ucar.nc2

Class Sequence

java.lang.Object

ucar.nc2.CDMNode

ucar.nc2.Variable

ucar.nc2.Structure

ucar.nc2.Sequence

All Implemented Interfaces:

java.lang.Comparable<VariableSimpleIF>, AttributeContainer, ProxyReader, VariableIF, VariableSimpleIF

public class Sequence
extends Structure

Sequence is a one-dimensional Structure with indeterminate length. The only data access is through getStructureIterator(). However, read() will read in the entire data and return an ArraySequence.

Since:

Feb 23, 2008

Nested Class Summary

Nested classes/interfaces inherited from class ucar.nc2.Variable

Variable.Cache

Field Summary

Fields inherited from class ucar.nc2.Structure

defaultBufferSize, isSubset, log, memberHash, members

Fields inherited from class ucar.nc2.Variable

attributes, cache, dataType, debugCaching, defaultCoordsSizeToCache, defaultSizeToCache, dimensions, elementSize, hashCode, isMetadata, isVariableLength, ncfile, permitCaching, proxyReader, shape, shapeAsSection, sizeToCache, spiObject

Fields inherited from class ucar.nc2.CDMNode

annotations, dodsname, group, immutable, parentstruct, shortName, sort

Constructor Summary

Constructors

Constructor and Description
Sequence(NetcdfFile ncfile, Group group, Structure parent, java.lang.String shortName)

Method Summary

Modifier and Type	Method and Description
StructureDataIterator	getStructureIterator(int bufferSize) Get an efficient iterator over all the data in the Structure.
Array	read(int[] origin, int[] shape) UnsupportedOperation
Array	read(java.util.List<Range> ranges) UnsupportedOperation
Array	read(Section section) UnsupportedOperation
Array	read(java.lang.String sectionSpec) UnsupportedOperation
StructureData	readStructure() UnsupportedOperation
StructureData	readStructure(int index) UnsupportedOperation
ArrayStructure	readStructure(int start, int count) UnsupportedOperation
Variable	section(Section subsection) UnsupportedOperation
Variable	slice(int dim, int value) UnsupportedOperation

Methods inherited from class ucar.nc2.Structure

addMemberVariable, calcElementSize, calcStructureSize, copy, findVariable, getElementSize, getNameAndAttributes, getNumberOfMemberVariables, getStructureIterator, getVariableNames, getVariables, isCaching, isSubset, makeStructureMembers, removeMemberVariable, replaceMemberVariable, select, select, setCaching, setImmutable, setMemberVariables, setParentGroup, writeCDL

Methods inherited from class ucar.nc2.Variable

_read, _read, addAll, addAttribute, compareTo, createNewCache, equals, extraInfo, findAttribute, findAttributeIgnoreCase, findDimensionIndex, getAttributes, getDAPName, getDAPName, getDatasetLocation, getDataType, getDescription, getDimension, getDimensions, getDimensionsAll, getDimensionsString, getEnumTypedef, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNetcdfFile, getParentGroup, getProxyReader, getRanges, getRank, getScalarData, getShape, getShape, getShapeAll, getShapeAsSection, getShapeNotScalar, getSize, getSizeToCache, getSPobject, getUnitsString, hasCachedData, hashCode, hashCodeShow, invalidateCache, isCoordinateVariable, isImmutable, isMetadata, isScalar, isUnknownLength, isUnlimited, isUnsigned, isVariableLength, lookupEnumString, read, readScalarByte, readScalarDouble, readScalarFloat, readScalarInt, readScalarLong, readScalarShort, readScalarString, readToByteChannel, readToStream, reallyRead, reallyRead, reduce, remove, removeAttribute, removeAttributeIgnoreCase, resetDimensions, resetShape, section, setCachedData, setCachedData, setDataType, setDimension, setDimensions, setDimensions, setDimensionsAnonymous, setElementSize, setEnumTypedef, setIsScalar, setName, setProxyReader, setSizeToCache, setSPobject, setUnsigned, setValues, setValues, toString, toStringDebug, writeCDL

Methods inherited from class ucar.nc2.CDMNode

annotate, getAnnotation, getAnnotations, getDODSName, getFullName, getFullNameEscaped, getGroup, getImmutable, getName, getParentStructure, getShortName, getSort, isMemberOfStructure, localhash, setDODSName, setImmutable, setParentStructure, setShortName, setSort, unwrap

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ucar.nc2.VariableIF

getFullName, getFullNameEscaped, getParentStructure, getShortName, isMemberOfStructure

Methods inherited from interface ucar.nc2.VariableSimpleIF

getName

Constructor Detail

Sequence

public Sequence(NetcdfFile ncfile,
                Group group,
                Structure parent,
                java.lang.String shortName)

Method Detail

getStructureIterator

public StructureDataIterator getStructureIterator(int bufferSize)
                                           throws java.io.IOException

Description copied from class: Structure

Get an efficient iterator over all the data in the Structure. This is the efficient way to get all the data, it can be much faster than reading one record at a time, and is optimized for large datasets. This is accomplished by buffering bufferSize amount of data at once.

