com.compomics.util.experiment.identification.IdentificationDB.addMatchParameter(String, UrParameter)
use match specific mapping instead
|
com.compomics.util.experiment.identification.Identification.addMatchParameter(String, UrParameter)
use the database match specific methods instead
|
com.compomics.util.experiment.identification.matches.ProteinMatch.addPeptideMatch(String)
renamed addPeptideMatchKey
|
com.compomics.util.experiment.massspectrometry.SpectrumFactory.addSpectra(File)
use the version with the waiting handler instead
|
com.compomics.util.preferences.PTMScoringPreferences.aScoreCalculation()
use isProbabilitsticScoreCalculation instead
|
com.compomics.software.CompomicsWrapper.checkForNewVersion(String, String, String)
use the Maven repository option instead:
checkForNewDeployedVersion
|
com.compomics.software.CompomicsWrapper.checkForNewVersion(String, String, String, boolean, String, String)
use the Maven repository option instead:
checkForNewDeployedVersion
|
com.compomics.util.experiment.identification.SearchParameters.correctPrecursorMass(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.gui.spectrum.SpectrumPanel.determineColorOfPeak(String)
it is advised to use methods based on the ion type rather
than on the peak label
|
com.compomics.util.gui.spectrum.SpectrumPanel.determineFragmentIonColor(String)
use the method based on the Ion class instead
|
com.compomics.util.experiment.biology.Enzyme.enzymeCleaves()
use isSemiSpecific instead
|
com.compomics.util.preferences.ProcessingPreferences.estimateAScore(boolean)
use the PTM scoring preferences instead
|
com.compomics.util.gui.spectrum.SpectrumPanel.filterAnnotations(Vector, HashMap>, ArrayList, boolean, boolean, boolean)
don't use method based on the peak labels but on the data
type
|
com.compomics.util.experiment.identification.SearchParameters.generateQuery()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.biology.AminoAcidPattern.getAaExcluded()
use targeted amino acids only
|
com.compomics.util.experiment.identification.SearchParameters.getDiscardLowQualitySpectra()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.preferences.GenePreferences.getEnsemblDatabaseName(String)
use the one with the Ensembl type parameter instead
|
com.compomics.util.preferences.GenePreferences.getEnsemblSpeciesVersion(String)
use getEnsemblSpeciesVersion(String ensemblType, String
speciesName) instead
|
com.compomics.util.experiment.identification.matches.IonMatch.getError()
replaced by getAbsoluteError() and getRelativeError()
|
com.compomics.util.experiment.identification.PeptideAssumption.getEValue()
use getScore instead
|
com.compomics.util.experiment.identification.Identification.getFileName(String)
use the database methods instead
|
com.compomics.util.experiment.identification.SearchParameters.getFractionMolecularWeights()
use getFractionMolecularWeightRanges instead
|
com.compomics.util.experiment.identification.SearchParameters.getFragmentationModel()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.getHitListLength()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.getHitListLengthDeNovo()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.Identification.getMatchParameter(String, UrParameter)
use the database match specific methods instead
|
com.compomics.util.experiment.identification.IdentificationDB.getMatchPArameter(String, UrParameter, boolean)
use match specific mapping instead
|
com.compomics.util.experiment.identification.SearchParameters.getMaxEValue()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.getMaxPeptideLength()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.getMinimalChargeForMultipleChargedFragments()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.getMinPeptideLength()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.identification_parameters.MsgfParameters.getNumberOfSpectrumMarches()
use getNumberOfSpectrumMatches (without the typo) instead
|
com.compomics.util.experiment.identification.IdentificationDB.getParameterTable(UrParameter)
use match specific mapping instead
|
com.compomics.util.experiment.identification.SearchParameters.getPepNovoPtmMap()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.preferences.ProcessingPreferences.getPeptideFDR()
use the IdValidationPreferences instead
|
com.compomics.util.experiment.identification.matches.ProteinMatch.getPeptideMatches()
renamed getPeptideMatchesKeys()
|
com.compomics.util.preferences.ProcessingPreferences.getProteinConfidenceMwPlots()
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.getProteinFDR()
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.getPsmFDR()
use the IdValidationPreferences instead
|
com.compomics.util.experiment.biology.PTM.getResidues()
use amino acid pattern instead
|
com.compomics.util.preferences.ProcessingPreferences.getScores(int)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.GenePreferences.getSpecies()
use getAllSpecies instead
|
com.compomics.util.preferences.GenePreferences.getSpeciesMap()
use getAllSpeciesMap instead
|
com.compomics.util.experiment.identification.Identification.getSpectrumIdentification()
use file specific names instead
|
com.compomics.util.preferences.ProcessingPreferences.initializeAlgorithmScores()
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.isAScoreCalculated()
use the PTM scoring preferences instead
|
com.compomics.util.preferences.PTMScoringPreferences.isaScoreNeutralLosses()
use isProbabilisticScoreNeutralLosses instead
|
com.compomics.util.experiment.identification.SearchParameters.isCorrectPrecursorMass()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SequenceFactory.isDecoy(String)
deprecated, use the isDecoy(proteinAccession, flag) with file
dependent flag or isDecoyAccession(String proteinAccession) instead.
|
com.compomics.util.experiment.identification.SearchParameters.isEstimateCharge()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.isRemovePrecursor()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.isScalePrecursor()
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.preferences.ProcessingPreferences.isScoringNeeded(ArrayList)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.isScoringNeeded(int)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.isTargetDecoyNeededForPsmScoring(ArrayList)
use the IdValidationPreferences instead
|
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.loadProperties(File)
use the SearchParameters class instead
|
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.parseModificationLine(String)
use the SearchParameters class instead
|
com.compomics.util.experiment.identification.IdentificationDB.removeMatch(String)
it is advised to use the specific psm/peptide/protein method
instead
|
com.compomics.util.experiment.identification.Identification.removeMatch(String)
it is advised to use the specific psm/peptide/protein method
instead
|
com.compomics.util.preferences.PTMScoringPreferences.setaScoreCalculation(boolean)
use setProbabilitsticScoreCalculation instead
|
com.compomics.util.preferences.PTMScoringPreferences.setaScoreNeutralLosses(boolean)
use setProbabilisticScoreNeutralLosses instead
|
com.compomics.util.experiment.identification.Identification.setDirectory(String, boolean)
use establishConnection(String dbFolder) instead
|
com.compomics.util.experiment.identification.SearchParameters.setDiscardLowQualitySpectra(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setEstimateCharge(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setFractionMolecularWeights(HashMap)
use setFractionMolecularWeightRanges instead
|
com.compomics.util.experiment.identification.SearchParameters.setFragmentationModel(String)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setGenerateQuery(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setHitListLength(Integer)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setHitListLengthDeNovo(Integer)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setMaxEValue(Double)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setMaxPeptideLength(Integer)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setMinimalChargeForMultipleChargedFragments(Charge)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setMinPeptideLength(Integer)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setPepNovoPtmMap(Map)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.preferences.ProcessingPreferences.setPeptideFDR(double)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.setProteinConfidenceMwPlots(Double)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.setProteinFDR(double)
use the IdValidationPreferences instead
|
com.compomics.util.preferences.ProcessingPreferences.setPsmFDR(double)
use the IdValidationPreferences instead
|
com.compomics.util.experiment.identification.SearchParameters.setRemovePrecursor(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.experiment.identification.SearchParameters.setScalePrecursor(Boolean)
use the appropriated IdentificationAlgorithmParameters
instead
|
com.compomics.util.preferences.ProcessingPreferences.setScoresForAlgorithm(int, ArrayList)
use the IdValidationPreferences instead
|