From 599b2354eeddc0edf4119e8464f4d10cbcd06d1c Mon Sep 17 00:00:00 2001
From: ribeaudc <ribeaudc>
Date: Wed, 20 Aug 2008 08:15:08 +0000
Subject: [PATCH] [LMS-559] change: - Move all the methods to
'IDataStructureV1_X' interface.
SVN: 7979
---
.../systemsx/cisd/bds/DataStructureV1_0.java | 34 ++---------------
.../systemsx/cisd/bds/IDataStructureV1_X.java | 38 ++++++++++++++++++-
.../cisd/bds/DataStructureV1_0Test.java | 2 +
3 files changed, 41 insertions(+), 33 deletions(-)
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 0a9a55193f4..6dcd8838091 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.bds;
import java.util.Set;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.handler.ChecksumHandler;
import ch.systemsx.cisd.bds.handler.MappingFileHandler;
@@ -84,7 +85,8 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
/**
* Returns the directory containing the standardized data.
*/
- public final IDirectory getStandardData()
+ @Private
+ final IDirectory getStandardData()
{
assertOpenOrCreated();
return Utilities.getOrCreateSubDirectory(getDataDirectory(), DIR_STANDARD);
@@ -162,21 +164,12 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
this.annotations = annotations;
}
- /**
- * Returns the experiment identifier.
- *
- * @throws DataStructureException if the experiment identifier hasn't be loaded nor hasn't be
- * set by {@link #setExperimentIdentifier(ExperimentIdentifier)}.
- */
public ExperimentIdentifier getExperimentIdentifier()
{
assertOpenOrCreated();
return ExperimentIdentifier.loadFrom(getMetaDataDirectory());
}
- /**
- * Sets the experiment identifier. Overwrites an already set or loaded value.
- */
public void setExperimentIdentifier(final ExperimentIdentifier experimentIdentifier)
{
assert experimentIdentifier != null : "Unspecified experiment identifier";
@@ -184,33 +177,18 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
experimentIdentifier.saveTo(getMetaDataDirectory());
}
- /**
- * Returns the date of registration of the experiment.
- *
- * @throws DataStructureException if the processing type hasn't be loaded nor hasn't be set by
- * {@link #setExperimentRegistrationTimestamp(ExperimentRegistrationTimestamp)}.
- */
public final ExperimentRegistrationTimestamp getExperimentRegistratorTimestamp()
{
assertOpenOrCreated();
return ExperimentRegistrationTimestamp.loadFrom(getMetaDataDirectory());
}
- /**
- * Sets the date of registration of the experiment.
- */
public final void setExperimentRegistrationTimestamp(final ExperimentRegistrationTimestamp date)
{
assertOpenOrCreated();
date.saveTo(getMetaDataDirectory());
}
- /**
- * Returns the experiment registrator.
- *
- * @throws DataStructureException if the processing type hasn't be loaded nor hasn't be set by
- * {@link #setExperimentRegistrator(ExperimentRegistrator)}.
- */
public final ExperimentRegistrator getExperimentRegistrator()
{
assertOpenOrCreated();
@@ -224,12 +202,6 @@ public class DataStructureV1_0 extends AbstractDataStructure implements IDataStr
registrator.saveTo(getMetaDataDirectory());
}
- /**
- * Returns the sample.
- *
- * @throws DataStructureException if the sample hasn't be loaded nor hasn't be set by
- * {@link #setSample(Sample)}.
- */
public Sample getSample()
{
assertOpenOrCreated();
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_X.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_X.java
index f88ff6b290e..6dd33d505ec 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_X.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_X.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.bds;
+import java.util.Set;
+
+import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
@@ -43,6 +46,9 @@ public interface IDataStructureV1_X extends IDataStructure
/**
* Returns the experiment registrator.
+ *
+ * @throws DataStructureException if the processing type hasn't be loaded nor hasn't be set by
+ * {@link #setExperimentRegistrator(ExperimentRegistrator)}.
*/
public ExperimentRegistrator getExperimentRegistrator();
@@ -77,10 +83,31 @@ public interface IDataStructureV1_X extends IDataStructure
public void addReference(final Reference reference);
/**
- * Sets the experiment identifier.
+ * Returns the standard-original mapping.
+ */
+ public Set<Reference> getStandardOriginalMapping();
+
+ /**
+ * Sets the experiment identifier. Overwrites an already set or loaded value.
*/
public void setExperimentIdentifier(final ExperimentIdentifier experimentIdentifier);
+ /**
+ * Returns the experiment identifier.
+ *
+ * @throws DataStructureException if the experiment identifier hasn't be loaded nor hasn't be
+ * set by {@link #setExperimentIdentifier(ExperimentIdentifier)}.
+ */
+ public ExperimentIdentifier getExperimentIdentifier();
+
+ /**
+ * Returns the date of registration of the experiment.
+ *
+ * @throws DataStructureException if the processing type hasn't be loaded nor hasn't be set by
+ * {@link #setExperimentRegistrationTimestamp(ExperimentRegistrationTimestamp)}.
+ */
+ public ExperimentRegistrationTimestamp getExperimentRegistratorTimestamp();
+
/**
* Sets the experiment registration timestamp.
*/
@@ -88,8 +115,15 @@ public interface IDataStructureV1_X extends IDataStructure
final ExperimentRegistrationTimestamp experimentRegistrationTimestamp);
/**
- * Sets the sample.
+ * Sets the measurement entity. Overwrites an already set or loaded value.
*/
public void setSample(final Sample sample);
+ /**
+ * Returns the sample.
+ *
+ * @throws DataStructureException if the sample hasn't be loaded nor hasn't be set by
+ * {@link #setSample(Sample)}.
+ */
+ public Sample getSample();
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
index ee4d83f580f..c794072023f 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -30,6 +30,7 @@ import java.util.Set;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.exception.StorageException;
import ch.systemsx.cisd.bds.handler.ChecksumHandler;
@@ -44,6 +45,7 @@ import ch.systemsx.cisd.common.filesystem.AbstractFileSystemTestCase;
*
* @author Franz-Josef Elmer
*/
+@Friend(toClasses = DataStructureV1_0.class)
public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
private static void assertPartOfString(final String part, final String string)
--
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