Deprecated API

Contents

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

Deprecated Classes

Class and Description
ome.xml.About The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ArcNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.AuxLightSourceRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ChannelComponentNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ChannelInfoNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ChannelSpecTypeNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ContactNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.CustomNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DatasetNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DatasetRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DescriptionNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DetectorNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DetectorRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DichroicNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.DisplayOptionsNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.DOMUtil The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.EmFilterNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExFilterNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExperimenterNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExperimenterRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExperimenterTypeNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExperimentNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ExperimentRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FeatureNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FilamentNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FilterNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FilterRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FilterSetNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.FilterSpecNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.GreyChannelNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.GroupNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.GroupRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ImageNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ImagingEnvironmentNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.InstrumentNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.InstrumentRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.LaserNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.LeaderNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.LightSourceNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.LightSourceRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ManufactSpecNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.MicroscopeNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ObjectiveNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ObjectiveRefNode The r2003fc classes are replaced by the ome.xml.model classes
loci.formats.ome.OmeisImporter The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.OMENode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.OMEXMLFactory The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.OMEXMLNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.OTFNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.OTFRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.PixelsNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.PlateNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.PlateRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ProjectionNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ProjectNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ProjectRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.PumpNode The r2003fc classes are replaced by the ome.xml.model classes
loci.poi.hssf.record.RecordFactory use EventRecordFactory instead
ome.xml.r2003fc.ome.ReferenceNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ROINode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ScreenNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ScreenRefNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.StageLabelNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.ThumbnailNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.TiffDataNode The r2003fc classes are replaced by the ome.xml.model classes
ome.xml.r2003fc.ome.TimeNode The r2003fc classes are replaced by the ome.xml.model classes

Deprecated Exceptions

Exceptions and Description
loci.formats.ome.OmeisException The r2003fc classes are replaced by the ome.xml.model classes

Deprecated Fields

Field and Description
loci.poi.hssf.usermodel.HSSFWorkbook.ENCODING_COMPRESSED_UNICODE POI will now properly handle unicode strings without forceing an encoding
loci.poi.hssf.usermodel.HSSFWorkbook.ENCODING_UTF_16 POI will now properly handle unicode strings without forceing an encoding
loci.formats.FormatTools.SVN_REVISION After Git move, deprecated in favour of FormatTools.VCS_REVISION.
com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.TAG_GPS_INFO_IFD_POINTER Superseded by EXIFParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER
com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.TAG_MARKER_NOTE Superseded by EXIFTIFFTagSet.TAG_MAKER_NOTE.
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.VERSION_2
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.VERSION_3
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.VERSION_4
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.VERSION_5

