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Packages that use PTM | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.gui.dialogs | This package contains GUI dialogs. |
com.compomics.util.preferences |
Uses of PTM in com.compomics.util.experiment.biology |
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Fields in com.compomics.util.experiment.biology declared as PTM | |
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static PTM |
PTMFactory.unknownPTM
Unknown modification to be returned when the modification is not found. |
Methods in com.compomics.util.experiment.biology that return PTM | |
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PTM |
PTMFactory.getPTM(double mass,
String location,
String sequence)
Deprecated. This method can generate inconsistent results in case a measurement matches to various PTMs. |
PTM |
PTMFactory.getPTM(int index)
Get a PTM according to its omssa index. |
PTM |
PTMFactory.getPTM(String name)
Returns the PTM indexed by its name. |
PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern. |
PTM |
PTMFactory.getSearchedPTM(String modificationName)
Returns the standard search compatible PTM corresponding to this pattern. |
Methods in com.compomics.util.experiment.biology with parameters of type PTM | |
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void |
PTMFactory.addUserPTM(PTM ptm)
Adds a new user modification. |
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm)
Returns the potential modification sites as an ordered list of string. 0 is the first aa. an empty list is returned if no possibility was found. |
static ArrayList<Integer> |
Peptide.getPotentialModificationSites(String sequence,
PTM ptm)
Returns the potential modification sites as an ordered list of string. 0 is the first aa. an empty list is returned if no possibility was found. |
PTM |
PTMFactory.getSearchedPTM(PTM modification)
Returns the standard search compatible PTM corresponding to this pattern. |
boolean |
Peptide.isModifiable(PTM ptm)
Indicates whether the given modification can be found on the peptide. |
boolean |
PTM.isSameAs(PTM anotherPTM)
Compares two PTMs. |
Uses of PTM in com.compomics.util.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type PTM | |
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static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location. |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the ptm plot series in the jfreechart format for one psm. |
static PtmtableContent |
PTMLocationScores.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content. |
Uses of PTM in com.compomics.util.gui.dialogs |
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Constructors in com.compomics.util.gui.dialogs with parameters of type PTM | |
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PtmDialog(JDialog parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog. |
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PtmDialog(JFrame parent,
PtmDialogParent ptmDialogParent,
PtmToPrideMap ptmToPrideMap,
PTM currentPTM,
boolean editable)
Creates a new PTM dialog. |
Uses of PTM in com.compomics.util.preferences |
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Methods in com.compomics.util.preferences that return PTM | |
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PTM |
ModificationProfile.getPtm(String modName)
Returns the back-ed up PTM with the given name |
Methods in com.compomics.util.preferences with parameters of type PTM | |
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void |
ModificationProfile.addFixedModification(PTM modification)
Adds a fixed modification. |
void |
ModificationProfile.addVariableModification(PTM modification)
Adds a variable modification. |
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