Deprecated API

Contents

• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Classes

Class and Description
com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog no longer used
com.compomics.util.preferences.PSProcessingPreferences replaced by utilities processing preferences and fraction preferences
com.compomics.util.gui.genes.SpeciesDialog use the GenePreferencesDialog instead

Deprecated Fields

Field and Description
com.compomics.util.preferences.GenePreferences.GENE_MAPPING_FILE_SUFFIX use the gene factory.
com.compomics.util.preferences.GenePreferences.GO_MAPPING_FILE_SUFFIX use the gene factory.
com.compomics.util.experiment.biology.AminoAcid.monoisotopicMass use the atomchain

Deprecated Methods

Method and Description
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.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.spectrum.SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation>, HashMap<Ion.IonType, ArrayList<Integer>>, ArrayList<NeutralLoss>, boolean, boolean, boolean) don't use method based on the peak labels but on the data type
com.compomics.util.pride.PtmToPrideMap.getDefaultCVTerm(String) use the getCvTerm method for the PTM instead
com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters.getUseSparseMatrix() from Comet release 2015.02 all searches use this internal data representation by default
com.compomics.util.pride.PtmToPrideMap.loadPtmToPrideMap(SearchParameters) the CV term is now part of the PTM object
com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters.setUseSparseMatrix(Boolean) from Comet release 2015.02 all searches use this internal data representation by default

Deprecated Constructors

Constructor and Description
com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog(JFrame, String, String) use ProgressDialogX instead
com.compomics.util.gui.spectrum.SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, boolean, PtmSettings) use the panel with ion selection instead