ru.biosoft.access
Class FileEntryCollection

java.lang.Object
  ru.biosoft.access.DataElementSupport
      ru.biosoft.access.AbstractDataCollection
          ru.biosoft.access.EntryCollection
              ru.biosoft.access.FileEntryCollection

All Implemented Interfaces:

DataCollection, DataElement

public class FileEntryCollection

extends EntryCollection

Implements simple access procedures to databases in EMBL-like format.

To do:

it is necessary to implement JobControl for index building

Field Summary

protected java.lang.String	end End tag of Entry.
protected java.io.RandomAccessFile	file The data collection file.
protected IndexTable	idxTable Indexes for entry searching by identificator (primary key).
static int	MAX_ENTRY_STR_LENGTH If size of entry more than this constant then Entry store its data in file.
protected java.util.List	nameList Unmodefiable list of names.
static java.lang.String	USE_INDEX_FILE Property to indicate whether index file should be used (by default it is true).

Fields inherited from class ru.biosoft.access.EntryCollection

ENTRY_DELIMITERS_PROPERTY, ENTRY_END_PROPERTY, ENTRY_ID_PROPERTY, ENTRY_START_PROPERTY

Fields inherited from class ru.biosoft.access.AbstractDataCollection

cat, info, notificationEnabled, path, propagationEnabled, v_cache

Fields inherited from interface ru.biosoft.access.DataCollection

CHILDREN_NODE_IMAGE, CHILDREN_NODE_VISIBLE, CLASS_PROPERTY, CLASSPATH_JAR_PROPERTY, COMPARATOR_OBJECT, CONFIG_FILE_PROPERTY, CONFIG_PATH_PROPERTY, DATA_ELEMENT_CLASS_PROPERTY, DEFAULT_CONFIG_FILE, DEFAULT_CONFIG_SUFFIX, DEFAULT_FILTER_CONFIG_SUFFIX, DEFAULT_FORMAT_CONFIG_SUFFIX, DEFAULT_NODE_CONFIG_SUFFIX, DEFAULT_REPOSITORY, DESCRIPTION_PROPERTY, DISPLAY_NAME_PROPERTY, FILE_PATH_PROPERTY, FILE_PROPERTY, FILTER_PROPERTY, ID_FORMAT, IS_ROOT, JOB_CONTROL_PROPERTY, LATE_CHILDREN_INITIALIZATION, MUTABLE, NAME_PROPERTY, NEXT_CONFIG, NODE_IMAGE, NODE_VISIBLE, PRIMARY_COLLECTION, REMOVE_CHILDREN, TRANSFORMER_CLASS

Constructor Summary

FileEntryCollection(DataCollection parent, java.util.Properties properties)
Loads the data collection and its indexes (currently only for id).

Method Summary

void	close() Closes data collection, releases all resources.
boolean	contains(java.lang.String name) Check is file entry collection contains data element with specified name.
protected DataElement	doGet(java.lang.String name) Read entry with specified name from file.
protected void	doPut(DataElement element, boolean isNew) Write entry into the file.
protected void	doRemove(java.lang.String name) Remove entry from the data collection.
java.util.List	getNameList() Gets list of all names in data collection.
int	getSize() Return size of data collection.
boolean	isMutable() Determine is this collection mutable (writable).
java.util.Iterator	iterator() Return iterator for data collection.

Methods inherited from class ru.biosoft.access.EntryCollection

getDataElementType

Methods inherited from class ru.biosoft.access.AbstractDataCollection

addDataCollectionListener, cachePut, checkMutable, contains, doAddPostNotify, doAddPreNotify, doRemovePostNotify, doRemovePreNotify, finalize, fireElementAdded, fireElementChanged, fireElementRemoved, fireElementWillAdd, fireElementWillChange, fireElementWillRemove, get, getCompleteName, getDescription, getInfo, initLog, isNotificationEnabled, isPropagationEnabled, makeInfo, propagateElementChanged, propagateElementWillChange, put, registerRoot, release, remove, removeDataCollectionListener, setNotificationEnabled, setPropagationEnabled, toString

Methods inherited from class ru.biosoft.access.DataElementSupport

getName, getOrigin, registerConstructorWithBadEqual

Methods inherited from class java.lang.Object

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

Methods inherited from interface ru.biosoft.access.DataElement

getName, getOrigin

Field Detail

USE_INDEX_FILE

public static final java.lang.String USE_INDEX_FILE

Property to indicate whether index file should be used (by default it is true).

