Deprecated API

Contents

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

Deprecated Classes

Class and Description
loci.formats.ome.OmeisImporter The OME server is no longer supported.
loci.poi.hssf.record.RecordFactory use EventRecordFactory instead

Deprecated Exceptions

Exceptions and Description
loci.formats.ome.OmeisException The OME server is no longer supported.

Deprecated Fields

Field and Description
loci.formats.CoreMetadata.cLengths use CoreMetadata.moduloC instead
loci.formats.CoreMetadata.cTypes use CoreMetadata.moduloC instead
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com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.TAG_GPS_INFO_IFD_POINTER Superseded by EXIFParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER
com.sun.media.imageio.plugins.tiff.EXIFTIFFTagSet.TAG_MARKER_NOTE Superseded by EXIFTIFFTagSet.TAG_MAKER_NOTE.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
loci.formats.MetadataTools.asRetrieve(MetadataStore) This method is not thread-safe; use OMEXMLService.asRetrieve(MetadataStore) instead.
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.plugins.util.RecordedImageProcessor.drawDot2(int, int)
loci.poi.hpsf.wellknown.SectionIDMap.get(Object) Use SectionIDMap.get(byte[]) instead!
loci.formats.IFormatReader.getChannelDimLengths()
loci.formats.IFormatReader.getChannelDimTypes()
loci.formats.DimensionSwapper.getCoreMetadata()
loci.formats.ReaderWrapper.getCoreMetadata()
loci.formats.IFormatReader.getCoreMetadata() Use #getCoreMetadataList instead.
loci.formats.ImageReader.getCoreMetadata()
loci.formats.FormatReader.getCoreMetadata()
loci.formats.FileStitcher.getCoreMetadata()
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.
ome.scifio.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.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
com.sun.media.imageio.plugins.bmp.BMPImageWriteParam.getVersion()
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.
ome.scifio.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.meta.AggregateMetadata.setRoot(Object)
loci.formats.meta.MetadataStore.setRoot(Object)
loci.formats.meta.FilterMetadata.setRoot(Object)
loci.formats.meta.DummyMetadata.setRoot(Object)
loci.formats.ome.OMEXMLMetadataImpl.setRoot(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.common.DataTools.unpackShort(short, byte[], int, boolean) Use {@link #unpackBytes(long, byte[], int, int, boolean)
ome.scifio.common.DataTools.unpackShort(short, byte[], int, boolean) Use {@link #unpackBytes(long, byte[], int, int, boolean)
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).