Example:

  StructureDataIterator ii = structVariable.getStructureIterator(100 * 1000);
  while (ii.hasNext()) {
    StructureData sdata = ii.next();
  }
 

Overrides:

getStructureIterator in class Structure

Parameters:

bufferSize - size in bytes to buffer, set < 0 to use default size

Returns:

StructureDataIterator over type StructureData

Throws:

java.io.IOException - on read error

read

public Array read(int[] origin,
                  int[] shape)
           throws java.io.IOException,
                  InvalidRangeException

UnsupportedOperation

Specified by:

read in interface VariableIF

Overrides:

read in class Variable

Parameters:

origin - int array specifying the starting index. If null, assume all zeroes.

shape - int array specifying the extents in each dimension. This becomes the shape of the returned Array.

Returns:

the requested data in a memory-resident Array

Throws:

java.lang.UnsupportedOperationException

java.io.IOException

InvalidRangeException

read

public Array read(java.lang.String sectionSpec)
           throws java.io.IOException,
                  InvalidRangeException

UnsupportedOperation

Specified by:

read in interface VariableIF

Overrides:

read in class Variable

Parameters:

sectionSpec - specification string, eg "1:2,10,:,1:100:10". May optionally have ().

Returns:

the requested data in a memory-resident Array

Throws:

java.lang.UnsupportedOperationException

java.io.IOException

InvalidRangeException

See Also:

for sectionSpec syntax

read

public Array read(java.util.List<Range> ranges)
           throws java.io.IOException,
                  InvalidRangeException

UnsupportedOperation

Overrides:

read in class Variable

Parameters:

ranges - list of Range specifying the section of data to read.

Returns:

the requested data in a memory-resident Array

Throws:

java.lang.UnsupportedOperationException

java.io.IOException - if error

InvalidRangeException - if ranges is invalid

See Also:

Variable.read(Section)

read

public Array read(Section section)
           throws java.io.IOException,
                  InvalidRangeException

UnsupportedOperation

Specified by:

read in interface VariableIF

Overrides:

read in class Variable

Parameters:

section - list of Range specifying the section of data to read. Must be null or same rank as variable. If list is null, assume all data. Each Range corresponds to a Dimension. If the Range object is null, it means use the entire dimension.

Returns:

the requested data in a memory-resident Array

Throws:

java.lang.UnsupportedOperationException

java.io.IOException - if error

InvalidRangeException - if section is invalid

readStructure

public StructureData readStructure()
                            throws java.io.IOException

UnsupportedOperation

Overrides:

readStructure in class Structure

Returns:

StructureData for a scalar

Throws:

java.lang.UnsupportedOperationException

java.io.IOException - on read error

readStructure

public StructureData readStructure(int index)
                            throws java.io.IOException,
                                   InvalidRangeException

UnsupportedOperation

Overrides:

readStructure in class Structure

Parameters:

index - index into 1D array

Returns:

ith StructureData

Throws:

java.lang.UnsupportedOperationException

java.io.IOException - on read error

InvalidRangeException - if index out of range

readStructure

public ArrayStructure readStructure(int start,
                                    int count)
                             throws java.io.IOException,
                                    InvalidRangeException

UnsupportedOperation

Overrides:

readStructure in class Structure

Parameters:

start - start at this index

count - return this many StructureData

Returns:

the StructureData recordsfrom start to start+count-1

Throws:

java.lang.UnsupportedOperationException

java.io.IOException - on read error

InvalidRangeException - if start, count out of range

slice

public Variable slice(int dim,
                      int value)
               throws InvalidRangeException

UnsupportedOperation

Overrides:

slice in class Variable

Parameters:

dim - which dimension to fix

value - at what index value

Returns:

a new Variable which is a logical slice of this Variable.

Throws:

java.lang.UnsupportedOperationException

InvalidRangeException - if dimension or value is illegal

section

public Variable section(Section subsection)
                 throws InvalidRangeException

UnsupportedOperation

Overrides:

section in class Variable

Parameters:

subsection - Section of this variable. Each Range in the section corresponds to a Dimension, and specifies the section of data to read in that Dimension. A Range object may be null, which means use the entire dimension.

Returns:

a new Variable which is a logical section of this Variable.

Throws:

java.lang.UnsupportedOperationException

InvalidRangeException - if section not compatible with shape