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 |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.tags |
Tag classes.
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com.compomics.util.gui.searchsettings.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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com.compomics.util.preferences |
Utilities preferences classes.
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Modifier and Type | Method and Description |
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void |
PTMFactory.checkFixedModifications(ModificationProfile 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(ModificationProfile 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,
ModificationProfile modProfile,
ArrayList<String> unknownPtms,
boolean isFixed)
Tries to convert a PRIDE PTM to utilities PTM name, and add it to the
modification profile.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile 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(ModificationProfile 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.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(Double ptmMass,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
ModificationProfile modificationProfile)
Returns the potential modification sites as an ordered list of string.
|
PTM |
PTMFactory.getPTM(ModificationProfile modificationProfile,
int index)
Get a PTM according to its OMSSA index.
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static String |
AminoAcidPattern.getTaggedModifiedSequence(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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,
ModificationProfile modificationProfile,
int localizationConfidenceLevel,
boolean useHtmlColorCoding,
boolean useShortName)
Returns the single residue as a tagged string (HTML color or PTM tag).
|
void |
PTMFactory.setSearchedOMSSAIndexes(ModificationProfile modificationProfile)
Set the OMSSA indexes used for this search.
|
Modifier and Type | Method and Description |
---|---|
ModificationProfile |
SearchParameters.getModificationProfile()
Returns the modification profile of the project.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project.
|
Modifier and Type | Method and Description |
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String |
Tag.getTaggedModifiedSequence(ModificationProfile 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(ModificationProfile 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(ModificationProfile 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>.
|
Modifier and Type | Method and Description |
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ModificationProfile |
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(Frame parent,
XtandemParameters xtandemParameters,
ModificationProfile modificationProfile,
double fragmentIonMassAccuracy)
Creates new form XtandemParametersDialog.
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Constructor and Description |
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile 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,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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Modifier and Type | Method and Description |
---|---|
boolean |
ModificationProfile.equals(ModificationProfile otherProfile)
Returns true of the two profiles are identical.
|
boolean |
IdFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
ModificationProfile modificationProfile)
Validates the modifications of a peptide.
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Constructor and Description |
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ModificationProfile(ModificationProfile modificationProfile)
Constructor creating a new Modification profile based on the given one.
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