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# Serialized Form

Package ncsa.hdf.hdf5lib

Class ncsa.hdf.hdf5lib.H5 extends java.lang.Object implements Serializable

serialVersionUID: 6129888282117053288L

Package ncsa.hdf.hdf5lib.exceptions

Class ncsa.hdf.hdf5lib.exceptions.HDF5AtomException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5AttributeException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5BtreeException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataFiltersException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DatasetInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataStorageException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5Exception extends java.lang.Exception implements Serializable

Serialized Fields

### detailMessage

    java.lang.String detailMessage

Class ncsa.hdf.hdf5lib.exceptions.HDF5ExternalFileListException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FileInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FunctionArgumentException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FunctionEntryExitException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5HeapException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5InternalErrorException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5JavaException extends HDF5Exception implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException extends HDF5Exception implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5LowLevelIOException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5MetaDataCacheException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ObjectHeaderException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5PropertyListInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ReferenceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ResourceUnavailableException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException extends HDF5LibraryException implements Serializable

Package ncsa.hdf.hdf5lib.structs

Class ncsa.hdf.hdf5lib.structs.H5_ih_info_t extends java.lang.Object implements Serializable

serialVersionUID: -142238015615462707L

Serialized Fields

### index_size

    long index_size

### heap_size

    long heap_size

Class ncsa.hdf.hdf5lib.structs.H5A_info_t extends java.lang.Object implements Serializable

serialVersionUID: 2791443594041667613L

Serialized Fields

### corder_valid

    boolean corder_valid

### corder

    long corder

### cset

    int cset

### data_size

    long data_size

Class ncsa.hdf.hdf5lib.structs.H5AC_cache_config_t extends java.lang.Object implements Serializable

serialVersionUID: -6748085696476149972L

Serialized Fields

### version

    int version

### rpt_fcn_enabled

    boolean rpt_fcn_enabled

### open_trace_file

    boolean open_trace_file

### close_trace_file

    boolean close_trace_file

### trace_file_name

    java.lang.String trace_file_name

### evictions_enabled

    boolean evictions_enabled

### set_initial_size

    boolean set_initial_size

### initial_size

    long initial_size

### min_clean_fraction

    double min_clean_fraction

### max_size

    long max_size

### min_size

    long min_size

### epoch_length

    long epoch_length

### incr_mode

    int incr_mode

### lower_hr_threshold

    double lower_hr_threshold

### increment

    double increment

### apply_max_increment

    boolean apply_max_increment

### max_increment

    long max_increment

### flash_incr_mode

    int flash_incr_mode

### flash_multiple

    double flash_multiple

### flash_threshold

    double flash_threshold

### decr_mode

    int decr_mode

### upper_hr_threshold

    double upper_hr_threshold

### decrement

    double decrement

### apply_max_decrement

    boolean apply_max_decrement

### max_decrement

    long max_decrement

### epochs_before_eviction

    int epochs_before_eviction

### apply_empty_reserve

    boolean apply_empty_reserve

### empty_reserve

    double empty_reserve

### dirty_bytes_threshold

    int dirty_bytes_threshold

### metadata_write_strategy

    int metadata_write_strategy

Class ncsa.hdf.hdf5lib.structs.H5G_info_t extends java.lang.Object implements Serializable

serialVersionUID: -3746463015312132912L

Serialized Fields

### storage_type

    int storage_type

### nlinks

    long nlinks

### max_corder

    long max_corder

### mounted

    boolean mounted

Class ncsa.hdf.hdf5lib.structs.H5L_info_t extends java.lang.Object implements Serializable

serialVersionUID: -4754320605310155033L

Serialized Fields

### type

    int type

### corder_valid

    boolean corder_valid

### corder

    long corder

### cset

    int cset

### address_val_size

    long address_val_size

Class ncsa.hdf.hdf5lib.structs.H5O_hdr_info_t extends java.lang.Object implements Serializable

serialVersionUID: 7883826382952577189L

Serialized Fields

### version

    int version

### nmesgs

    int nmesgs

### nchunks

    int nchunks

### flags

    int flags

### space_total

    long space_total

### space_meta

    long space_meta

### space_mesg

    long space_mesg

### space_free

    long space_free

### mesg_present

    long mesg_present

### mesg_shared

    long mesg_shared

Class ncsa.hdf.hdf5lib.structs.H5O_info_t extends java.lang.Object implements Serializable

