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org.eclipse.dawnsci.nexus
Interface NexusFile






All Superinterfaces:
java.lang.AutoCloseable


All Known Implementing Classes:
NexusFileHDF5




public interface NexusFile
extends java.lang.AutoCloseable
Replacement for old Nexus file interface
 
 All elements of a path can be augmented with an optional NX_class string appended on
 with a ":". If the NX_class attribute does not match then an
 IllegalArgumentException will be thrown.











Field Summary

Fields 

Modifier and Type
Field and Description


static int
COMPRESSION_LZW_L1
Compression using LZW level 1



static int
COMPRESSION_NONE
No compression



static java.lang.String
NX_URL_SCHEME
Scheme for NeXus URI used to refer to external files



static java.lang.String
NXCLASS
Deprecated. 
Use NexusConstants.NXCLASS




static java.lang.String
NXCLASS_SEPARATOR 









Method Summary

All Methods Instance Methods Abstract Methods 

Modifier and Type
Method and Description


void
activateSwmrMode()
Activates SWMR mode.



void
addAttribute(Node node,
            Attribute... attribute)
Add (and write) attribute(s) to given node



void
addAttribute(java.lang.String path,
            Attribute... attribute)
Add (and write) attribute(s) to given path



void
addNode(GroupNode group,
       java.lang.String name,
       Node node)
Add node to group.



void
addNode(java.lang.String path,
       Node node)
Add node to given path.



void
close()
Close file



void
createAndOpenToWrite()
Create file and open to write



Attribute
createAttribute(IDataset attr)
Create attribute



DataNode
createData(GroupNode group,
          IDataset data)
Create data node in given group



DataNode
createData(GroupNode group,
          ILazyWriteableDataset data)
Create data node in given group



DataNode
createData(GroupNode group,
          ILazyWriteableDataset data,
          int compression)
Create data node in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          IDataset data)
Create data node with given name in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          ILazyWriteableDataset data)
Create data node with given name in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          ILazyWriteableDataset data,
          int compression)
Create data node with given name in given group



DataNode
createData(java.lang.String path,
          IDataset data,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary



DataNode
createData(java.lang.String path,
          ILazyWriteableDataset data,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.



DataNode
createData(java.lang.String path,
          ILazyWriteableDataset data,
          int compression,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary



DataNode
createData(java.lang.String path,
          java.lang.String name,
          IDataset data,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary



DataNode
createData(java.lang.String path,
          java.lang.String name,
          ILazyWriteableDataset data,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary.



DataNode
createData(java.lang.String path,
          java.lang.String name,
          ILazyWriteableDataset data,
          int compression,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary



int
flush()
Flush data to filesystem



void
flushAllCachedDatasets()
Flush datasets cached when setCacheDataset(boolean) is set true



java.lang.String
getAttributeValue(java.lang.String path)
The full attribute key is: @
 e.g.



DataNode
getData(GroupNode group,
       java.lang.String name)
Get data node in group with given name



DataNode
getData(java.lang.String path)
Get data node with given path



java.lang.String
getFilePath()
Returns the file path of this NexusFile



GroupNode
getGroup(GroupNode group,
        java.lang.String name,
        java.lang.String nxClass,
        boolean createPathIfNecessary)
Get group in group with given name and create path if necessary



GroupNode
getGroup(java.lang.String path,
        boolean createPathIfNecessary)
Get group with given path and create path if necessary



Node
getNode(java.lang.String path)
Get Node with given path.



java.lang.String
getPath(Node node)
Get path of node from internal tree



java.lang.String
getRoot()
Get the path of root node from internal tree



Tree
getTree()
Get the complete tree of data.



boolean
isPathValid(java.lang.String path)
Checks if a path within the file exists



void
link(java.lang.String source,
    java.lang.String destination)
Link source to a destination.



void
linkExternal(java.net.URI source,
            java.lang.String destination,
            boolean isGroup)
Link source in another file to a destination.



void
openToRead()
Open file to only read



void
openToWrite(boolean createIfNecessary)
Open file to write



void
removeNode(GroupNode group,
          java.lang.String name)
Remove node from given group.



void
removeNode(java.lang.String path,
          java.lang.String name)
Remove node from given path.



void
setCacheDataset(boolean cacheDataset)
Sets the datasets written to to be held open until the file is closed
 
 With this value set to true, datasets will not be flushed until the file is closed,
 call flushAllCachedDatasets() to flush



void
setDebug(boolean debug)
Set to instrument some method calls via logging at the DEBUG level



void
setWritesAsync(boolean async)
Set to writes to be performed asynchronously for data nodes created after calling this
















