cross.datastructures.fragments

Class FileFragment

java.lang.Object

cross.datastructures.fragments.FileFragment

All Implemented Interfaces:

IFileFragment, IFragment, IGroupFragment, IIterableFragment, IXMLSerializable, Externalizable, Serializable, Comparable<Object>, Iterable<IVariableFragment>, Comparator<IFragment>

public class FileFragment
extends Object
implements IFileFragment

FileFragment can be considered the root element of a Tree of VariableFragments, where each VariableFragment represents one Variable within the (possibly not yet existing) File F. FileFragments should be created and registered by calling FragmentTools.create(String filename) or appropriate get(...) methods, which create and return a new FileFragment, if not previously existent, or return the Fragment matching the given filename. Filenames can be local or global, since the IO-mechanism decides, whether a file given by filename already exists in input or output location. Files already existing in output location are overwritten by default, but this behavior can be changed by setting the configuration option output.overwrite to false. Then, files are created in the default location for temporary files.

Author:

Nils Hoffmann

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	NUMBERFORMAT

Constructor Summary

Constructors

Constructor and Description
FileFragment() Create a FileFragment
FileFragment(File f) Create a FileFragment connected to File f.
FileFragment(File basedir, String name) Create a plain FileFragment at basedir with name.
FileFragment(URI u) Create a FileFragment connected to URI u.

Method Summary

Methods

Modifier and Type	Method and Description
void	addAttribute(Attribute a) Add an attribute
IVariableFragment	addChild(String name) Add a child of given name or return already existing one.
void	addChildren(IVariableFragment... fragments) Add a number of children.
void	addDimensions(Dimension... dims1) Add dimensions to this IFileFragment.
void	addSourceFile(Collection<IFileFragment> c) Add source FileFragments contained in Collection c to this FileFragment.
void	addSourceFile(IFileFragment... ff) Add source FileFragments contained in ff to this FileFragment.
void	appendXML(org.jdom.Element e) Append structural information of this FileFragment to Element e.
void	clearArrays() Iterates through all VariableFragments, clearing in memory arrays, except for source_files.
void	clearDimensions() Resets all dimensions of this fragment.
int	compare(IFragment arg0, IFragment arg1) Compare Fragments by comparing their string representations.
int	compareTo(Object arg0) Only perform comparison on instances of Fragment.
boolean	equals(Object obj)
String	getAbsolutePath() Return this FileFragment's storage location as string representation.
Attribute	getAttribute(Attribute a) Return a given Attribute.
Attribute	getAttribute(String name) Return a given Attribute by name.
List<Attribute>	getAttributes() Return attributes of Fragment.
ICacheDelegate<IVariableFragment,List<Array>>	getCache() Return a Cache for variable fragment array data for this fragment.
IVariableFragment	getChild(String varname) Returns the child with name varname.
IVariableFragment	getChild(String varname, boolean loadStructureOnly) Returns the child with name varname.
Set<Dimension>	getDimensions() The registered dimensions of this FileFragment as an unmodifiable Set.
long	getID() The unique ID (between runs) of this FileFragment.
List<IVariableFragment>	getImmediateChildren() Returns the immediate children of this fileFragment.
String	getName() Return the name of this FileFragment, does not include directory or other prefixed information.
IGroupFragment	getParent()
int	getSize() Return the number of children of this FileFragment.
Collection<IFileFragment>	getSourceFiles() Use this method with caution!
StatsMap	getStats() Retrieve statistics from a Fragment.
URI	getUri() Get the uniform resource identifier for this FileFragment.
boolean	hasAttribute(Attribute a) Query for an Attribute.
boolean	hasAttribute(String name) Query for an Attribute by name.
boolean	hasChild(IVariableFragment vf) Query this fragment for knowledge of a given VariableFragment.
boolean	hasChild(String varname) Query this fragment for knowledge of a child variable with the given name.
boolean	hasChildren(IVariableFragment... vf) Query FileFragment for the given VariableFragments.
boolean	hasChildren(String... s) Query FileFragment for children with the given strings as names.
int	hashCode()
boolean	isModified()
Iterator<IVariableFragment>	iterator() Creates an iterator over all children of this FileFragment by the time of creation of the iterator.
long	nextGID()
static String	printFragment(IFileFragment ff)
void	readExternal(ObjectInput in)
void	readStructure() Call the IDataSource for this FileFragment and load the structural information for this fragment.
void	removeChild(IVariableFragment variableFragment) Remove the given IVariableFragment from the list of this FileFragment's children.
void	removeSourceFile(IFileFragment ff) Remove the given source file.
void	removeSourceFiles() Removes all currently associated source files.
boolean	save() Store this fragment using the IDataSource responsible for handling this fragment name's extension.
void	setAttributes(Attribute... a) Set attributes on a fragment.
void	setCache(ICacheDelegate<IVariableFragment,List<Array>> persistentCache) Sets the array cache of this FileFragment as specified if the current cache has not yet been initialized (is null).
void	setFile(File f1) Change the filename of this Fragment.
void	setFile(String file) Change the filename of this Fragment.
void	setID(long id)
void	setStats(StatsMap stats1) Set statistics on a Fragment.
String	toString()
void	writeExternal(ObjectOutput out)