See Also:

Constant Field Values

MAX_ENTRY_STR_LENGTH

public static final int MAX_ENTRY_STR_LENGTH

If size of entry more than this constant then Entry store its data in file.

See Also:

Constant Field Values

file

protected java.io.RandomAccessFile file

The data collection file.

idxTable

protected IndexTable idxTable

Indexes for entry searching by identificator (primary key).

See Also:

IndexTable

nameList

protected java.util.List nameList

Unmodefiable list of names.

end

protected java.lang.String end

End tag of Entry. (e.g // - for EMBL).

Constructor Detail

FileEntryCollection

public FileEntryCollection(DataCollection parent,
                           java.util.Properties properties)
                    throws java.lang.Exception

Loads the data collection and its indexes (currently only for id). Used by CollectionFactory

Parameters:

parent - Parent data collection.

properties - Properties for creating FileEntryCollection

Throws:

java.lang.Exception

See Also:

CollectionFactory

To do:

"see Format of config file"

Method Detail

doGet

protected DataElement doGet(java.lang.String name)
                     throws java.lang.Exception

Read entry with specified name from file. Use index file for navigation through data file.

Overrides:

doGet in class AbstractDataCollection

Parameters:

name - Name (PK) of the data element that should be extract from data collection.

Returns:

DataElement with specified name.

Throws:

java.lang.Exception

See Also:

AbstractDataCollection.get(String)

doPut

protected void doPut(DataElement element,
                     boolean isNew)
              throws java.lang.Exception

Write entry into the file.

Overrides:

doPut in class AbstractDataCollection

Parameters:

element - Element that should be added into collection.

Throws:

java.lang.Exception - If data element cann't be added.

See Also:

AbstractDataCollection.put(DataElement), IndexTable.put(java.io.RandomAccessFile,String)

doRemove

protected void doRemove(java.lang.String name)
                 throws java.lang.Exception

Remove entry from the data collection. Current implementation not remove entry from the file, but only add 'deleted' after entry.

Overrides:

doRemove in class AbstractDataCollection

Throws:

java.io.IOException - If data element cann't be removed.

java.lang.Exception

See Also:

AbstractDataCollection.remove(String), IndexTable.removeIndex(String)

getSize

public int getSize()

Return size of data collection.

Specified by:

getSize in interface DataCollection

Overrides:

getSize in class AbstractDataCollection

Returns:

Size of data collection.

isMutable

public boolean isMutable()

Determine is this collection mutable (writable).

Specified by:

isMutable in interface DataCollection

Overrides:

isMutable in class AbstractDataCollection

Returns:

Always return TRUE.

contains

public boolean contains(java.lang.String name)

Check is file entry collection contains data element with specified name.

Specified by:

contains in interface DataCollection

Overrides:

contains in class AbstractDataCollection

Parameters:

name - Name of data element.

Returns:

true - if contains, false otherwise.

See Also:

AbstractDataCollection.contains(ru.biosoft.access.DataElement)

iterator

public java.util.Iterator iterator()

Return iterator for data collection. Method remove() supported only for mutable collections. After remove(),put(),get() iterator will be invalid.

Returns:

Iterator

getNameList

public java.util.List getNameList()

Description copied from class: AbstractDataCollection

Gets list of all names in data collection.

Specified by:

getNameList in interface DataCollection

Overrides:

getNameList in class AbstractDataCollection

Returns:

Names of all elements in the data collection.

close

public void close()
           throws java.lang.Exception

Closes data collection, releases all resources. Close data file and index file. This method invalidates DataCollection instance.

Specified by:

close in interface DataCollection

Overrides:

close in class AbstractDataCollection

Throws:

java.io.IOException - When io error occured.

java.lang.Exception