Deprecated Methods

Method and Description
loci.poi.hssf.usermodel.HSSFWorkbook.addSSTString(String) Do not call this method from your applications. Use the methods available in the HSSFRow to add string HSSFCells
ome.xml.model.primitives.Timestamp.asCalendar() In version 5.0, java.util.Calendar usage is replaced by org.joda.time.DateTime.
ome.xml.model.primitives.Timestamp.asDate() In version 5.0, java.util.Date usage is replaced by org.joda.time.DateTime.
loci.formats.MetadataTools.asRetrieve(MetadataStore) This method is not thread-safe; use OMEXMLService.asRetrieve(MetadataStore) instead.
ome.xml.model.primitives.Timestamp.asSqlDate() In version 5.0, java.sql.Date usage is replaced by org.joda.time.DateTime.
loci.formats.ome.AbstractOMEXMLMetadata.booleanToInteger(Boolean) This method will be removed in 5.0.
loci.formats.MetadataTools.createOMEXMLMetadata(String) This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String) instead.
loci.formats.MetadataTools.createOMEXMLMetadata(String, String) This method is not thread-safe; use OMEXMLService.createOMEXMLMetadata(String, String) instead.
loci.formats.MetadataTools.createOMEXMLRoot(String) This method is not thread-safe; use OMEXMLService.createOMEXMLRoot(String) instead.
loci.formats.ome.AbstractOMEXMLMetadata.doubleToInteger(Double) This method will be removed in 5.0.
loci.plugins.util.RecordedImageProcessor.drawDot2(int, int)
loci.poi.hpsf.wellknown.SectionIDMap.get(Object) Use SectionIDMap.get(byte[]) instead!
ome.xml.OMEXMLNode.getChildNodes() NB: This method exists only for legacy reasons, and usage is discouraged.
loci.poi.hssf.usermodel.HSSFCell.getEncoding() As of 3-Jan-06 POI now automatically handles Unicode without forcing the encoding.
loci.common.DataTools.getHexString(byte[]) Use DataTools.bytesToHex(byte[]) instead.
loci.formats.MetadataTools.getLatestVersion() This method is not thread-safe; use OMEXMLService.getLatestVersion() instead.
loci.formats.ReaderWrapper.getMetadata()
loci.formats.IFormatReader.getMetadata() Use #getGlobalMetadata() or #getSeriesMetadata() instead.
loci.formats.ImageReader.getMetadata()
loci.formats.FormatReader.getMetadata()
loci.formats.MetadataTools.getOMEMetadata(MetadataRetrieve) This method is not thread-safe; use OMEXMLService.getOMEMetadata(MetadataRetrieve) instead.
loci.formats.MetadataTools.getOMEXML(MetadataRetrieve) This method is not thread-safe; use OMEXMLService.getOMEXML(MetadataRetrieve) instead.
loci.formats.MetadataTools.getOMEXMLVersion(Object) This method is not thread-safe; use OMEXMLService.getOMEXMLVersion(Object) instead.
loci.formats.ome.AbstractOMEXMLMetadata.getRoot() This method will be removed in 5.0, but the abstract method is still present, but returning loci.formats.meta.MetadataRoot rather than Object.
loci.poi.hssf.usermodel.HSSFWorkbook.getSSTString(int) Do not call this method from your applications. Use the methods available in the HSSFRow to get string HSSFCells
loci.poi.hssf.usermodel.HSSFCell.getStringCellValue() Use the HSSFRichTextString return
loci.formats.ome.AbstractOMEXMLMetadata.getUUID() This method will be removed in 5.0, but the abstract method is still present.
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.getVersion()
loci.formats.ome.AbstractOMEXMLMetadata.integerToBoolean(Integer) This method will be removed in 5.0.
loci.formats.ome.AbstractOMEXMLMetadata.integerToDouble(Integer) This method will be removed in 5.0.
loci.plugins.util.RecordedImageProcessor.isKillable()
loci.formats.ReaderWrapper.isMetadataCollected()
loci.formats.IFormatReader.isMetadataCollected() Use IMetadataConfigurable.getMetadataOptions() instead.
loci.formats.ImageReader.isMetadataCollected()
loci.formats.FormatReader.isMetadataCollected()
loci.formats.MetadataTools.isOMEXMLMetadata(Object) This method is not thread-safe; use OMEXMLService.isOMEXMLMetadata(Object) instead.
loci.formats.MetadataTools.isOMEXMLRoot(Object) This method is not thread-safe; use OMEXMLService.isOMEXMLRoot(Object) instead.
loci.common.DataTools.makeDataArray(byte[], int, boolean, boolean, boolean) Use DataTools.makeDataArray(byte[], int, boolean, boolean) regardless of signedness.
loci.poi.hpsf.wellknown.SectionIDMap.put(Object, Object) Use SectionIDMap.put(byte[], PropertyIDMap) instead!
loci.poi.hssf.record.RecordInputStream.readAllContinuedRemainder() Best to write a input stream that wraps this one where there is special sub record that may overlap continue records.
loci.formats.IFormatWriter.saveBytes(byte[], boolean) Please use saveBytes(int, byte[]) instead.
loci.formats.FormatWriter.saveBytes(byte[], boolean)
loci.formats.WriterWrapper.saveBytes(byte[], boolean)
