diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
index 5b2028d56feacf59810d93766abb8dac5fb0fa94..fd046108e8de26409d5fcc9d9a5dd54f21a05377 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
@@ -21,6 +21,8 @@ import java.util.Collections;
import java.util.Date;
import java.util.List;
+import types.BooleanOrUnknown;
+
import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.common.collections.CollectionIO;
@@ -47,6 +49,8 @@ public final class DataSet implements IStorable
static final String OBSERVABLE_TYPE = "observable_type";
static final String IS_MEASURED = "is_measured";
+
+ static final String IS_COMPLETE = "is_complete";
static final String PARENT_CODES = "parent_codes";
@@ -67,10 +71,12 @@ public final class DataSet implements IStorable
* by means of some calculation from another data set.
*/
private final boolean isMeasured;
-
+
/** The list of parent codes. Never <code>null</code> but could be empty. */
private final List<String> parentCodes;
+ private BooleanOrUnknown isComplete = BooleanOrUnknown.UNKNOWN;
+
/**
* Creates an instance of data set.
*
@@ -141,6 +147,11 @@ public final class DataSet implements IStorable
{
return parentCodes;
}
+
+ public final void setComplete(boolean complete)
+ {
+ isComplete = BooleanOrUnknown.resolve(complete);
+ }
/**
* Loads the experiment identifier from the specified directory.
@@ -176,6 +187,7 @@ public final class DataSet implements IStorable
folder.addKeyValuePair(PRODUCER_CODE, StringUtils.emptyIfNull(producerCode));
folder.addKeyValuePair(IS_MEASURED, Boolean.toString(isMeasured).toUpperCase());
folder.addKeyValuePair(OBSERVABLE_TYPE, observableTypeCode);
+ folder.addKeyValuePair(IS_COMPLETE, isComplete.toString());
final String value;
if (parentCodes.size() > 0)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
index d38400f12eff3eb6712e17f320f6c1f7651d3454..ba1d20fdebb67bef82a8009e546e3aae1c4885c9 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
@@ -52,10 +52,8 @@ public final class HCSImageFormatV1_0 extends Format
* These parameters are located in <code>metadata/parameters</code>.
* </p>
*/
- private final static String[] FORMAT_PARAMETERS =
- new String[]
- { PlateGeometry.PLATE_GEOMETRY, WellGeometry.WELL_GEOMETRY, NUMBER_OF_CHANNELS,
- CONTAINS_ORIGINAL_DATA };
+ private final static String[] FORMAT_PARAMETERS = new String[]
+ { WellGeometry.WELL_GEOMETRY, NUMBER_OF_CHANNELS, CONTAINS_ORIGINAL_DATA };
/**
* The one and only one instance.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
index 30a53c9252e4699ccea69e8938e78ae783340137..1431c801929ed71bf19930abd7eb58eb26b4a86f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -59,17 +59,17 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
return (Boolean) getFormatParameters().getValue(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA);
}
- private final Geometry getWellGeometry()
+ public final Geometry getWellGeometry()
{
return (Geometry) getFormatParameters().getValue(WellGeometry.WELL_GEOMETRY);
}
- private final Geometry getPlateGeometry()
+ public final Geometry getPlateGeometry()
{
return (Geometry) getFormatParameters().getValue(PlateGeometry.PLATE_GEOMETRY);
}
- private final int getChannelCount()
+ public final int getChannelCount()
{
return ((Integer) getFormatParameters().getValue(HCSImageFormatV1_0.NUMBER_OF_CHANNELS))
.intValue();
@@ -169,20 +169,20 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
// IHCSFormattedData
//
- public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation,
- final Location wellLocation)
+ public final INode tryGetStandardNodeAt(final int channel, final Location wellLocation,
+ final Location tileLocation)
{
- checkCoordinates(channel, plateLocation, wellLocation);
+ checkCoordinates(channel, wellLocation, tileLocation);
try
{
final IDirectory standardDir = getStandardDataDirectory();
final IDirectory channelDir =
Utilities.getSubDirectory(standardDir, getChannelName(channel));
final IDirectory plateRowDir =
- Utilities.getSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ Utilities.getSubDirectory(channelDir, getPlateRowDirName(wellLocation));
final IDirectory plateColumnDir =
- Utilities.getSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
- return plateColumnDir.tryGetNode(createWellFileName(wellLocation));