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

NUMBERFORMAT

public static final String NUMBERFORMAT

See Also:

Constant Field Values

Constructor Detail

FileFragment

public FileFragment()

Create a FileFragment

FileFragment

public FileFragment(File f)

Create a FileFragment connected to File f.

Parameters:

f -

FileFragment

public FileFragment(URI u)

Create a FileFragment connected to URI u.

Parameters:

u -

FileFragment

public FileFragment(File basedir,
            String name)

Create a plain FileFragment at basedir with name. If name is null, uses a default filename.

Parameters:

basedir -

name -

Method Detail

printFragment

public static String printFragment(IFileFragment ff)

setCache

public void setCache(ICacheDelegate<IVariableFragment,List<Array>> persistentCache)

Sets the array cache of this FileFragment as specified if the current cache has not yet been initialized (is null). Throws an IllegalStateException otherwise to prevent loss of cached data.

Specified by:

setCache in interface IFileFragment

Throws:

IllegalStateException

addChild

public IVariableFragment addChild(String name)

Description copied from interface: IFileFragment

Add a child of given name or return already existing one.

Specified by:

addChild in interface IFileFragment

Returns:

variableFragment

addChildren

public void addChildren(IVariableFragment... fragments)

Description copied from interface: IFileFragment

Add a number of children.

Specified by:

addChildren in interface IFileFragment

Specified by:

addChildren in interface IGroupFragment

addDimensions

public void addDimensions(Dimension... dims1)

Description copied from interface: IFileFragment

Add dimensions to this IFileFragment.

Specified by:

addDimensions in interface IFileFragment

addSourceFile

public void addSourceFile(Collection<IFileFragment> c)

Description copied from interface: IFileFragment

Add source FileFragments contained in Collection c to this FileFragment.

Specified by:

addSourceFile in interface IFileFragment

addSourceFile

public void addSourceFile(IFileFragment... ff)

Description copied from interface: IFileFragment

Add source FileFragments contained in ff to this FileFragment.

Specified by:

addSourceFile in interface IFileFragment

appendXML

public void appendXML(org.jdom.Element e)

Description copied from interface: IFileFragment

Append structural information of this FileFragment to Element e.

Specified by:

appendXML in interface IFileFragment

Specified by:

appendXML in interface IXMLSerializable

clearArrays

public void clearArrays()
                 throws IllegalStateException

Description copied from interface: IFileFragment

Iterates through all VariableFragments, clearing in memory arrays, except for source_files. Throws IllegalStateException if VariableData has been altered.

Specified by:

clearArrays in interface IFileFragment

Throws:

IllegalStateException

clearDimensions

public void clearDimensions()

Description copied from interface: IFileFragment

Resets all dimensions of this fragment. Does not set Dimensions to null in IVariableFragments having these Dimensions!

Specified by:

clearDimensions in interface IFileFragment

compare

public int compare(IFragment arg0,
          IFragment arg1)

Description copied from interface: IFragment

Compare Fragments by comparing their string representations.

Specified by:

compare in interface IFragment

Specified by:

compare in interface Comparator<IFragment>

Parameters:

arg0 -

arg1 -

Returns:

See Also:

Fragment.compare(cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IFragment)

compareTo

public int compareTo(Object arg0)

Description copied from interface: IFragment

Only perform comparison on instances of Fragment.

Specified by:

compareTo in interface IFragment

Specified by:

compareTo in interface Comparable<Object>

Parameters:

arg0 -

Returns:

See Also:

Fragment.compareTo(java.lang.Object)

getAbsolutePath

public String getAbsolutePath()

Description copied from interface: IFileFragment

Return this FileFragment's storage location as string representation.

