern |
PTM.getPattern()
Returns the amino acid pattern targeted by this modification.
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AminoAcidPattern |
Peptide.getSequenceAsPattern()
Returns the sequence of this peptide as AminoAcidPattern.
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static AminoAcidPattern |
Peptide.getSequenceAsPattern(String sequence)
Returns the given sequence as AminoAcidPattern.
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AminoAcidPattern |
AminoAcidPattern.getStandardSearchPattern()
Computes a pattern which can be searched by standard search engines,
i.e., a pattern targeting a single amino-acid and not a complex pattern.
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static AminoAcidPattern |
AminoAcidPattern.getTrypsinExample()
Returns the trypsin example as amino acid pattern.
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static AminoAcidPattern |
AminoAcidPattern.merge(AminoAcidPattern pattern1,
AminoAcidPattern pattern2)
Convenience method merging two different patterns (see public void
merge(AminoAcidPattern otherPattern) for detailed information of the
merging procedure).
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Modifier and Type | Method and Description |
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void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
AminoAcidPattern aminoAcidPattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
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ArrayList<Integer> |
Protein.getPeptideStart(String peptideSequence,
AminoAcidPattern pattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the list of indexes where a peptide can be found in the protein
sequence.
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HashMap<Integer,String[]> |
Protein.getSurroundingAA(String peptide,
AminoAcidPattern pattern,
int patternLength,
int nAA,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the amino acids surrounding a peptide in the sequence of the
given protein in a map: peptide start index -> (amino acids before, amino
acids after).
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ArrayList<String> |
Peptide.isCterm(AminoAcidPattern pattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the
C-terminus.
|
boolean |
Protein.isCTerm(String peptideSequence,
AminoAcidPattern pattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein ends with the given
peptide.
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boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
AminoAcidPattern pattern,
int patternLength,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
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ArrayList<String> |
Peptide.isNterm(AminoAcidPattern pattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the
N-terminus.
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boolean |
Protein.isNTerm(String peptideSequence,
AminoAcidPattern pattern,
int patternLength,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein starts with the given
peptide.
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boolean |
AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern)
Indicates whether another AminoAcidPattern targets the same pattern.
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void |
AminoAcidPattern.merge(AminoAcidPattern otherPattern)
Simple merger for two patterns.
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static AminoAcidPattern |
AminoAcidPattern.merge(AminoAcidPattern pattern1,
AminoAcidPattern pattern2)
Convenience method merging two different patterns (see public void
merge(AminoAcidPattern otherPattern) for detailed information of the
merging procedure).
|
void |
PTM.setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification.
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Constructor and Description |
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AminoAcidPattern(AminoAcidPattern aminoAcidPattern)
Creates a pattern from another pattern.
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PTM(int type,
String name,
double mass,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
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PTM(int type,
String name,
String shortName,
double mass,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
---|---|
AminoAcidPattern |
AminoAcidPatternDialog.getPattern()
Returns the pattern as edited by the user.
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Constructor and Description |
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AminoAcidPatternDialog(Frame parent,
AminoAcidPattern pattern,
boolean editable)
Creates a new AminoAcidPatternDialog.
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