serialVersionUID: 4691681163544054518L

Serialized Fields

### fileno

    long fileno

### addr

    long addr

### type

    int type

### rc

    int rc

### atime

    long atime

### mtime

    long mtime

### ctime

    long ctime

### btime

    long btime

### num_attrs

    long num_attrs

### hdr

    H5O_hdr_info_t hdr

### meta_size_obj

    H5_ih_info_t meta_size_obj

### meta_size_attr

    H5_ih_info_t meta_size_attr

Package ncsa.hdf.hdflib

Class ncsa.hdf.hdflib.HDFDeprecated extends HDFLibrary implements Serializable

Class ncsa.hdf.hdflib.HDFException extends java.lang.Exception implements Serializable

Serialized Fields

### HDFerror

    int HDFerror

### msg

    java.lang.String msg

Class ncsa.hdf.hdflib.HDFJavaException extends HDFException implements Serializable

Serialized Fields

### msg

    java.lang.String msg

Class ncsa.hdf.hdflib.HDFLibrary extends java.lang.Object implements Serializable

serialVersionUID: -1695429510319126910L

Class ncsa.hdf.hdflib.HDFLibraryException extends HDFException implements Serializable

Serialized Fields

### HDFerror

    int HDFerror

### msg

    java.lang.String msg

Class ncsa.hdf.hdflib.HDFNotImplementedException extends HDFJavaException implements Serializable

Serialized Fields

### msg

    java.lang.String msg

Package ncsa.hdf.object

Class ncsa.hdf.object.Attribute extends java.lang.Object implements Serializable

serialVersionUID: 2072473407027648309L

Serialized Fields

### name

    java.lang.String name

  The name of the attribute.

### type

    Datatype type

  The datatype of the attribute.

### rank

    int rank

  The rank of the data value of the attribute.

### dims

    long[] dims

  The dimension sizes of the attribute.

### value

    java.lang.Object value

  The value of the attribute.

### isUnsigned

    boolean isUnsigned

  Flag to indicate if the datatype is an unsigned integer.

### isScalar

    boolean isScalar

  flag to indicate if the dataset is a single scalar point

Class ncsa.hdf.object.CompoundDS extends Dataset implements Serializable

serialVersionUID: -4880399929644095662L

Serialized Fields

### numberOfMembers

    int numberOfMembers

  The number of members of the compound dataset.

### memberNames

    java.lang.String[] memberNames

  The names of members of the compound dataset.

### memberOrders

    int[] memberOrders

  Returns array containing the total number of elements of the members of compound.

  For example, a compound dataset COMP has members of A, B and C as

           COMP {
               int A;
               float B[5];
               double C[2][3];
           }

  memberOrders is an integer array of {1, 5, 6} to indicate that member A has one element, member B has 5 elements, and member C has 6 elements.

### memberDims

    java.lang.Object[] memberDims

  The dimension sizes of each member.

  The i-th element of the Object[] is an integer array (int[]) that contains the dimension sizes of the i-th member.

### memberTypes

    Datatype[] memberTypes

  The datatypes of compound members.

### isMemberSelected

    boolean[] isMemberSelected

  The array to store flags to indicate if a member of compound dataset is selected for read/write.

  If a member is selected, the read/write will perform on the member. Applications such as HDFView will only display the selected members of the compound dataset.

       For example, if a compound dataset has four members
           String[] memberNames = {"X", "Y", "Z", "TIME"};
       and
           boolean[] isMemberSelected = {true, false, false, true};
       members "X" and "TIME" are selected for read and write.

Class ncsa.hdf.object.Dataset extends HObject implements Serializable

serialVersionUID: -3360885430038261178L

Serialized Fields

### data

    java.lang.Object data

  The memory buffer that holds the raw data of the dataset.

### rank

    int rank

  The number of dimensions of the dataset.

### dims

    long[] dims

  The current dimension sizes of the dataset

### maxDims

    long[] maxDims

  The max dimension sizes of the dataset

### selectedDims

    long[] selectedDims

  Array that contains the number of data points selected (for read/write) in each dimension.

  The select size must be less than or equal to the current dimension size. A subset of a rectangle selection is defined by the starting position and selected sizes.

