de.mpg.biochem.mars.io

Class MoleculeArchiveFSSource

java.lang.Object

de.mpg.biochem.mars.io.MoleculeArchiveFSSource

All Implemented Interfaces:

MoleculeArchiveSource, MoleculeArchiveStorage, java.lang.AutoCloseable

public class MoleculeArchiveFSSource
extends java.lang.Object
implements MoleculeArchiveSource

Field Summary

Fields inherited from interface de.mpg.biochem.mars.io.MoleculeArchiveSource

INDEXES_FILE_NAME, METADATA_SUBDIRECTORY_NAME, MOLECULES_SUBDIRECTORY_NAME, PROPERTIES_FILE_NAME, ROVER_FILE_EXTENSION

Fields inherited from interface de.mpg.biochem.mars.io.MoleculeArchiveStorage

MOLECULE_ARCHIVE_ENDING, MOLECULE_ARCHIVE_STORE_ENDING, N5_DATASET_DIRECTORY_ENDING

Constructor Summary

Constructors

Constructor and Description
MoleculeArchiveFSSource(java.io.File file) Use to read from an archive or create one.
MoleculeArchiveFSSource(java.lang.String path) Use to read from an archive or create one.

Method Summary

Modifier and Type	Method and Description
boolean	exists(java.lang.String pathName) Test whether a group or dataset exists at a given path.
java.lang.String	getArchiveType()
java.lang.String	getFileExtension()
java.io.InputStream	getIndexesInputStream()
java.io.OutputStream	getIndexesOutputStream()
java.io.InputStream	getInputStream()
java.io.InputStream	getMetadataInputStream(java.lang.String metaUID)
java.io.OutputStream	getMetadataOutputStream(java.lang.String metaUID)
java.util.List<java.lang.String>	getMetadataUIDs()
java.io.InputStream	getMoleculeInputStream(java.lang.String UID)
java.io.OutputStream	getMoleculeOutputStream(java.lang.String UID)
java.util.List<java.lang.String>	getMoleculeUIDs()
java.lang.String	getName()
java.io.OutputStream	getOutputStream()
java.lang.String	getPath()
java.io.InputStream	getPropertiesInputStream()
java.io.OutputStream	getPropertiesOutputStream()
java.io.InputStream	getRoverInputStream()
java.io.OutputStream	getRoverOutputStream()
java.lang.String	getURI()
void	initializeLocation()
boolean	isReachable()
boolean	isVirtual()
java.lang.String[]	list(java.lang.String pathName) List all groups (including datasets) in a group.
java.lang.String[]	listDirectories(java.lang.String pathName) List all groups (including datasets) in a group.
java.lang.String[]	listFiles(java.lang.String pathName) List all groups (including datasets) in a group.
void	removeMetadata(java.lang.String metaUID)
void	removeMolecule(java.lang.String UID)
void	setPath(java.lang.String path)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface de.mpg.biochem.mars.io.MoleculeArchiveStorage

close, deepList, deepList, deepList, deepList, deepList, deepListHelper, getGroupSeparator, groupPath

Constructor Detail

MoleculeArchiveFSSource

public MoleculeArchiveFSSource(java.io.File file)

Use to read from an archive or create one.

Parameters:

file - the file or directory.

MoleculeArchiveFSSource

public MoleculeArchiveFSSource(java.lang.String path)

Use to read from an archive or create one.

Parameters:

path - the full file path.

Method Detail

initializeLocation

public void initializeLocation()

Specified by:

initializeLocation in interface MoleculeArchiveSource

setPath

public void setPath(java.lang.String path)

Specified by:

setPath in interface MoleculeArchiveSource

getPath

public java.lang.String getPath()

Specified by:

getPath in interface MoleculeArchiveSource

getName

public java.lang.String getName()

Specified by:

getName in interface MoleculeArchiveSource

isVirtual

public boolean isVirtual()

Specified by:

isVirtual in interface MoleculeArchiveSource

isReachable

public boolean isReachable()

Specified by:

isReachable in interface MoleculeArchiveSource

getInputStream

public java.io.InputStream getInputStream()
                                   throws java.io.IOException

