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jalview.util.LinkedIdentityHashSet
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jalview.ws.jws2.jabaws2.Jws2InstanceFactory
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jalview.io.AlignFile
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jalview.util.Comparison
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jalview.datamodel.SequenceCursor
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jalview.datamodel.Sequence
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jalview.util.MessageManager
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jalview.util.MapList
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jalview.util.MappingUtils
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jalview.io.FormatAdapter
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jalview.log.JLogger
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jalview.viewmodel.styles.ViewStyle
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jalview.datamodel.ColumnSelection.IntList
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jalview.io.FileParse
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jalview.schemes.ColourSchemeProperty
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jalview.datamodel.Alignment
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jalview.log.JLoggerLog4j
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jalview.viewmodel.AlignmentViewport
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jalview.datamodel.AlignedCodonFrame
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jalview.bin.Console
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jalview.io.AppletFormatAdapter
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jalview.datamodel.AlignmentAnnotation
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jalview.bin.Cache
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jalview.io.FileFormat
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jalview.datamodel.ColumnSelection
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jalview.util.StringUtils
jalview.util.StringUtils
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jalview.viewmodel.ViewportRanges
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jalview.util.ColorUtils
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jalview.util.Platform
jalview.util.Platform
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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jalview.datamodel.HiddenColumnsCursor
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jalview.datamodel.HiddenColumns
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jalview.analysis.AlignSeq
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jalview.analysis.AlignmentUtils
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jalview.gui.Desktop
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