loci.formats.ImageWriter.saveBytes(byte[], boolean)
loci.formats.IFormatWriter.saveBytes(byte[], int, boolean, boolean) Please use saveBytes(int, byte[]) and setSeries(int) instead.
loci.formats.FormatWriter.saveBytes(byte[], int, boolean, boolean)
loci.formats.WriterWrapper.saveBytes(byte[], int, boolean, boolean)
loci.formats.ImageWriter.saveBytes(byte[], int, boolean, boolean)
loci.formats.gui.BufferedImageWriter.saveImage(BufferedImage, boolean) Please use saveImage(int, BufferedImage) instead. Saves the given BufferedImage to the current file. Note that this method will append the image plane to the file; it will not overwrite previously saved image planes. If this image plane is the last one in the file, the last flag must be set.
loci.formats.gui.BufferedImageWriter.saveImage(BufferedImage, int, boolean, boolean) Please use saveImage(int, BufferedImage) instead. Saves the given BufferedImage to the given series in the current file. Note that this method will append the image plane to the file; it will not overwrite previously saved image planes. If this image plane is the last one in the series, the lastInSeries flag must be set. If this image plane is the last one in the file, the last flag must be set.
loci.formats.IFormatWriter.savePlane(Object, boolean) Please use savePlane(int, Object) instead.
loci.formats.FormatWriter.savePlane(Object, boolean)
loci.formats.WriterWrapper.savePlane(Object, boolean)
loci.formats.ImageWriter.savePlane(Object, boolean)
loci.formats.IFormatWriter.savePlane(Object, int, boolean, boolean) Please use savePlane(int, Object) and setSeries(int) instead.
loci.formats.FormatWriter.savePlane(Object, int, boolean, boolean)
loci.formats.WriterWrapper.savePlane(Object, int, boolean, boolean)
loci.formats.ImageWriter.savePlane(Object, int, boolean, boolean)
loci.poi.hssf.usermodel.HSSFCell.setCellValue(String) Use setCellValue(HSSFRichTextString) instead.
loci.poi.hssf.usermodel.HSSFCell.setEncoding(short) As of 3-Jan-06 POI now automatically handles Unicode without forcing the encoding.
loci.formats.ReaderWrapper.setMetadataCollected(boolean)
loci.formats.IFormatReader.setMetadataCollected(boolean) Use IMetadataConfigurable.setMetadataOptions(MetadataOptions) instead.
loci.formats.ImageReader.setMetadataCollected(boolean)
loci.formats.FormatReader.setMetadataCollected(boolean)
loci.formats.DelegateReader.setMetadataCollected(boolean)
loci.formats.FileStitcher.setMetadataCollected(boolean)
loci.poi.hssf.record.MergeCellsRecord.setNumAreas(short) We now link the size to the actual array of merged regions
loci.poi.hssf.usermodel.HSSFSheet.setProtect(boolean) use protectSheet(String, boolean, boolean)
loci.formats.ome.AbstractOMEXMLMetadata.setRoot(Object) This method will be removed in 5.0, but the abstract method is still present, but requiring loci.formats.meta.MetadataRoot rather than Object.
loci.poi.hssf.model.Workbook.setSheetName(int, String, short) 3-Jan-06 Simply use setSheetNam e(int sheetnum, String sheetname)
loci.poi.hssf.usermodel.HSSFWorkbook.setSheetName(int, String, short) 3-Jan-2006 POI now automatically detects unicode and sets the encoding appropriately. Simply use setSheetName(int sheet, String encoding)
loci.formats.ome.AbstractOMEXMLMetadata.setUUID(String) This method will be removed in 5.0, but the abstract method is still present.
loci.common.DataTools.unpackShort(short, byte[], int, boolean) Use {@link #unpackBytes(long, byte[], int, int, boolean)
ome.xml.model.AbstractOMEModelObject.update(Element) Use {@link #update(Element, Model)
loci.formats.MetadataTools.validateOMEXML(String) This method is not thread-safe; use OMEXMLService.validateOMEXML(String) instead.
loci.formats.MetadataTools.validateOMEXML(String, boolean) This method is not thread-safe; use OMEXMLService.validateOMEXML(String, boolean) instead.
loci.formats.services.JAIIIOServiceImpl.writeImage(OutputStream, BufferedImage, boolean, int[], double)
loci.formats.services.JAIIIOService.writeImage(OutputStream, BufferedImage, boolean, int[], double) Replaced by JAIIIOService.writeImage(OutputStream, BufferedImage, JPEG2000CodecOptions).

Deprecated Constructors

Constructor and Description
ome.xml.model.AbstractOMEModelObject() Subclasses should not chain up to any constructor of this class
ome.xml.model.AbstractOMEModelObject(Element) Subclasses should not chain up to any constructor of this class
ome.xml.model.primitives.Timestamp(Calendar) In version 5.0, java.util.Calendar usage is replaced by org.joda.time.DateTime.
ome.xml.model.primitives.Timestamp(Date) In version 5.0, java.util.Date usage is replaced by org.joda.time.DateTime.