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Packages that use com.compomics.util.experiment.identification | |
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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.scoring | |
com.compomics.util.experiment.io.identifications | |
com.compomics.util.experiment.quantification | This package contains experiment classes related to quantification. |
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 | |
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Identification
This class contains identification results. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.biology | |
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SearchParameters
This class groups the parameters used for identification. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification | |
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Advocate
The advocate of a hit can be a search engine, a re-scoring algorithm, etc. |
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AdvocateFactory
This factory will provide adapted advocates when required. |
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FastaIndex
This class contains the index of a FASTA file. |
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IdentificationMatch
This is an abstract class for an identification match. |
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IdentificationMatch.MatchType
The type of match. |
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NeutralLossesMap
This class contains the informations relative to the accounting of neutral losses |
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SearchParameters
This class groups the parameters used for identification. |
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SearchParameters.PrecursorAccuracyType
Possible mass accuracy types. |
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SearchParametersCLIParams
Enum class specifying the SearchParameter command line option parameters for SearchCLI and DeNovoCLI. |
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SearchParametersInputBean.ToolType
The tool type. |
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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 | |
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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 | |
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Identification
This class contains identification results. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.identification.matches | |
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IdentificationMatch
This is an abstract class for an identification match. |
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IdentificationMatch.MatchType
The type of match. |
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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 | |
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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.scoring | |
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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 | |
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SearchParameters
This class groups the parameters used for identification. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.experiment.quantification | |
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Identification
This class contains identification results. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.gui.spectrum | |
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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 | |
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NeutralLossesMap
This class contains the informations relative to the accounting of neutral losses |
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PeptideAssumption
This object will models the assumption made by an advocate. |
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SearchParameters
This class groups the parameters used for identification. |
Classes in com.compomics.util.experiment.identification used by com.compomics.util.pride | |
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SearchParameters
This class groups the parameters used for identification. |
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