Specified by:

getInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getOutputStream

public java.io.OutputStream getOutputStream()
                                     throws java.io.IOException

Specified by:

getOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getRoverInputStream

public java.io.InputStream getRoverInputStream()
                                        throws java.io.IOException

Specified by:

getRoverInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getRoverOutputStream

public java.io.OutputStream getRoverOutputStream()
                                          throws java.io.IOException

Specified by:

getRoverOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getArchiveType

public java.lang.String getArchiveType()
                                throws java.io.IOException

Specified by:

getArchiveType in interface MoleculeArchiveSource

Throws:

java.io.IOException

getPropertiesInputStream

public java.io.InputStream getPropertiesInputStream()
                                             throws java.io.IOException

Specified by:

getPropertiesInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getPropertiesOutputStream

public java.io.OutputStream getPropertiesOutputStream()
                                               throws java.io.IOException

Specified by:

getPropertiesOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getIndexesInputStream

public java.io.InputStream getIndexesInputStream()
                                          throws java.io.IOException

Specified by:

getIndexesInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getIndexesOutputStream

public java.io.OutputStream getIndexesOutputStream()
                                            throws java.io.IOException

Specified by:

getIndexesOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getMoleculeInputStream

public java.io.InputStream getMoleculeInputStream(java.lang.String UID)
                                           throws java.io.IOException

Specified by:

getMoleculeInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getMoleculeOutputStream

public java.io.OutputStream getMoleculeOutputStream(java.lang.String UID)
                                             throws java.io.IOException

Specified by:

getMoleculeOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

removeMolecule

public void removeMolecule(java.lang.String UID)

Specified by:

removeMolecule in interface MoleculeArchiveSource

getMetadataInputStream

public java.io.InputStream getMetadataInputStream(java.lang.String metaUID)
                                           throws java.io.IOException

Specified by:

getMetadataInputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

getMetadataOutputStream

public java.io.OutputStream getMetadataOutputStream(java.lang.String metaUID)
                                             throws java.io.IOException

Specified by:

getMetadataOutputStream in interface MoleculeArchiveSource

Throws:

java.io.IOException

removeMetadata

public void removeMetadata(java.lang.String metaUID)

Specified by:

removeMetadata in interface MoleculeArchiveSource

getMoleculeUIDs

public java.util.List<java.lang.String> getMoleculeUIDs()

Specified by:

getMoleculeUIDs in interface MoleculeArchiveSource

getMetadataUIDs

public java.util.List<java.lang.String> getMetadataUIDs()

Specified by:

getMetadataUIDs in interface MoleculeArchiveSource

getFileExtension

public java.lang.String getFileExtension()

getURI

public java.lang.String getURI()

Specified by:

getURI in interface MoleculeArchiveStorage

exists

public boolean exists(java.lang.String pathName)
               throws java.io.IOException

Description copied from interface: MoleculeArchiveStorage

Test whether a group or dataset exists at a given path.

Specified by:

exists in interface MoleculeArchiveStorage

Parameters:

pathName - group path

Returns:

true if the path exists

Throws:

java.io.IOException - an exception is thrown if the source is not accessible

list

public java.lang.String[] list(java.lang.String pathName)
                        throws java.io.IOException

Description copied from interface: MoleculeArchiveStorage

List all groups (including datasets) in a group.

Specified by:

list in interface MoleculeArchiveStorage

Parameters:

pathName - group path

Returns:

list of children

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

listDirectories

public java.lang.String[] listDirectories(java.lang.String pathName)
                                   throws java.io.IOException

Description copied from interface: MoleculeArchiveStorage

List all groups (including datasets) in a group.

Specified by:

listDirectories in interface MoleculeArchiveStorage

Parameters:

pathName - group path

Returns:

list of directories

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

listFiles

public java.lang.String[] listFiles(java.lang.String pathName)
                             throws java.io.IOException

Description copied from interface: MoleculeArchiveStorage

List all groups (including datasets) in a group.

Specified by:

listFiles in interface MoleculeArchiveStorage

Parameters:

pathName - group path

Returns:

list of files

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group