  For example, a 4 X 5 dataset

           0,  1,  2,  3,  4
          10, 11, 12, 13, 14
          20, 21, 22, 23, 24
          30, 31, 32, 33, 34
       long[] dims = {4, 5};
       long[] startDims = {1, 2};
       long[] selectedDims = {3, 3};
       then the following subset is selected by the startDims and selectedDims above
           12, 13, 14
           22, 23, 24
       32, 33, 34

### startDims

    long[] startDims

  The starting position of each dimension of a selected subset. With both the starting position and selected sizes, the subset of a rectangle selection is fully defined.

### selectedIndex

    int[] selectedIndex

  Array that contains the indices of the dimensions selected for display.

  selectedIndex[] is provied for two purpose:

  1. selectedIndex[] is used to indicate the order of dimensions for display, i.e. selectedIndex[0] = row, selectedIndex[1] = column and selectedIndex[2] = depth. For example, for a four dimesion dataset, if selectedIndex[] is {1, 2, 3}, then dim[1] is selected as row index, dim[2] is selected as column index and dim[3] is selected as depth index.
  2. selectedIndex[] is also used to select dimensions for display for datasets with three or more dimensions. We assume that applications such as HDFView can only display data up to three dimensions (a 2D spreadsheet/image with a third dimension that the 2D spreadsheet/image is cut from). For dataset with more than three dimensions, we need selectedIndex[] to store which three dimensions are chosen for display. For example, for a four dimesion dataset, if selectedIndex[] = {1, 2, 3}, then dim[1] is selected as row index, dim[2] is selected as column index and dim[3] is selected as depth index. dim[0] is not selected. Its location is fixed at 0 by default.

### selectedStride

    long[] selectedStride

  The number of elements to move from the start location in each dimension. For example, if selectedStride[0] = 2, every other data point is selected along dim[0].

### chunkSize

    long[] chunkSize

  The array of dimension sizes for a chunk.

### compression

    java.lang.String compression

  The GZIP compression level.

### datatype

    Datatype datatype

  The datatype object of the dataset.

### dimNames

    java.lang.String[] dimNames

  Array of strings that represent the dimension names. It is null if dimension names do not exist.

### convertByteToString

    boolean convertByteToString

  Flag to indicate if the byte[] array is converted to strings

### isDataLoaded

    boolean isDataLoaded

  Flag to indicate if data values are loaded into memory.

### nPoints

    long nPoints

  The number of data points in the memory buffer.

### originalBuf

    java.lang.Object originalBuf

  The data buffer that contains the raw data directly reading from file (before any data conversion).

### convertedBuf

    java.lang.Object convertedBuf

  The array that holds the converted data of unsigned C-type integers.

  For example, Suppose that the original data is an array of unsigned 16-bit short integers. Since Java does not support unsigned integer, the data is converted to an array of 32-bit singed integer. In that case, the converted buffer is the array of 32-bit singed integer.

### enumConverted

    boolean enumConverted

  Flag to indicate if the enum data is converted to strings.

Class ncsa.hdf.object.Datatype extends HObject implements Serializable

serialVersionUID: -581324710549963177L

Serialized Fields

### datatypeClass

    int datatypeClass

  The class of the datatype.

### datatypeSize

    int datatypeSize

  The size (in bytes) of the datatype.

### datatypeOrder

    int datatypeOrder

  The byte order of the datatype. Valid values are ORDER_LE, ORDER_BE, and ORDER_VAX.

### datatypeSign

    int datatypeSign

  The sign of the datatype.

### enumMembers

    java.lang.String enumMembers

  The (name, value) pairs of enum members

### baseType

    Datatype baseType

  The base datatype of every element of the array (for CLASS_ARRAY datatype).

### dims

    long[] dims

Class ncsa.hdf.object.FileFormat extends java.io.File implements Serializable

serialVersionUID: -4700692313888420796L

Serialized Fields

### max_members

    int max_members

  Current Java applications, such as HDFView, cannot handle files with large numbers of objects due to JVM memory limitations. For example, 1,000,000 objects is too many. max_members is defined so that applications such as HDFView will load up to max_members objects starting with the start_members -th object. The implementing class has freedom in its interpretation of how to "count" objects in the file.

### start_members

    int start_members

### fid

    int fid

  File identifier. -1 indicates the file is not open.

### fullFileName

    java.lang.String fullFileName

  The absolute pathname (path+name) of the file.

### isReadOnly

    boolean isReadOnly

  Flag indicating if the file access is read-only.

