ucar.nc2.dataset
Class SequenceDS

java.lang.Object
  ucar.nc2.Variable
      ucar.nc2.Structure
          ucar.nc2.dataset.StructureDS
              ucar.nc2.dataset.SequenceDS

All Implemented Interfaces:

Comparable<VariableSimpleIF>, Enhancements, VariableEnhanced, ProxyReader, VariableIF, VariableSimpleIF

public class SequenceDS
extends StructureDS

Enhance sequence

Since:

Nov 10, 2009

Author:

caron

Nested Class Summary

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

Variable.Cache

Field Summary

Fields inherited from class ucar.nc2.dataset.StructureDS

orgVar

Fields inherited from class ucar.nc2.Structure

defaultBufferSize, isSubset, memberHash, members

Fields inherited from class ucar.nc2.Variable

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

Constructor Summary

SequenceDS(Group g, Sequence orgSeq)

Method Summary

StructureDataIterator	getStructureIterator(int bufferSize) Get an efficient iterator over all the data in the Structure.
Array	read() Read all the data for this Variable and return a memory resident Array.
Array	read(Section section) Read a section of the data for this Variable from the netcdf file and return a memory resident Array.

Methods inherited from class ucar.nc2.dataset.StructureDS

addCoordinateSystem, clearCoordinateSystems, convert, convert, copy, enhance, getCoordinateSystems, getDescription, getOriginalDataType, getOriginalName, getOriginalVariable, getUnitsString, reallyRead, reallyRead, removeCoordinateSystem, select, setName, setOriginalVariable, setUnitsString

Methods inherited from class ucar.nc2.Structure

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

Methods inherited from class ucar.nc2.Variable

_read, _read, addAttribute, clone, compareTo, createNewCache, equals, extraInfo, findAttribute, findAttributeIgnoreCase, findDimensionIndex, getAttributes, getDataType, getDimension, getDimensions, getDimensionsAll, getDimensionsString, getEnumTypedef, getName, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameAndDimensions, getNameEscaped, getParentGroup, getParentStructure, getProxyReader, getRanges, getRank, getScalarData, getShape, getShape, getShapeAll, getShapeAsSection, getShortName, getSize, getSizeToCache, getSPobject, hasCachedData, hashCode, invalidateCache, isCoordinateVariable, isImmutable, isMemberOfStructure, isMetadata, isScalar, isUnknownLength, isUnlimited, isUnsigned, isVariableLength, lookupEnumString, read, read, read, readScalarByte, readScalarDouble, readScalarFloat, readScalarInt, readScalarLong, readScalarShort, readScalarString, readToByteChannel, remove, removeAttribute, removeAttributeIgnoreCase, resetDimensions, resetShape, section, section, setCachedData, setCachedData, setDataType, setDimension, setDimensions, setDimensions, setDimensionsAnonymous, setElementSize, setEnumTypedef, setIsScalar, setParentStructure, setProxyReader, setSizeToCache, setSPobject, setValues, setValues, slice, toString, toStringDebug, writeCDL

Methods inherited from class java.lang.Object

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

Methods inherited from interface ucar.nc2.VariableIF

findAttribute, findAttributeIgnoreCase, findDimensionIndex, getAttributes, getDataType, getDimension, getDimensions, getDimensionsAll, getElementSize, getName, getNameAndDimensions, getNameEscaped, getParentGroup, getParentStructure, getRanges, getRank, getShape, getShapeAsSection, getShortName, getSize, isCoordinateVariable, isMemberOfStructure, isMetadata, isScalar, isUnlimited, isUnsigned, isVariableLength, read, read, readScalarByte, readScalarDouble, readScalarFloat, readScalarInt, readScalarLong, readScalarShort, readScalarString, section, toStringDebug

Methods inherited from interface java.lang.Comparable

compareTo

Constructor Detail

SequenceDS

public SequenceDS(Group g,
                  Sequence orgSeq)

Method Detail

getStructureIterator

public StructureDataIterator getStructureIterator(int bufferSize)
                                           throws 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:

IOException - on read error

read

public Array read(Section section)
           throws IOException,
                  InvalidRangeException

Description copied from class: Variable

Read a section of the data for this Variable from the netcdf file and return a memory resident Array. The Array has the same element type as the Variable, and the requested shape. Note that this does not do rank reduction, so the returned Array has the same rank as the Variable. Use Array.reduce() for rank reduction.

If the Variable is a member of an array of Structures, this returns only the variable's data in the first Structure, so that the Array shape is the same as the Variable. To read the data in all structures, use readAllStructures().

Note this only allows you to specify a subset of this variable. If the variable is nested in a array of structures and you want to subset that, use NetcdfFile.read(String sectionSpec, boolean flatten);

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:

IOException - if error

InvalidRangeException - if section is invalid

read

public Array read()
           throws IOException

Description copied from class: Variable

Read all the data for this Variable and return a memory resident Array. The Array has the same element type and shape as the Variable.

If the Variable is a member of an array of Structures, this returns only the variable's data in the first Structure, so that the Array shape is the same as the Variable. To read the data in all structures, use readAllStructures().

Specified by:

read in interface VariableIF

Overrides:

read in class Variable

Returns:

the requested data in a memory-resident Array.

Throws:

IOException