Uses of Class
com.compomics.util.preferences.ModificationProfile

Packages that use ModificationProfile
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
 

Methods in com.compomics.util.experiment.biology with parameters of type ModificationProfile
 void PTMFactory.checkFixedModifications(ModificationProfile modificationProfile, Peptide peptide, ProteinMatch.MatchingType matchingType, Double massTolerance)
          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, ProteinMatch.MatchingType matchingType)
          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, ProteinMatch.MatchingType matchingType, Double massTolerance)
          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>.
 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>> 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
 

Methods in com.compomics.util.experiment.identification that return ModificationProfile
 ModificationProfile SearchParameters.getModificationProfile()
          Returns the modification profile of the project.
 

Methods in com.compomics.util.experiment.identification with parameters of type ModificationProfile
 void SearchParameters.setModificationProfile(ModificationProfile modificationProfile)
          Sets the modification profile of the project.
 

Uses of ModificationProfile in com.compomics.util.gui.spectrum
 

Constructors in com.compomics.util.gui.spectrum with parameters of type ModificationProfile
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.
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
 

Methods in com.compomics.util.preferences with parameters of type ModificationProfile
 boolean ModificationProfile.equals(ModificationProfile otherProfile)
          Returns true of the two profiles are identical.
 



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