de.mpg.biochem.mars.io

Interface MoleculeArchiveSource

All Superinterfaces:

java.lang.AutoCloseable, MoleculeArchiveStorage

All Known Implementing Classes:

MoleculeArchiveAmazonS3Source, MoleculeArchiveFSSource

public interface MoleculeArchiveSource
extends MoleculeArchiveStorage

Basic interface for

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INDEXES_FILE_NAME
static java.lang.String	METADATA_SUBDIRECTORY_NAME
static java.lang.String	MOLECULES_SUBDIRECTORY_NAME
static java.lang.String	PROPERTIES_FILE_NAME
static java.lang.String	ROVER_FILE_EXTENSION

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

MOLECULE_ARCHIVE_ENDING, MOLECULE_ARCHIVE_STORE_ENDING, N5_DATASET_DIRECTORY_ENDING

Method Summary

Modifier and Type	Method and Description
java.lang.String	getArchiveType()
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()
void	initializeLocation()
boolean	isReachable()
boolean	isVirtual()
void	removeMetadata(java.lang.String metaUID)
void	removeMolecule(java.lang.String UID)
void	setPath(java.lang.String path)

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

close, deepList, deepList, deepList, deepList, deepList, deepListHelper, exists, getGroupSeparator, getURI, groupPath, list, listDirectories, listFiles

Field Detail

PROPERTIES_FILE_NAME

static final java.lang.String PROPERTIES_FILE_NAME

See Also:

Constant Field Values

INDEXES_FILE_NAME

static final java.lang.String INDEXES_FILE_NAME

See Also:

Constant Field Values

MOLECULES_SUBDIRECTORY_NAME

static final java.lang.String MOLECULES_SUBDIRECTORY_NAME

See Also:

Constant Field Values

METADATA_SUBDIRECTORY_NAME

static final java.lang.String METADATA_SUBDIRECTORY_NAME

See Also:

Constant Field Values

ROVER_FILE_EXTENSION

static final java.lang.String ROVER_FILE_EXTENSION

See Also:

Constant Field Values

Method Detail

setPath

void setPath(java.lang.String path)

getPath

java.lang.String getPath()

getName

java.lang.String getName()

initializeLocation

void initializeLocation()
                 throws java.io.IOException

Throws:

java.io.IOException

isVirtual

boolean isVirtual()

isReachable

boolean isReachable()

getArchiveType

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

Throws:

java.io.IOException

getInputStream

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

Throws:

java.io.IOException

getOutputStream

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

Throws:

java.io.IOException

getRoverInputStream

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

Throws:

java.io.IOException

getRoverOutputStream

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

Throws:

java.io.IOException

getPropertiesInputStream

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

Throws:

java.io.IOException

getPropertiesOutputStream

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

Throws:

java.io.IOException

getIndexesInputStream

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

Throws:

java.io.IOException

getIndexesOutputStream

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

Throws:

java.io.IOException

getMoleculeInputStream

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

Throws:

java.io.IOException

getMoleculeOutputStream

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

Throws:

java.io.IOException

removeMolecule

void removeMolecule(java.lang.String UID)
             throws java.io.IOException

Throws:

java.io.IOException

getMetadataInputStream

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

Throws:

java.io.IOException

getMetadataOutputStream

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

Throws:

java.io.IOException

getMoleculeUIDs

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

getMetadataUIDs

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

removeMetadata

void removeMetadata(java.lang.String metaUID)
             throws java.io.IOException

Throws:

java.io.IOException