Deprecated API

Contents

• Classes
• Fields
• Methods

Deprecated Classes

Class	Description
loci.formats.codec.BitBuffer	Use loci.common.RandomAccessInputStream instead
loci.formats.codec.BitWriter	Use loci.common.RandomAccessOutputStream instead
loci.formats.meta.MetadataConverter	Use ome.xml.meta.MetadataConverter.

Deprecated Fields

Field	Description
loci.formats.FormatTools.PROPERTY_FILE	The property file is no longer used.
loci.formats.FormatTools.VCS_SHORT_REVISION	Use the general FormatTools.VCS_REVISION field.
loci.formats.in.DeltavisionReader.DATE_FORMAT	Use DeltavisionReader.DATE_FORMATS instead
loci.formats.in.ND2Reader.USE_CHUNKMAP_LEGACY_KEY
loci.formats.UpgradeChecker.OLD_TOOLS	Removed in Bio-Formats 6.9.0
loci.formats.UpgradeChecker.STABLE_VERSION	As of release 6.6.0

Deprecated Methods

Method	Description
loci.formats.ClassList.isWhitelistedKey(String)	Use ClassList.isAllowedKey(String) instead.
loci.formats.codec.HuffmanCodec.getSample(BitBuffer, CodecOptions)
loci.formats.FormatReader.getAcquisitionMode(String)	Use MetadataTools.getAcquisitionMode(String).
loci.formats.FormatReader.getArcType(String)	Use MetadataTools.getArcType(String).
loci.formats.FormatReader.getBinning(String)	Use MetadataTools.getBinning(String).
loci.formats.FormatReader.getCompression(String)	Use MetadataTools.getCompression(String).
loci.formats.FormatReader.getContrastMethod(String)	Use MetadataTools.getContrastMethod(String).
loci.formats.FormatReader.getCorrection(String)	Use MetadataTools.getCorrection(String).
loci.formats.FormatReader.getDetectorType(String)	Use MetadataTools.getDetectorType(String).
loci.formats.FormatReader.getDimensionOrder(String)	Use MetadataTools.getDimensionOrder(String).
loci.formats.FormatReader.getExperimentType(String)	Use MetadataTools.getExperimentType(String).
loci.formats.FormatReader.getFilamentType(String)	Use MetadataTools.getFilamentType(String).
loci.formats.FormatReader.getFillRule(String)	Use MetadataTools.getFillRule(String).
loci.formats.FormatReader.getFilterType(String)	Use MetadataTools.getFilterType(String).
loci.formats.FormatReader.getFontFamily(String)	Use MetadataTools.getFontFamily(String).
loci.formats.FormatReader.getFontStyle(String)	Use MetadataTools.getFontStyle(String).
loci.formats.FormatReader.getIlluminationType(String)	Use MetadataTools.getIlluminationType(String).
loci.formats.FormatReader.getImmersion(String)	Use MetadataTools.getImmersion(String).
loci.formats.FormatReader.getLaserMedium(String)	Use MetadataTools.getLaserMedium(String).
loci.formats.FormatReader.getLaserType(String)	Use MetadataTools.getLaserType(String).
loci.formats.FormatReader.getMarker(String)	Use MetadataTools.getMarker(String).
loci.formats.FormatReader.getMedium(String)	Use MetadataTools.getMedium(String).
loci.formats.FormatReader.getMicrobeamManipulationType(String)	Use MetadataTools.getMicrobeamManipulationType(String).
loci.formats.FormatReader.getMicroscopeType(String)	Use MetadataTools.getMicroscopeType(String).
loci.formats.FormatReader.getNamingConvention(String)	Use MetadataTools.getNamingConvention(String).
loci.formats.FormatReader.getPixelType(String)	Use MetadataTools.getPixelType(String).
loci.formats.FormatReader.getPulse(String)	Use MetadataTools.getPulse(String).
loci.formats.FormatTools.loadProperties()	This method should no longer be used. The properties are now obtained from the jar manifest.
loci.formats.IFormatReader.coreIndexToSeries(int)	This method is no longer required for sub-resolution support.
loci.formats.IFormatReader.getCoreIndex()	This method is no longer required for sub-resolution support.
loci.formats.IFormatReader.getCoreMetadataList()	Reader internals should not be accessed by reader users
loci.formats.IFormatReader.seriesToCoreIndex(int)	This method is no longer required for sub-resolution support.
loci.formats.IFormatReader.setCoreIndex(int)	This method is no longer required for sub-resolution support.
loci.formats.in.OMETiffReader.getMetadataStoreForConversion()	Use the general FormatReader.getMetadataStore() method.
loci.formats.in.OMETiffReader.getMetadataStoreForDisplay()	Use the general FormatReader.getMetadataStore() method.
loci.formats.in.OperettaReader.getAcquisitionMode(String)
loci.formats.tiff.TiffParser.getIFDs()	Use TiffParser.getMainIFDs() and TiffParser.getSubIFDs(IFD) instead.
loci.formats.tools.EditTiffG.openFile(String)