Specified by:

getAbsolutePath in interface IFileFragment

Returns:

getAttribute

public Attribute getAttribute(Attribute a)

Description copied from interface: IFragment

Return a given Attribute.

Specified by:

getAttribute in interface IFragment

Parameters:

a -

Returns:

the attribute

See Also:

Fragment.getAttribute(ucar.nc2.Attribute)

getAttribute

public Attribute getAttribute(String name)

Description copied from interface: IFragment

Return a given Attribute by name.

Specified by:

getAttribute in interface IFragment

Parameters:

name -

Returns:

the named attribute

See Also:

Fragment.getAttribute(java.lang.String)

getAttributes

public List<Attribute> getAttributes()

Description copied from interface: IFragment

Return attributes of Fragment.

Specified by:

getAttributes in interface IFragment

Returns:

the list of attributes

See Also:

Fragment.getAttributes()

getCache

public ICacheDelegate<IVariableFragment,List<Array>> getCache()

Description copied from interface: IFileFragment

Return a Cache for variable fragment array data for this fragment.

Specified by:

getCache in interface IFileFragment

Returns:

the cache delegate

See Also:

cross.datastructures.fragments.Fragment#getCache()

getChild

public IVariableFragment getChild(String varname)
                           throws ResourceNotAvailableException

Description copied from interface: IFileFragment

Returns the child with name varname. If varname is not found in local structure, try to locate it in sourcefiles. First hit wins. Otherwise throw IllegalArgumentException.

Specified by:

getChild in interface IFileFragment

Specified by:

getChild in interface IGroupFragment

Parameters:

varname -

Returns:

the child fragment

Throws:

ResourceNotAvailableException

See Also:

IFileFragment.getChild(String)

getChild

public IVariableFragment getChild(String varname,
                         boolean loadStructureOnly)
                           throws ResourceNotAvailableException

Description copied from interface: IFileFragment

Returns the child with name varname. If varname is not found in local structure, try to locate it in sourcefiles. First hit wins. Otherwise throw IllegalArgumentException. If loadStructureOnly is true, only the variable structure is retrieved, not the data.

Specified by:

getChild in interface IFileFragment

Parameters:

varname -

loadStructureOnly -

Returns:

Throws:

ResourceNotAvailableException

See Also:

IFileFragment.getChild(String, boolean)

getImmediateChildren

public List<IVariableFragment> getImmediateChildren()

Description copied from interface: IFileFragment

Returns the immediate children of this fileFragment. Does not return children that are only found in referenced source files.

Specified by:

getImmediateChildren in interface IFileFragment

Returns:

getID

public long getID()

Description copied from interface: IFileFragment

The unique ID (between runs) of this FileFragment.

Specified by:

getID in interface IFileFragment

Returns:

getName

public String getName()

Description copied from interface: IFileFragment

Return the name of this FileFragment, does not include directory or other prefixed information.

Specified by:

getName in interface IFileFragment

Specified by:

getName in interface IGroupFragment

getParent

public IGroupFragment getParent()

Specified by:

getParent in interface IFileFragment

Specified by:

getParent in interface IGroupFragment

getSize

public int getSize()

Description copied from interface: IFileFragment

Return the number of children of this FileFragment.

Specified by:

getSize in interface IFileFragment

Specified by:

getSize in interface IGroupFragment

getSourceFiles

public Collection<IFileFragment> getSourceFiles()

Use this method with caution! It will only return the list of source files, if either an array from a parent file has been loaded, or if the sourcefiles have been loaded explicitly. If you want to obtain the list of source files, call: tools.FragmentTools.getSourceFiles(IFileFragment f).

Specified by:

getSourceFiles in interface IFileFragment

Returns:

getStats

public StatsMap getStats()

Description copied from interface: IFragment

Retrieve statistics from a Fragment.

Specified by:

getStats in interface IFragment

Returns:

@see cross.datastructures.fragments.Fragment#getStats()

getUri

public URI getUri()

Get the uniform resource identifier for this FileFragment.

Specified by:

getUri in interface IFileFragment

Returns:

u

hasAttribute

public boolean hasAttribute(Attribute a)

Description copied from interface: IFragment

Query for an Attribute.

Specified by:

hasAttribute in interface IFragment

Parameters:

a -

Returns:

whether the given attribute is known

See Also:

Fragment.hasAttribute(ucar.nc2.Attribute)

hasAttribute

public boolean hasAttribute(String name)

Description copied from interface: IFragment

Query for an Attribute by name.

