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.gui |
Basic GUI classes.
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Modifier and Type | Method and Description |
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AminoAcidPattern |
AminoAcidSequence.getAsAminoAcidPattern()
Returns this amino acid sequence as amino acid pattern.
|
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.
|
AminoAcidPattern |
AminoAcidPattern.getSubPattern(int startIndex,
boolean updateTarget)
Returns a sub pattern of the pattern.
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AminoAcidPattern |
AminoAcidPattern.getSubPattern(int startIndex,
int endIndex,
boolean updateTarget)
Returns a sub pattern of the 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).
|
AminoAcidPattern |
AminoAcidPattern.reverse()
Returns an amino acid pattern which is a reversed version of the current
pattern.
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Modifier and Type | Method and Description |
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void |
AminoAcidPattern.append(AminoAcidPattern otherPattern)
Appends another pattern at the end of this pattern.
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boolean |
AminoAcidPattern.contains(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern contains a subsequence of amino acids.
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int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
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int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences,
int startIndex)
Returns the first index where the amino acid pattern is found in the
given pattern.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(AminoAcidPattern input,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the indexes where the amino acid pattern was found in the input.
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static String |
AminoAcidPattern.getTaggedModifiedSequence(PtmSettings modificationProfile,
AminoAcidPattern aminoAcidPattern,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
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boolean |
AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence ends with the pattern.
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boolean |
AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same pattern.
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boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same sequence
without accounting for PTM localization.
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boolean |
AminoAcidPattern.isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same pattern
without accounting for PTM localization.
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boolean |
AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence starts with the pattern.
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boolean |
AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
|
boolean |
AminoAcidPattern.matchesIn(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
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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,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
|
PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm cvTerm)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
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void |
Tag.addAminoAcidPattern(AminoAcidPattern aminoAcidPattern)
Adds a sequence of amino acids to the tag.
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void |
SequenceSegment.appendTerminus(AminoAcidPattern aminoAcidPattern)
Appends an amino acid pattern to the terminus of sequencing.
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Constructor and Description |
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Tag(double nTermGap,
AminoAcidPattern sequenceTag,
double cTermGap)
Constructor for a tag consisting of a pattern tag between two mass tags.
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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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