Field Detail





NXCLASS
@Deprecated
static final java.lang.String NXCLASS
Deprecated. Use NexusConstants.NXCLASS

See Also:
Constant Field Values








NXCLASS_SEPARATOR
static final java.lang.String NXCLASS_SEPARATOR

See Also:
Constant Field Values








COMPRESSION_NONE
static final int COMPRESSION_NONE
No compression

See Also:
Constant Field Values








COMPRESSION_LZW_L1
static final int COMPRESSION_LZW_L1
Compression using LZW level 1

See Also:
Constant Field Values








NX_URL_SCHEME
static final java.lang.String NX_URL_SCHEME
Scheme for NeXus URI used to refer to external files

See Also:
Constant Field Values










Method Detail





getFilePath
java.lang.String getFilePath()
Returns the file path of this NexusFile

Returns:
file path








openToRead
void openToRead()
         throws NexusException
Open file to only read

Throws:
java.io.IOException
NexusException








openToWrite
void openToWrite(boolean createIfNecessary)
          throws NexusException
Open file to write

Parameters:
createIfNecessary - if true, then create file if it does not exist
Throws:
java.io.IOException
NexusException








createAndOpenToWrite
void createAndOpenToWrite()
                   throws NexusException
Create file and open to write

Throws:
java.io.IOException
NexusException








setWritesAsync
void setWritesAsync(boolean async)
Set to writes to be performed asynchronously for data nodes created after calling this

Parameters:
async - 








setCacheDataset
void setCacheDataset(boolean cacheDataset)
Sets the datasets written to to be held open until the file is closed
 
 With this value set to true, datasets will not be flushed until the file is closed,
 call flushAllCachedDatasets() to flush

Parameters:
cacheDataset - 








flushAllCachedDatasets
void flushAllCachedDatasets()
Flush datasets cached when setCacheDataset(boolean) is set true







setDebug
void setDebug(boolean debug)
Set to instrument some method calls via logging at the DEBUG level

Parameters:
debug - 








getRoot
java.lang.String getRoot()
Get the path of root node from internal tree

Returns:
root node path








getPath
java.lang.String getPath(Node node)
Get path of node from internal tree

Parameters:
node - 
Returns:
(depth-first) path of node








getGroup
GroupNode getGroup(java.lang.String path,
                   boolean createPathIfNecessary)
            throws NexusException
Get group with given path and create path if necessary

Parameters:
path - 
createPathIfNecessary - 
Returns:
node or null if group does not exist at specified path
Throws:
NexusException








getGroup
GroupNode getGroup(GroupNode group,
                   java.lang.String name,
                   java.lang.String nxClass,
                   boolean createPathIfNecessary)
            throws NexusException
Get group in group with given name and create path if necessary

Parameters:
group - 
name - 
nxClass - 
createPathIfNecessary - 
Returns:
node or null
Throws:
NexusException - if node is not a group at specified path or group does not exist and not creating path








getData
DataNode getData(java.lang.String path)
          throws NexusException
Get data node with given path

Parameters:
path - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException








getData
DataNode getData(GroupNode group,
                 java.lang.String name)
          throws NexusException
Get data node in group with given name

Parameters:
group - 
name - 
Returns:
node or null if data does not exist in group
Throws:
NexusException








addNode
void addNode(java.lang.String path,
             Node node)
      throws NexusException
Add node to given path. This will recursively add other nodes if the given node is a group node.

Parameters:
path - 
node - 
Throws:
NexusException - if node already exists at given path or parts of path does not exist








addNode
void addNode(GroupNode group,
             java.lang.String name,
             Node node)
      throws NexusException
Add node to group. This will recursively add other nodes if the given node is a group node.

Parameters:
group - 
name - 
node - 
Throws:
NexusException - if node already exists in group with name








removeNode
void removeNode(java.lang.String path,
                java.lang.String name)
         throws NexusException
Remove node from given path.
 

 Note, this will fail if the file is in SWMR node

Parameters:
path - path to parent group of node
name - name of node in parent group
Throws:
NexusException








removeNode
void removeNode(GroupNode group,
                java.lang.String name)
         throws NexusException
Remove node from given group.
 

 Note, this will fail if the file is in SWMR node

Parameters:
group - parent group of node
name - name of node in parent group
Throws:
NexusException








createData
DataNode createData(java.lang.String path,
                    ILazyWriteableDataset data,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.

