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Packages that use ModificationProfile | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
com.compomics.util.preferences |
Uses of ModificationProfile in com.compomics.util.experiment.biology |
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Methods in com.compomics.util.experiment.biology with parameters of type ModificationProfile | |
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void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide)
Removes the fixed modifications of the peptide 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 massTolerance)
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)
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. |
PTM |
PTMFactory.getPTM(ModificationProfile modificationProfile,
int index)
Get a PTM according to its OMSSA index. |
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>. |
static String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
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>. |
void |
PTMFactory.setSearchedOMSSAIndexes(ModificationProfile modificationProfile)
Set the OMSSA indexes used for this search. |
Uses of ModificationProfile in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return ModificationProfile | |
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ModificationProfile |
SearchParameters.getModificationProfile()
Returns the modification profile of the project. |
Methods in com.compomics.util.experiment.identification with parameters of type ModificationProfile | |
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void |
SearchParameters.setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project. |
Uses of ModificationProfile in com.compomics.util.gui.spectrum |
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Constructors in com.compomics.util.gui.spectrum with parameters of type ModificationProfile | |
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated. use the panel with ion selection instead |
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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. |
Uses of ModificationProfile in com.compomics.util.preferences |
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Methods in com.compomics.util.preferences with parameters of type ModificationProfile | |
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boolean |
ModificationProfile.equals(ModificationProfile otherProfile)
Returns true of the two profiles are identical. |
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