Specified by:

hasAttribute in interface IFragment

Parameters:

name -

Returns:

whether the named attribute is known

See Also:

Fragment.hasAttribute(java.lang.String)

hasChild

public boolean hasChild(IVariableFragment vf)

Description copied from interface: IGroupFragment

Query this fragment for knowledge of a given VariableFragment.

Specified by:

hasChild in interface IGroupFragment

Returns:

true if a child vf is attached to this FileFragment, else false.

hasChild

public boolean hasChild(String varname)

Description copied from interface: IGroupFragment

Query this fragment for knowledge of a child variable with the given name.

Specified by:

hasChild in interface IGroupFragment

Returns:

true if a child of this name is attached to this FileFragment, false else.

hasChildren

public boolean hasChildren(IVariableFragment... vf)

Description copied from interface: IFileFragment

Query FileFragment for the given VariableFragments.

Specified by:

hasChildren in interface IFileFragment

Returns:

hasChildren

public boolean hasChildren(String... s)

Description copied from interface: IFileFragment

Query FileFragment for children with the given strings as names.

Specified by:

hasChildren in interface IFileFragment

Returns:

isModified

public boolean isModified()

Specified by:

isModified in interface IFileFragment

Returns:

iterator

public Iterator<IVariableFragment> iterator()

Description copied from interface: IFileFragment

Creates an iterator over all children of this FileFragment by the time of creation of the iterator.

Specified by:

iterator in interface IFileFragment

Specified by:

iterator in interface Iterable<IVariableFragment>

nextGID

public long nextGID()

Specified by:

nextGID in interface IGroupFragment

Returns:

readStructure

public void readStructure()
                   throws IllegalStateException

Description copied from interface: IFileFragment

Call the IDataSource for this FileFragment and load the structural information for this fragment. This includes variable names and shapes as well as attributes.

Specified by:

readStructure in interface IFileFragment

Throws:

IllegalStateException - if this fragment has been modified to indicate possible loss of data.

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
                         ClassNotFoundException

Specified by:

readExternal in interface Externalizable

Parameters:

in -

Throws:

IOException

ClassNotFoundException

removeChild

public void removeChild(IVariableFragment variableFragment)

Description copied from interface: IFileFragment

Remove the given IVariableFragment from the list of this FileFragment's children.

Specified by:

removeChild in interface IFileFragment

removeSourceFile

public void removeSourceFile(IFileFragment ff)

Description copied from interface: IFileFragment

Remove the given source file.

Specified by:

removeSourceFile in interface IFileFragment

removeSourceFiles

public void removeSourceFiles()

Description copied from interface: IFileFragment

Removes all currently associated source files.

Specified by:

removeSourceFiles in interface IFileFragment

save

public boolean save()

Description copied from interface: IFileFragment

Store this fragment using the IDataSource responsible for handling this fragment name's extension.

Specified by:

save in interface IFileFragment

Returns:

setAttributes

public void setAttributes(Attribute... a)

Description copied from interface: IFragment

Set attributes on a fragment.

Specified by:

setAttributes in interface IFragment

Parameters:

a -

See Also:

Fragment.setAttributes(ucar.nc2.Attribute[])

addAttribute

public void addAttribute(Attribute a)

Description copied from interface: IFragment

Add an attribute

Specified by:

addAttribute in interface IFragment

setFile

public void setFile(File f1)

Description copied from interface: IFileFragment

Change the filename of this Fragment.

Specified by:

setFile in interface IFileFragment

setFile

public void setFile(String file)

Description copied from interface: IFileFragment

Change the filename of this Fragment.

Specified by:

setFile in interface IFileFragment

setID

public void setID(long id)

Specified by:

setID in interface IGroupFragment

Parameters:

id -

setStats

public void setStats(StatsMap stats1)

Description copied from interface: IFragment

Set statistics on a Fragment.

Specified by:

setStats in interface IFragment

Parameters:

stats1 -

See Also:

Fragment.setStats(cross.datastructures.StatsMap)

toString

public String toString()

Specified by:

toString in interface IFileFragment

Overrides:

toString in class Object

Returns:

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Specified by:

writeExternal in interface Externalizable

Parameters:

out -

Throws:

IOException

getDimensions

public Set<Dimension> getDimensions()

The registered dimensions of this FileFragment as an unmodifiable Set.

Specified by:

getDimensions in interface IFileFragment

Returns:

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Specified by:

equals in interface Comparator<IFragment>

Overrides:

equals in class Object