Parameters:
path - to group
data - 
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(java.lang.String path,
                    java.lang.String name,
                    ILazyWriteableDataset data,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given name and path to its group and create path if necessary.

Parameters:
path - to parent group
name - name within parent group
data - 
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(java.lang.String path,
                    ILazyWriteableDataset data,
                    int compression,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given path to its group and create path if necessary

Parameters:
path - to parent group
data - data
compression - 
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(java.lang.String path,
                    java.lang.String name,
                    ILazyWriteableDataset data,
                    int compression,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given name and path to its group and create path if necessary

Parameters:
path - to parent group
name - name within parent group
data - dataset
compression - 
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(java.lang.String path,
                    IDataset data,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given path to its group and create path if necessary

Parameters:
path - to group
data - dataset
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(java.lang.String path,
                    java.lang.String name,
                    IDataset data,
                    boolean createPathIfNecessary)
             throws NexusException
Create data node with given path to its group and create path if necessary

Parameters:
path - to group
name - name within parent group
data - dataset
createPathIfNecessary - 
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    ILazyWriteableDataset data)
             throws NexusException
Create data node in given group

Parameters:
group - parent group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    java.lang.String name,
                    ILazyWriteableDataset data)
             throws NexusException
Create data node with given name in given group

Parameters:
group - parent group
name - name within group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    ILazyWriteableDataset data,
                    int compression)
             throws NexusException
Create data node in given group

Parameters:
group - 
data - 
compression - 
Returns:
node
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    java.lang.String name,
                    ILazyWriteableDataset data,
                    int compression)
             throws NexusException
Create data node with given name in given group

Parameters:
group - parent group
data - dataset
compression - 
Returns:
node
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    IDataset data)
             throws NexusException
Create data node in given group

Parameters:
group - parent group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
DataNode createData(GroupNode group,
                    java.lang.String name,
                    IDataset data)
             throws NexusException
Create data node with given name in given group

Parameters:
group - parent group
name - name within group
data - dataset
Returns:
Throws:
NexusException








createAttribute
Attribute createAttribute(IDataset attr)
Create attribute

Parameters:
attr - 
Returns:
attribute








getAttributeValue
java.lang.String getAttributeValue(java.lang.String path)
                            throws NexusException
The full attribute key is: @
 e.g. /entry1/data@napimount

Parameters:
fullAttributeKey - 
Returns:
Throws:
NexusException








addAttribute
void addAttribute(Node node,
                  Attribute... attribute)
           throws NexusException
Add (and write) attribute(s) to given node

Parameters:
node - 
attribute - 
Throws:
NexusException








addAttribute
void addAttribute(java.lang.String path,
                  Attribute... attribute)
           throws NexusException
Add (and write) attribute(s) to given path

Parameters:
path - 
attribute - 
Throws:
NexusException








link
void link(java.lang.String source,
          java.lang.String destination)
   throws NexusException
Link source to a destination. If the destination ends in 
 then the source name is added to the destination.

Parameters:
source - 
destination - 
Throws:
NexusException








linkExternal
void linkExternal(java.net.URI source,
                  java.lang.String destination,
                  boolean isGroup)
           throws NexusException
Link source in another file to a destination. If the destination ends in 
 then the source name is added to the destination.

Parameters:
source - 
destination - 
isGroup - 
Throws:
NexusException








flush
int flush()
   throws NexusException
Flush data to filesystem

Returns:
the nexus int code for the flush or -1 if unsucessfull.
Throws:
NexusException








close
void close()
    throws NexusException
Close file

Specified by:
close in interface java.lang.AutoCloseable
Throws:
NexusException








isPathValid
boolean isPathValid(java.lang.String path)
Checks if a path within the file exists

Parameters:
path - 
Returns:
true if path exists








activateSwmrMode
void activateSwmrMode()
               throws NexusException
Activates SWMR mode. The file must have been created as
 with SWMR enabled.

Throws:
NexusException - if SWMR mode could not be activated








getNode
Node getNode(java.lang.String path)
      throws NexusException
Get Node with given path. Can be a GroupNode or a DataNode

Parameters:
path - 
Returns:
node or null if group does not exist at specified path
Throws:
NexusException








getTree
Tree getTree()
      throws NexusException
Get the complete tree of data.

Returns:
tree or null if none exists.
Throws:
NexusException














Skip navigation links




Overview
Package
Class
Tree
Deprecated
Index
Help




Prev Class
Next Class


Frames
No Frames


All Classes






Summary: 
Nested | 
Field | 
Constr | 
Method


Detail: 
Field | 
Constr | 
Method