Class ncsa.hdf.object.Group extends HObject implements Serializable

serialVersionUID: 3913174542591568052L

Serialized Fields

### memberList

    java.util.List<E> memberList

  The list of members (Groups and Datasets) of this group in memory.

### parent

    Group parent

  The parent group where this group is located. The parent of the root group is null.

### nMembersInFile

    int nMembersInFile

  Total number of (Groups and Datasets) of this group in file.

Class ncsa.hdf.object.HObject extends java.lang.Object implements Serializable

serialVersionUID: -1723666708199882519L

Serialized Fields

### filename

    java.lang.String filename

  The full path of the file that contains the object.

### fileFormat

    FileFormat fileFormat

  The file which contains the object

### name

    java.lang.String name

  The name of the data object. The root group has its default name, a slash. The name can be changed except the root group.

### path

    java.lang.String path

  The full path of the data object. The full path always starts with the root, a slash. The path cannot be changed. Also, a path must ended with a slash. For example, /arrays/ints/

### fullName

    java.lang.String fullName

  The full name of the data object, i.e. "path + name"

### oid

    long[] oid

  Array of long integer storing unique identifier for the object.

  HDF4 objects are uniquely identified by a (ref_id, tag_id) pair. i.e. oid[0]=tag, oid[1]=ref.
  HDF5 objects are uniquely identified by an object reference.

### linkTargetObjName

    java.lang.String linkTargetObjName

  The name of the Target Object that is being linked to.

Class ncsa.hdf.object.ScalarDS extends Dataset implements Serializable

serialVersionUID: 8925371455928203981L

Serialized Fields

### interlace

    int interlace

  The interlace mode of the stored raster image data. Valid values are INTERLACE_PIXEL, INTERLACE_LINE and INTERLACE_PLANE.

### imageDataRange

    double[] imageDataRange

  The min-max range of image data values. For example, [0, 255] indicates the min is 0, and the max is 255.

### palette

    byte[][] palette

  The indexed RGB color model with 256 colors.

  The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.

### isImage

    boolean isImage

  True if this dataset is an image.

### isTrueColor

    boolean isTrueColor

  True if this dataset is a true color image.

### isText

    boolean isText

  True if this dataset is ASCII text.

### isUnsigned

    boolean isUnsigned

  Flag to indicate if the original C data is unsigned integer.

### unsignedConverted

    boolean unsignedConverted

  Flag to indicate is the original unsigned C data is converted.

### fillValue

    java.lang.Object fillValue

  The fill value of the dataset.

### isImageDisplay

    boolean isImageDisplay

  Flag to indicate if the dataset is displayed as an image

### isDefaultImageOrder

    boolean isDefaultImageOrder

  Flag to indicate if the dataset is displayed as an image with default order of dimensions

### isFillValueConverted

    boolean isFillValueConverted

  Flag to indicate if the FillValue is converted from unsigned C.

Package ncsa.hdf.object.h4

Class ncsa.hdf.object.h4.H4Datatype extends Datatype implements Serializable

serialVersionUID: -1342029403385521874L

Class ncsa.hdf.object.h4.H4File extends FileFormat implements Serializable

serialVersionUID: 8985533001471224030L

Serialized Fields

### flag

    int flag

  the file access flag.

### rootNode

    javax.swing.tree.DefaultMutableTreeNode rootNode

  The root node of the tree structure of this file.

### objList

    java.util.List<E> objList

  The list of unique (tag, ref) pairs. It is used to avoid duplicate objects in memory.

### grid

    int grid

  The GR interface identifier. The identifier is returned by GRstart(fid), which initializes the GR interface for the file specified by the parameter. GRstart(fid) is an expensive call. It should be called only once. Calling GRstart(fid) in a loop should be avoided.

### isNetCDF

    boolean isNetCDF

### sdid

    int sdid

  The SDS interface identifier. The identifier is returned by SDstart(fname, flag), which initializes the SD interface for the file specified by the parameter. SDstart(fname, flag) is an expensive call. It should be called only once Calling SDstart(fname, flag) in a loop should be avoided.

