Deprecated API

Contents

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

Deprecated Classes

Class and Description
net.maizegenetics.analysis.filter.FilterSiteNamePlugin
net.maizegenetics.analysis.gbs.v2.GBSEnzyme
net.maizegenetics.analysis.distance.Kinship

Deprecated Fields

Field and Description
net.maizegenetics.dna.tag.AbstractTagsByTaxa.taxaNames

Deprecated Methods

Method and Description
net.maizegenetics.analysis.gbs.v2.EnzymeList.Enzyme.enzyme()
net.maizegenetics.util.Tassel5HDF5Constants.getGenotypesDepthPath(taxon)
net.maizegenetics.analysis.gbs.v2.EnzymeList.Enzyme.initialCutSiteRemnant()
net.maizegenetics.analysis.gbs.v2.EnzymeList.Enzyme.likelyReadEnd()
net.maizegenetics.dna.tag.AbstractPETags.mkFastaFile(tagsFFastaFileS, tagsBFastaFileS, contigFastaFileS)
net.maizegenetics.analysis.gbs.v2.EnzymeList.Enzyme.readEndCutSiteRemnantLength()
net.maizegenetics.dna.snp.ImportUtils.readGuessFormat(fileName)
net.maizegenetics.analysis.data.ExportPlugin.setAlignmentFileType(type)
net.maizegenetics.analysis.data.ExportPlugin.setSaveFile(saveFile)
net.maizegenetics.dna.tag.TagsByTaxa.truncateTaxonNames()

Deprecated Constructors

Constructor and Description
net.maizegenetics.analysis.gbs.v2.GBSEnzyme.<init>(enzyme)
net.maizegenetics.dna.map.Chromosome.<init>(name)
net.maizegenetics.analysis.filter.FilterAlignmentPlugin.<init>(parentFrame, isInteractive)