Modifier and Type | Method and Description |
---|---|
static String |
AminoAcidPattern.getTaggedModifiedSequence(ModificationParameters 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 Modification tags, e.g, <mox>.
|
String |
AminoAcidSequence.getTaggedModifiedSequence(ModificationParameters 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(ModificationParameters modificationProfile,
boolean useHtmlColorCoding,
boolean useShortName,
boolean excludeAllFixedPtms)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g, <mox>.
|
static String |
AminoAcidSequence.getTaggedModifiedSequence(ModificationParameters 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 modificationName,
ModificationParameters 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 |
---|---|
static ArrayList<NeutralLoss> |
IonFactory.getNeutralLosses(ModificationParameters ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
|
static HashSet<Integer> |
IonFactory.getReporterIons(ModificationParameters ptmSettings)
Returns the reporter ions to annotate with the given PTM settings.
|
Modifier and Type | Method and Description |
---|---|
String |
ModificationFactory.convertPridePtm(String pridePtmName,
ModificationParameters modProfile,
ArrayList<String> unknownPtms,
boolean isFixed)
Tries to convert a PRIDE Modification to utilities Modification name, and add it to the
modification profile.
|
Modifier and Type | Method and Description |
---|---|
String |
Peptide.getTaggedModifiedSequence(ModificationParameters modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g,
<mox>.
|
String |
Peptide.getTaggedModifiedSequence(ModificationParameters 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 Modification tags, e.g,
<mox>.
|
Modifier and Type | Method and Description |
---|---|
String |
Tag.getTaggedModifiedSequence(ModificationParameters 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 modification tags, e.g, <mox>.
|
String |
Tag.getTaggedModifiedSequence(ModificationParameters 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 modification tags, e.g, <mox>.
|
static String |
Tag.getTaggedModifiedSequence(ModificationParameters modificationProfile,
Tag tag,
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 modification tags, e.g, <mox>.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
ModificationParameters modificationProfile)
Verifies that the definition of every modification name is available.
|
Constructor and Description |
---|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
ModificationParameters modificationSettings,
PeptideVariantsParameters peptideVariantsPreferences)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
static String |
PeptideUtils.getTaggedModifiedSequence(Peptide peptide,
ModificationParameters modificationProfile,
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 Modification tags, e.g,
<mox>.
|
Modifier and Type | Method and Description |
---|---|
ModificationParameters |
XTandemParametersDialog.getModificationProfile()
Returns the modification profile corresponding to the input by the user.
|
Constructor and Description |
---|
XTandemParametersDialog(Dialog owner,
Frame parent,
XtandemParameters xtandemParameters,
ModificationParameters modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a dialog as owner.
|
XTandemParametersDialog(Frame parent,
XtandemParameters xtandemParameters,
ModificationParameters modificationProfile,
double fragmentIonMassAccuracyInDa,
boolean editable)
Creates new form XtandemParametersDialog with a frame as owner.
|
Constructor and Description |
---|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationParameters modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationParameters modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationParameters modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
Modifier and Type | Method and Description |
---|---|
ModificationParameters |
SearchParameters.getModificationParameters()
Returns the modification settings.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ModificationParameters.equals(ModificationParameters otherProfile)
Returns true of the two profiles are identical.
|
void |
SearchParameters.setModificationParameters(ModificationParameters modificationParameters)
Sets the modification settings.
|
Constructor and Description |
---|
ModificationParameters(ModificationParameters modificationParameters)
Constructor creating a new Modification profile based on the given one.
|
Modifier and Type | Method and Description |
---|---|
void |
OmssaParameters.setPtmIndexes(ModificationParameters modificationProfile)
Set the PTM indexes of the modifications searched.
|
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