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io.github.h5jan.core
Class NxsFile



java.lang.Object


io.github.h5jan.core.NxsFile







All Implemented Interfaces:
java.lang.AutoCloseable




public class NxsFile
extends java.lang.Object
implements java.lang.AutoCloseable
A simple delegate class which wraps the Dawnsci classes
 for easy reading and writing of datasets.
 
 You may also use the dawnsci classes directly
 however this API will be backwardsly compatible
 and not leak details of HDF5.











Method Summary

All Methods Static Methods Instance Methods Concrete 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() 


static NxsFile
create(java.lang.String path)
Create a new H5 file (overwriting any existing one)



static NxsFile
create(java.lang.String path,
      boolean enableSWMR)
Create a new Nexus file (overwriting any existing one)



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)
Get data node in group with given name



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



boolean
equals(java.lang.Object obj) 


int
flush()
Flush data to filesystem



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



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



DataNode
getData(GroupNode group,
       java.lang.String name) 


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



ILazyDataset
getDataset(java.lang.String path)
Read an ILazyDataset



java.lang.String
getFilePath() 


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 augmentedPath,
        boolean createPathIfNecessary)
Get/Create a group node.



Node
getNode(java.lang.String augmentedPath)
Get any node of any type.



java.lang.String
getPath(Node node)
Path of node



java.lang.String
getRoot()
Root node path



Tree
getTree()
Get the complete tree of data.



int
hashCode() 


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.



static NxsFile
open(java.lang.String path)
Open an existing Nexus file to modify



static NxsFile
reference(java.lang.String path)
Open an existing file read only



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



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)
Print more debuggined



java.lang.String
toString() 






Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait














Method Detail





create
public static NxsFile create(java.lang.String path)
                      throws NexusException,
                             java.io.IOException
Create a new H5 file (overwriting any existing one)

Parameters:
path - 
Returns:
Nexus formatted H5 file
Throws:
NexusException
java.io.IOException








create
public static NxsFile create(java.lang.String path,
                             boolean enableSWMR)
                      throws NexusException,
                             java.io.IOException
Create a new Nexus file (overwriting any existing one)

Parameters:
path - 
enableSWMR - 
Returns:
Nexus file
Throws:
NexusException
java.io.IOException








open
public static NxsFile open(java.lang.String path)
                    throws NexusException
Open an existing Nexus file to modify

Parameters:
path - 
Returns:
Nexus file
Throws:
NexusException








reference
public static NxsFile reference(java.lang.String path)
                         throws NexusException
Open an existing file read only

Parameters:
path - 
Returns:
Nexus file
Throws:
NexusException








hashCode
public int hashCode()

Overrides:
hashCode in class java.lang.Object








equals
public boolean equals(java.lang.Object obj)

Overrides:
equals in class java.lang.Object








getFilePath
public java.lang.String getFilePath()

Returns:
path to file








setDebug
public void setDebug(boolean debug)
Print more debuggined

Parameters:
debug - 








getPath
public java.lang.String getPath(Node node)
Path of node

Parameters:
node - 
Returns:
path








getRoot
public java.lang.String getRoot()
Root node path

Returns:
root








toString
public java.lang.String toString()

Overrides:
toString in class java.lang.Object








getGroup
public GroupNode getGroup(java.lang.String augmentedPath,
                          boolean createPathIfNecessary)
                   throws NexusException
Get/Create a group node.

Parameters:
augmentedPath - 
createPathIfNecessary - 
Returns:
Throws:
NexusException








getNode
public Node getNode(java.lang.String augmentedPath)
             throws NexusException
Get any node of any type.

Parameters:
augmentedPath - 
Returns:
Throws:
NexusException








getGroup
public 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
public 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
public DataNode getData(GroupNode group,
                        java.lang.String name)
                 throws NexusException

Throws:
NexusException








createData
public DataNode createData(java.lang.String path,
                           ILazyWriteableDataset data,
                           int compression,
                           boolean createPathIfNecessary)
                    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








createData
public 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
public 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
public 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
public 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
public 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
public 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
public 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
public 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
public 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
public 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
public 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








addNode
public 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








addNode
public 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








removeNode
public 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








createAttribute
public Attribute createAttribute(IDataset attr)
Create attribute

Parameters:
attr - 
Returns:
attribute








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

Parameters:
path - 
attribute - 
Throws:
NexusException








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

Parameters:
node - 
attribute - 
Throws:
NexusException








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

Parameters:
fullAttributeKey - 
Returns:
Throws:
NexusException








link
public 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
public 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








activateSwmrMode
public 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








flush
public int flush()
          throws NexusException
Flush data to filesystem

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








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







close
public void close()
           throws NexusException

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








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

Parameters:
path - 
Returns:
true if path exists








setCacheDataset
public 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 - 








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

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








getDataset
public ILazyDataset getDataset(java.lang.String path)
                        throws NexusException
Read an ILazyDataset

Parameters:
path - to read
Returns:
lazy dataset which does not use local memory.
Throws:
NexusException - - if cannot read.














Skip navigation links




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Package
Class
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Help




Prev Class
Next Class


Frames
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Summary: 
Nested | 
Field | 
Constr | 
Method


Detail: 
Field | 
Constr | 
Method