+ Utilities.getSubDirectory(plateRowDir, getPlateColumnDir(wellLocation));
+ return plateColumnDir.tryGetNode(createWellFileName(tileLocation));
} catch (final DataStructureException e)
{
return null;
@@ -190,28 +190,28 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
}
public final NodePath addStandardNode(final File imageRootDirectory,
- final String imageRelativePath, final int channel, final Location plateLocation,
- final Location wellLocation) throws DataStructureException
+ final String imageRelativePath, final int channel, final Location wellLocation,
+ final Location tileLocation) throws DataStructureException
{
assert imageRootDirectory != null : "Given image root directory can not be null.";
assert imageRelativePath != null : "Given image relative path can not be null.";
- INode node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
+ INode node = tryGetStandardNodeAt(channel, wellLocation, tileLocation);
if (node != null)
{
throw new DataStructureException(
String
.format(
"A node already exists at channel %d, plate location '%s' and well location '%s'.",
- channel, plateLocation, wellLocation));
+ channel, wellLocation, tileLocation));
}
final IDirectory standardDir = getStandardDataDirectory();
final IDirectory channelDir =
Utilities.getOrCreateSubDirectory(standardDir, getChannelName(channel));
final IDirectory plateRowDir =
- Utilities.getOrCreateSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ Utilities.getOrCreateSubDirectory(channelDir, getPlateRowDirName(wellLocation));
final IDirectory plateColumnDir =
- Utilities.getOrCreateSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
- final String wellFileName = createWellFileName(wellLocation);
+ Utilities.getOrCreateSubDirectory(plateRowDir, getPlateColumnDir(wellLocation));
+ final String wellFileName = createWellFileName(tileLocation);
if (containsOriginalData())
{
final IDirectory imageRootDirectoryNode = getImageRootDirectoryNode(imageRootDirectory);
@@ -236,7 +236,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
String
.format(
"Original file name '%s' could not be added at channel %d, plate location '%s' and well location '%s'.",
- imageRelativePath, channel, plateLocation, wellLocation));
+ imageRelativePath, channel, wellLocation, tileLocation));
}
final char sep = Constants.PATH_SEPARATOR;
final String standardNodePath =
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
index 5848633e11c91a358b02b51152dce73801582732..090fe2d423d61d4b7023d16e39b3308f38d10708 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -31,9 +31,29 @@ import ch.systemsx.cisd.bds.storage.INode;
*/
public interface IHCSImageFormattedData extends IFormattedData
{
+ /**
+ * Returns <code>true</code> if the data structure contains the original data.
+ */
+ public boolean containsOriginalData();
+
+ /**
+ * Returns the number of channels.
+ */
+ public int getChannelCount();
+
+ /**
+ * Returns the geometric arrangement of the tiles of a well.
+ */
+ public Geometry getWellGeometry();
+
+ /**
+ * Returns the geometric arrangement of the wells of a plate.
+ */
+ public Geometry getPlateGeometry();
+
/**
- * For given <var>channel</var>, given <var>plateLocation</var> and given <var>wellLocation</var>
+ * For given <var>channel</var>, given <var>wellLocation</var> and given <var>tileLocation</var>
* returns the corresponding <code>INode</code> (found in <code>data/standard</code>
* directory).
*
@@ -41,8 +61,8 @@ public interface IHCSImageFormattedData extends IFormattedData
* <code>data/original</code> directory or a {@link IFile} that can be extracted
* somewhere. Might return <code>null</code>.
*/
- public INode tryGetStandardNodeAt(final int channel, final Location plateLocation,
- final Location wellLocation);
+ public INode tryGetStandardNodeAt(final int channel, final Location wellLocation,
+ final Location tileLocation);
/**
* Adds a new image file at given coordinates.
@@ -57,8 +77,9 @@ public interface IHCSImageFormattedData extends IFormattedData
* @throws DataStructureException if a node already exists at given coordinates.
*/
public NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath,
- final int channel, final Location plateLocation, final Location wellLocation)
+ final int channel, final Location wellLocation, final Location tileLocation)
throws DataStructureException;
+
//
// Helper classes