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.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.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.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.IdentificationDB.getParameterTable(UrParameter)
use match specific mapping instead
|
com.compomics.util.experiment.biology.PTMFactory.getPTM(double, String, String)
This method can generate inconsistent results in case a
measurement matches to various PTMs.
|
com.compomics.util.experiment.biology.PTM.getResidues()
use amino acid pattern 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.isAScoreCalculated()
use the PTM scoring preferences instead
|
com.compomics.util.experiment.biology.Enzyme.isCleavageSite(String, String)
use the isCleavageSite method using chars as input 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.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.experiment.identification.Identification.setDirectory(String, boolean)
use establishConnection(String dbFolder) instead
|
com.compomics.util.experiment.identification.SearchParameters.setFractionMolecularWeights(HashMap)
use setFractionMolecularWeightRanges instead
|
com.compomics.software.ToolFactory.startRelims(JFrame)
use PeptideShaker's own Reshake option instead.
|