Uses of Package
com.compomics.util.experiment.identification

Packages that use com.compomics.util.experiment.identification
com.compomics.util.experiment This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment. 
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.experiment.identification.advocates This package contains experiment classes related to modeling identifications. 
com.compomics.util.experiment.identification.identifications This package contains experiment classes related to MS/MS identifications. 
com.compomics.util.experiment.identification.matches This package contains experiment classes releated to matches. 
com.compomics.util.experiment.identification.ptm   
com.compomics.util.experiment.identification.ptm.ptmscores   
com.compomics.util.experiment.identification.scoring   
com.compomics.util.experiment.io.identifications   
com.compomics.util.experiment.quantification This package contains experiment classes related to quantification. 
com.compomics.util.gui.searchsettings   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.preferences   
com.compomics.util.pride   
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment
Identification
          This class contains identification results.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.biology
SearchParameters
          This class groups the parameters used for identification.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification
Advocate
          The advocate of a hit can be a search engine, a re-scoring algorithm, etc.
AdvocateFactory
          This factory will provide adapted advocates when required.
FastaIndex
          This class contains the index of a FASTA file.
IdentificationMatch
          This is an abstract class for an identification match.
IdentificationMatch.MatchType
          The type of match.
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
SearchParameters
          This class groups the parameters used for identification.
SearchParameters.PrecursorAccuracyType
          Possible mass accuracy types.
SearchParametersCLIParams
          Enum class specifying the SearchParameter command line option parameters for SearchCLI and DeNovoCLI.
SearchParametersInputBean.ToolType
          The tool type.
SequenceFactory
          Factory retrieving the information of the loaded FASTA file.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.advocates
Advocate
          The advocate of a hit can be a search engine, a re-scoring algorithm, etc.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.identifications
Identification
          This class contains identification results.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.matches
IdentificationMatch
          This is an abstract class for an identification match.
IdentificationMatch.MatchType
          The type of match.
PeptideAssumption
          This object will models the assumption made by an advocate.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.ptm
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.ptm.ptmscores
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
SpectrumAnnotator
          The spectrum annotator annotates peaks in a spectrum.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.scoring
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.io.identifications
SearchParameters
          This class groups the parameters used for identification.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.quantification
Identification
          This class contains identification results.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.gui.searchsettings
SearchParameters
          This class groups the parameters used for identification.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.gui.spectrum
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.preferences
NeutralLossesMap
          This class contains the informations relative to the accounting of neutral losses
PeptideAssumption
          This object will models the assumption made by an advocate.
SearchParameters
          This class groups the parameters used for identification.
 

Classes in com.compomics.util.experiment.identification used by com.compomics.util.pride
SearchParameters
          This class groups the parameters used for identification.
 



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