Deprecated API


Contents
Deprecated Classes
com.compomics.util.experiment.io.identifications.IdentificationParametersReader
          use the SearchParameters class instead 
 

Deprecated Fields
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.CHARGE_ESTIMATION
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.DATABASE_FILE
          use the SearchParameters class instead Reference for the database file 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.ENZYME
          use the SearchParameters class instead Reference for the enzyme 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.EVALUE_CUTOFF
          use the SearchParameters class instead 
com.compomics.util.experiment.identification.Identification.EXTENTION
          use the database methods instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.FIXED_MODIFICATIONS
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.FRAGMENT_ION_MASS_ACCURACY
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.FRAGMENT_ION_TYPE_1
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.FRAGMENT_ION_TYPE_2
          use the SearchParameters class instead 
com.compomics.util.experiment.identification.Identification.longKeys
          use the database instead @TODO implement this for db keys 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MAX_PEPTIDE_SIZE
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MAXIMUM_HITLIST_LENGTH
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MIN_PEPTIDE_SIZE
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MISSED_CLEAVAGES
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MODIFICATION_SEPARATOR
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.MODIFICATION_USE_SEPARATOR
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_CHARGE_LOWER_BOUND
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_CHARGE_UPPER_BOUND
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_ELIMINATION
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_MASS_ACCURACY_UNIT
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_MASS_TOLERANCE
          use the SearchParameters class instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.PRECURSOR_SCALING
          use the SearchParameters class instead 
com.compomics.util.experiment.identification.Identification.spectrumIdentification
          use file specific mapping instead 
com.compomics.util.experiment.identification.Identification.urParameters
          use the database instead 
com.compomics.util.experiment.io.identifications.IdentificationParametersReader.VARIABLE_MODIFICATIONS
          use the SearchParameters class instead 
 

Deprecated Methods
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.gui.waiting.waitinghandlers.ProgressDialogX.doNothingOnClose()
          replace by setUnstoppable 
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.matches.IonMatch.getError()
          replaced by getAbsoluteError() and getRelativeError() 
com.compomics.util.experiment.identification.Identification.getFileName(String)
          use the database methods 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)
          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.experiment.identification.Identification.getSpectrumIdentification()
          use file specific names instead 
com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX.incrementValue()
          use waiting handler method instead 
com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX.incrementValue(int)
          use waiting handler method 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.gui.waiting.waitinghandlers.ProgressDialogX.setIntermidiate(boolean)
          Replaced by setIndeterminate, from utilities 3.1.17. 
com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX.setMax(int)
          use waiting handler method instead 
com.compomics.software.ToolFactory.startRelims(JFrame)
          use PeptideShaker's own Reshake option instead. 
 

Deprecated Constructors
com.compomics.util.experiment.biology.Peptide(String, Double, ArrayList, ArrayList)
          use the constructor without mass. The mass will be recalculated. 
com.compomics.util.gui.waiting.ProgressDialog(JFrame, String, String)
          use ProgressDialogX instead 
com.compomics.util.experiment.biology.PTM(int, String, double, ArrayList)
          use amino acid pattern instead 
com.compomics.util.experiment.biology.PTM(int, String, String, double, ArrayList)
          use amino acid pattern instead 
com.compomics.util.gui.spectrum.SequenceFragmentationPanel(String, ArrayList, boolean, boolean, ModificationProfile)
          use the panel with ion selection instead 
 



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