public class PeptideShakerMethods extends Object
| Constructor and Description |
|---|
PeptideShakerMethods() |
| Modifier and Type | Method and Description |
|---|---|
static String |
getDatabaseText(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary)
Returns the database usage details.
|
static String |
getDecoyType()
Returns the decoy sequences creation details.
|
static String |
getGeneAnnotation()
Returns the gene annotation method usage details.
|
static String |
getIdentificationSettings(com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
Returns the identification settings details.
|
static String |
getPeptideShaker()
Returns the PeptideShaker usage details.
|
static String |
getProteomeXchange()
Returns the ProteomeXchange upload details.
|
static String |
getPtmScoring(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters ptmScoringPreferences)
Returns the PTM scoring methods used.
|
static String |
getSearchEnginesText(ProjectDetails projectDetails)
Returns the search engines usage details.
|
static String |
getSearchGUIText()
Returns the SearchGUI usage details.
|
static String |
getSpectrumCounting(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)
Returns the spectrum counting method usage details.
|
static String |
getValidation(com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters idMatchValidationPreferences)
Returns the validation thresholds used.
|
public static String getSearchEnginesText(ProjectDetails projectDetails)
projectDetails - the PeptideShaker project detailspublic static String getSearchGUIText()
public static String getDatabaseText(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary)
fastaParameters - the FASTA parametersfastaSummary - the FASTA summarypublic static String getDecoyType()
public static String getIdentificationSettings(com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
searchParameters - the search parameterspublic static String getPeptideShaker()
public static String getValidation(com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters idMatchValidationPreferences)
idMatchValidationPreferences - the match validation preferencespublic static String getPtmScoring(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters ptmScoringPreferences)
ptmScoringPreferences - the PTM localization scoring preferencespublic static String getGeneAnnotation()
public static String getSpectrumCounting(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)
spectrumCountingPreferences - the spectrum counting preferences usedpublic static String getProteomeXchange()
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