com.compomics.software.CompomicsWrapper.checkForNewVersion(String, String, String)
use the Maven repository option instead:
checkForNewDeployedVersion
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com.compomics.software.CompomicsWrapper.checkForNewVersion(String, String, String, boolean, String, String)
use the Maven repository option instead:
checkForNewDeployedVersion
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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
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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
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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
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