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.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
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com.compomics.util.gui.parameters.identification_parameters.algorithm_settings |
Search algorithm settings dialogs.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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Modifier and Type | Method and Description |
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void |
PTMFactory.checkFixedModifications(PtmSettings modificationProfile,
Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
void |
PTMFactory.checkFixedModifications(PtmSettings modificationProfile,
Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Removes the fixed modifications of the given tag and remaps the one
searched for according to the ModificationProfile.
|
String |
PTMFactory.convertPridePtm(String pridePtmName,
PtmSettings modProfile,
ArrayList<String> unknownPtms,
boolean isFixed)
Tries to convert a PRIDE PTM to utilities PTM name, and add it to the
modification profile.
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HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
String ptmName,
Double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
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static ArrayList<NeutralLoss> |
IonFactory.getNeutralLosses(PtmSettings ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
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ArrayList<Integer> |
Peptide.getPotentialModificationSites(Double ptmMass,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Returns the potential modification sites as an ordered list of string.
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static HashSet<Integer> |
IonFactory.getReporterIons(PtmSettings ptmSettings)
Returns the reporter ions to annotate with the given PTM settings.
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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>.
|
String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
AminoAcidSequence.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
AminoAcidPattern.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
Peptide.getTaggedModifiedSequence(PtmSettings modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
AminoAcidSequence.getTaggedModifiedSequence(PtmSettings modificationProfile,
String sequence,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
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>.
|
static String |
AminoAcidSequence.getTaggedResidue(char residue,
String ptmName,
PtmSettings modificationProfile,
int localizationConfidenceLevel,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the single residue as a tagged string (HTML color or PTM tag).
|
Modifier and Type | Method and Description |
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String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedModifications,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
static String |
Tag.getTaggedModifiedSequence(PtmSettings modificationProfile,
Tag tag,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms,
boolean includeTerminalGaps)
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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Modifier and Type | Method and Description |
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boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Validates the modifications of a peptide.
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Modifier and Type | Method and Description |
---|---|
PtmSettings |
SearchParameters.getPtmSettings()
Returns the PTM settings.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PtmSettings.equals(PtmSettings otherProfile)
Returns true of the two profiles are identical.
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void |
SearchParameters.setPtmSettings(PtmSettings ptmSettings)
Sets the PTM settings.
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Constructor and Description |
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PtmSettings(PtmSettings modificationProfile)
Constructor creating a new Modification profile based on the given one.
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Modifier and Type | Method and Description |
---|---|
void |
OmssaParameters.setPtmIndexes(PtmSettings modificationProfile)
Set the PTM indexes of the modifications searched.
|
Modifier and Type | Method and Description |
---|---|
PtmSettings |
XTandemSettingsDialog.getModificationProfile()
Returns the modification profile corresponding to the input by the user.
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Constructor and Description |
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XTandemSettingsDialog(Dialog owner,
Frame parent,
XtandemParameters xtandemParameters,
PtmSettings modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a dialog as owner.
|
XTandemSettingsDialog(Frame parent,
XtandemParameters xtandemParameters,
PtmSettings modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a frame as owner.
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Constructor and Description |
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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