diff --git a/bds/source/java/ch/systemsx/cisd/bds/container/Container.java b/bds/source/java/ch/systemsx/cisd/bds/container/Container.java
deleted file mode 100644
index 0db93992aff0bf8e9e8edaf1ecdfab9a8fb52d2d..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/container/Container.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.container;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.AbstractDataStructure;
-import ch.systemsx.cisd.bds.DataStructureFactory;
-import ch.systemsx.cisd.bds.IStorage;
-import ch.systemsx.cisd.bds.Version;
-import ch.systemsx.cisd.bds.fs.FileStorage;
-import ch.systemsx.cisd.bds.hdf5.HDF5Storage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class Container
-{
- private final File baseDir;
-
- public Container(File baseDir)
- {
- assert baseDir != null : "Unspecified base directory.";
- assert baseDir.isDirectory() : "Is not a directory : " + baseDir.getAbsolutePath();
- this.baseDir = baseDir;
- }
-
- public AbstractDataStructure load(String name)
- {
- IStorage storage = createStorage(name);
- storage.load();
- Version version = Version.loadFrom(storage.getRoot());
- return DataStructureFactory.createDataStructure(storage, version);
- }
-
- private IStorage createStorage(String name)
- {
- File file = new File(baseDir, name);
- if (file.exists() == false)
- {
- throw new UserFailureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
- }
- if (file.isDirectory())
- {
- return new FileStorage(file);
- }
- File hdf5File = new File(baseDir, name + ".hdf5");
- if (hdf5File.exists())
- {
- return new HDF5Storage(hdf5File);
- }
- throw new UserFailureException("Couldn't found appropriate container named '" + name + "' in "
- + baseDir.getAbsolutePath());
-
- }
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/AbstractNode.java b/bds/source/java/ch/systemsx/cisd/bds/fs/AbstractNode.java
deleted file mode 100644
index befbaa1da9af312a99f584eda60ba33d391129b0..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/AbstractNode.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.INode;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-abstract class AbstractNode implements INode
-{
- protected final File fileNode;
-
- AbstractNode(File file)
- {
- assert file != null : "Unspecified file";
- this.fileNode = file;
- }
-
- public String getName()
- {
- return fileNode.getName();
- }
-
- public IDirectory tryToGetParent()
- {
- File dir = fileNode.getParentFile();
- return dir == null ? null : new Directory(dir);
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java
deleted file mode 100644
index b7ecbc8c26268d3934424751f36a5bca0c8f6cbd..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.INode;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class Directory extends AbstractNode implements IDirectory
-{
- public Directory(File directory)
- {
- super(directory);
- assert directory.isDirectory() : "Not a directory: " + directory.getAbsolutePath();
- }
-
- public INode getNode(String name)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public IDirectory appendDirectory(String name)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public void appendKeyValuePair(String key, String value)
- {
- File file = new File(fileNode, key);
- try
- {
- FileWriter fileWriter = new FileWriter(file);
- fileWriter.write(value);
- fileWriter.close();
- } catch (IOException ex)
- {
- file.delete();
- throw new EnvironmentFailureException("Can not create " + file.getAbsolutePath() + ": " + ex);
- }
- }
-
- public void appendNode(INode node)
- {
- // TODO Auto-generated method stub
-
- }
-
- public void appendRealFile(File file)
- {
- File newFile = new File(fileNode, file.getName());
- if (file.renameTo(newFile) == false)
- {
- throw new EnvironmentFailureException("Couldn't move file " + file.getAbsolutePath() + " to "
- + fileNode.getAbsolutePath());
- }
- }
-
- public void appendLink(String name, INode node)
- {
- // TODO Auto-generated method stub
-
- }
-
- public Iterator<INode> iterator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
- {
- // TODO Auto-generated method stub
-
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java b/bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java
deleted file mode 100644
index aefe534501bb6dc334b11d82e8bfeda9aa480175..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.IStorage;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class FileStorage implements IStorage
-{
- private Directory root;
-
- public FileStorage(File folder)
- {
- root = new Directory(folder);
- }
-
- public IDirectory getRoot()
- {
- return root;
- }
-
- public void load()
- {
- }
-
- public void save()
- {
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java b/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java
deleted file mode 100644
index 09dc58b4e50ad35385a01b5cedca166ef44e63d0..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.ILink;
-import ch.systemsx.cisd.bds.INode;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class Link implements ILink
-{
-
- private final String name;
- private IDirectory parent;
- private final INode reference;
-
- Link(String name, INode reference)
- {
- this.name = name;
- this.reference = reference;
- }
-
- public String getName()
- {
- return name;
- }
-
- void setParent(IDirectory parentOrNull)
- {
- parent = parentOrNull;
- }
-
- public IDirectory tryToGetParent()
- {
- return parent;
- }
-
- public INode getReference()
- {
- return reference;
- }
-
- public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
- {
- // TODO Auto-generated method stub
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/fs/NodeFactory.java
deleted file mode 100644
index b23c7aa6b4a3c1767e7d8e4b4dbaeacb26198dbf..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/NodeFactory.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-import java.io.IOException;
-
-import ch.systemsx.cisd.bds.INode;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class NodeFactory
-{
- static INode createNode(File file)
- {
- assert file != null : "Unspecified node";
- String absolutePath = file.getAbsolutePath();
- try
- {
- String canonicalPath = file.getCanonicalPath();
- if (absolutePath.equals(canonicalPath) == false)
- {
- return new Link(file.getName(), createNode(new File(canonicalPath)));
- }
- if (file.isDirectory())
- {
- return new Directory(file);
- }
- return new StringFile(file);
- } catch (IOException ex)
- {
- throw new EnvironmentFailureException("Couldn't get canonical path of file " + absolutePath);
- }
- }
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java b/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java
deleted file mode 100644
index 1061b43852b58a8946c25744fc16f4cbeccb02d1..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.fs;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.IFile;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.utilities.FileUtilities;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class StringFile extends AbstractNode implements IFile<String>
-{
- StringFile(File file)
- {
- super(file);
- assert file.isFile() : "Not a file " + file.getAbsolutePath();
- }
-
- public String getValue()
- {
- return FileUtilities.loadToString(fileNode);
- }
-
- public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
- {
- // TODO Auto-generated method stub
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java b/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java
deleted file mode 100644
index 04c04c6c3bcf508c693cd6dbc398f85837ca57ce..0000000000000000000000000000000000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.bds.hdf5;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.IStorage;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class HDF5Storage implements IStorage
-{
- public HDF5Storage(File hdf5File)
- {
- assert hdf5File != null : "Unspecified HDF5 file.";
- }
-
- public IDirectory getRoot()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public void load()
- {
- // TODO Auto-generated method stub
-
- }
-
- public void save()
- {
- // TODO Auto-generated method stub
-
- }
-
-}