### showAll

    boolean showAll

Class ncsa.hdf.object.h4.H4GRImage extends ScalarDS implements Serializable

serialVersionUID: 1029672744963360976L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### grid

    int grid

  The GR interface identifier obtained from GRstart(fid)

### ncomp

    int ncomp

  The number of components in the raster image

### datatypeID

    int datatypeID

  the datatype identifier

### nAttributes

    int nAttributes

Class ncsa.hdf.object.h4.H4Group extends Group implements Serializable

serialVersionUID: 3785240955078867900L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### nAttributes

    int nAttributes

Class ncsa.hdf.object.h4.H4SDS extends ScalarDS implements Serializable

serialVersionUID: 2557157923292438696L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### sdid

    int sdid

  The SDS interface identifier obtained from SDstart(filename, access)

### datatypeID

    int datatypeID

  the datatype identifier

### nAttributes

    int nAttributes

Class ncsa.hdf.object.h4.H4Vdata extends CompoundDS implements Serializable

serialVersionUID: -5978700886955419959L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### numberOfRecords

    int numberOfRecords

  Number of records of this Vdata table.

### memberTIDs

    int[] memberTIDs

  The data types of the members of the compound dataset.

### nAttributes

    int nAttributes

Package ncsa.hdf.object.h5

Class ncsa.hdf.object.h5.H5CompoundDS extends CompoundDS implements Serializable

serialVersionUID: -5968625125574032736L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes attached data object.

### nAttributes

    int nAttributes

### obj_info

    H5O_info_t obj_info

### flatNameList

    java.util.List<E> flatNameList

  A list of names of all fields including nested fields.

  The nested names are separated by CompoundDs.separator. For example, if compound dataset "A" has the following nested structure,

       A --> m01
       A --> m02
       A --> nest1 --> m11
       A --> nest1 --> m12
       A --> nest1 --> nest2 --> m21
       A --> nest1 --> nest2 --> m22
       i.e.
       A = { m01, m02, nest1{m11, m12, nest2{ m21, m22}}}

  The flatNameList of compound dataset "A" will be {m01, m02, nest1[m11, nest1[m12, nest1[nest2[m21, nest1[nest2[m22}

### flatTypeList

    java.util.List<E> flatTypeList

  A list of datatypes of all fields including nested fields.

### isExternal

    boolean isExternal

  flag to indicate is the dataset is an external dataset

Class ncsa.hdf.object.h5.H5Datatype extends Datatype implements Serializable

serialVersionUID: -750546422258749792L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object.

### isNamed

    boolean isNamed

  Flag to indicate if this datatype is a named datatype

### nAttributes

    int nAttributes

### obj_info

    H5O_info_t obj_info

### isVLEN

    boolean isVLEN

### description

    java.lang.String description

Class ncsa.hdf.object.h5.H5File extends FileFormat implements Serializable

serialVersionUID: 6247335559471526045L

Serialized Fields

### flag

    int flag

  the file access flag. Valid values are HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5F_ACC_RDWR and HDF5Constants.H5F_ACC_CREAT.

### indexType

    int indexType

  The index type. Valid values are HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_INDEX_CRT_ORDER.

### rootNode

    javax.swing.tree.DefaultMutableTreeNode rootNode

  The root node of the file hierarchy.

### libver

    int[] libver

  The library version bounds

### attrFlag

    boolean attrFlag

Class ncsa.hdf.object.h5.H5Group extends Group implements Serializable

serialVersionUID: -951164512330444150L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### nAttributes

    int nAttributes

### obj_info

    H5O_info_t obj_info

Class ncsa.hdf.object.h5.H5Link extends HObject implements Serializable

serialVersionUID: -8137277460521594367L

Serialized Fields

### obj_info

    H5O_info_t obj_info

Class ncsa.hdf.object.h5.H5ScalarDS extends ScalarDS implements Serializable

serialVersionUID: 2887517608230611642L

Serialized Fields

### attributeList

    java.util.List<E> attributeList

  The list of attributes of this data object. Members of the list are instance of Attribute.

### paletteRefs

    byte[] paletteRefs

  The byte array containing references of palettes. Each reference requires eight bytes storage. Therefore, the array length is 8*numberOfPalettes.

### isVLEN

    boolean isVLEN

  flag to indicate if the dataset is a variable length

### isEnum

    boolean isEnum

  flag to indicate if the dataset is enum

### isExternal

    boolean isExternal

  flag to indicate if the dataset is an external dataset

### isArrayOfCompound

    boolean isArrayOfCompound

### isNativeDatatype

    boolean isNativeDatatype

  flag to indicate if the datatype in file is the same as dataype in memory

### isRegRef

    boolean isRegRef

  flag to indicate is the datatype is reg. ref.

### nAttributes

    int nAttributes

### obj_info

    H5O_info_t obj_info

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