diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
index 48a917329dafaec87ff32ffe9443d5ea01928558..0e8f1c9c0ca168b028613c2c0089c4ad7d1fd5ee 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IStorage;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Container.java b/bds/source/java/ch/systemsx/cisd/bds/Container.java
new file mode 100644
index 0000000000000000000000000000000000000000..d161d843fa0f06ed5ae2047171cd14bc5e498299
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/Container.java
@@ -0,0 +1,70 @@
+/*
+ * 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;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.IStorage;
+import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
+import ch.systemsx.cisd.bds.storage.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/DataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
index b039165e2e4d17ae62f32c5cd58f8cb925283843..9a3c2d56438e47f2347c1f5cef0d91a6bf6dfbca 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
@@ -21,6 +21,7 @@ import java.lang.reflect.InvocationTargetException;
import java.util.HashMap;
import java.util.Map;
+import ch.systemsx.cisd.bds.storage.IStorage;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index bbbfa6a4f98544976699123dae3ed5d68437bbb2..97139abbe4d12bf480bbe05056a187d595b1238b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IStorage;
+
/**
*
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index 73c4353f586726cdb4fd37359ba24a7e8104078b..53e3a16ce6b8d8aafc74df11334198d93d0449e1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
/**
* Identifier of the experiment which corresponds to the data. This is an immutable but extendable value object class.
* An instance of this class allows unique identification in the database.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_0.java
index 82219390b36901eda5cbed101254083b8bcb162c..2a6eb2643a1dcdab0a387c361bd5eb8333d0dd6e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_0.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
/**
* Data structure interface for Version 1.0.
*
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
index 6717aff94faff53b928941feda9f52e9f1dff846..c84a55cb218ae36406b3c6cb023828a6197e1bd6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+
/**
* Enumeration of processing types.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index a352ebc55ad3d9f2b40c8b57cc5ebc9b7f5ce617..fff492ed4639b13adfc92226e8e0f7586eceaa27 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IFile;
+import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 4bc6052125efa968d0dd6e211c6893205c6fa1c5..0770d4e4e48b5c6c0def65e2e38422dafb20e2be 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Version.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
new file mode 100644
index 0000000000000000000000000000000000000000..98c493481acfde313b49ee24f5934ebe671e1aa1
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
@@ -0,0 +1,39 @@
+/*
+ * 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.storage;
+
+import java.io.File;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IDirectory extends INode, Iterable<INode>
+{
+ public INode getNode(String name);
+
+ public IDirectory appendDirectory(String name);
+
+ public void appendNode(INode node);
+
+ public void appendRealFile(File file);
+
+ public void appendKeyValuePair(String key, String value);
+
+ public void appendLink(String name, INode node);
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java
new file mode 100644
index 0000000000000000000000000000000000000000..c657dcbb2d422445390c6c2fabe94ac48a96c9d3
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java
@@ -0,0 +1,30 @@
+/*
+ * 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.storage;
+
+/**
+ * Role of a file with a value (content) of type <code>T</code>.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IFile<T> extends INode
+{
+ /**
+ * Returns the value (or content) of this file node.
+ */
+ public T getValue();
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java b/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java
new file mode 100644
index 0000000000000000000000000000000000000000..c533b230cb2100540b96b9423c76b26c3c5ed7a5
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java
@@ -0,0 +1,27 @@
+/*
+ * 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.storage;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ILink extends INode
+{
+ public INode getReference();
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java b/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
new file mode 100644
index 0000000000000000000000000000000000000000..42cf6ca8943308ff5b585936432aa55027608339
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
@@ -0,0 +1,49 @@
+/*
+ * 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.storage;
+
+import java.io.File;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Role of a node in the data structure.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface INode
+{
+ /**
+ * Returns the name of this node.
+ */
+ public String getName();
+
+ /**
+ * Returns the parent directory of this node or <code>null</code> if it is the root node.
+ */
+ public IDirectory tryToGetParent();
+
+ /**
+ * Extracts this node to the specified directory of the file system. All descendants are also extracted.
+ *
+ * @throws UserFailureException if this or a descended node is a link referring to a node which is not this
+ * node or a descended node.
+ * @throws EnvironmentFailureException if extraction causes an IOException.
+ */
+ public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException;
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
new file mode 100644
index 0000000000000000000000000000000000000000..b02fd16a11c6885d65633e11f15c17fdc5c14097
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
@@ -0,0 +1,31 @@
+/*
+ * 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.storage;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IStorage
+{
+ public void load();
+
+ public IDirectory getRoot();
+
+ public void save();
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
new file mode 100644
index 0000000000000000000000000000000000000000..80c8e52c16a88585bad2b74d0404998675ba9040
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
@@ -0,0 +1,50 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.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/storage/filesystem/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
new file mode 100644
index 0000000000000000000000000000000000000000..d59a75491c048c589f6c88a7898d6814af0fa5b7
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
@@ -0,0 +1,103 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Iterator;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.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/storage/filesystem/FileStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
new file mode 100644
index 0000000000000000000000000000000000000000..d5e74a49073344e67d220dd2064cc9b79e72e478
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
@@ -0,0 +1,51 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.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/storage/filesystem/Link.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
new file mode 100644
index 0000000000000000000000000000000000000000..87deccea4553589f18214cb01c1d7be46ad92ff1
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
@@ -0,0 +1,70 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.ILink;
+import ch.systemsx.cisd.bds.storage.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/storage/filesystem/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..1f14d22468102abeeaffce7ca37bf6e246ffc32e
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
@@ -0,0 +1,53 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+import java.io.IOException;
+
+import ch.systemsx.cisd.bds.storage.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/storage/filesystem/StringFile.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/StringFile.java
new file mode 100644
index 0000000000000000000000000000000000000000..394e11a20f6b51968beac405bc42bd06801481e3
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/StringFile.java
@@ -0,0 +1,49 @@
+/*
+ * 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.storage.filesystem;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.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/storage/hdf5/HDF5Storage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java
new file mode 100644
index 0000000000000000000000000000000000000000..55f2a8a9c07ab409f80645fe027bdc557418357c
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java
@@ -0,0 +1,54 @@
+/*
+ * 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.storage.hdf5;
+
+import java.io.File;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.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
+
+ }
+
+}