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 3d63e11c84e31ce536962c97d9f67f1c83988ce5..0021df7caecaaaa34ec3730fabf4599717625a22 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -115,7 +115,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
/**
* Returns the formatted data. This method can be called only after method {@link #setFormat(Format)} has been
- * invoked. If the format is not known {@link UnknownFormat1_0} will be assumed.
+ * invoked. If the format is not known {@link UnknownFormatV1_0} will be assumed.
*
* @throws DataStructureException if this method has been invoked before the format has been set.
*/
@@ -126,7 +126,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
{
throw new DataStructureException("Couldn't create formatted data because of unspecified format.");
}
- return FormattedDataFactory.createFormattedData(getDataDirectory(), format, UnknownFormat1_0.UNKNOWN_1_0,
+ return FormattedDataFactory.createFormattedData(getDataDirectory(), format, UnknownFormatV1_0.UNKNOWN_1_0,
formatParameters);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
index 93bc71a699dcb5ee455871ba937c84484f290838..f3d1aed1ca994ba448cbc574117f10522ca22f7a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
@@ -20,7 +20,7 @@ import java.util.HashMap;
import java.util.Map;
import ch.systemsx.cisd.bds.exception.DataStructureException;
-import ch.systemsx.cisd.bds.hcs.HCSImageFormat1_0;
+import ch.systemsx.cisd.bds.hcs.HCSImageFormatV1_0;
/**
* A store of all active formats.
@@ -40,8 +40,8 @@ public final class FormatStore
private final static Map<String, Format> createFormats()
{
final Map<String, Format> map = new HashMap<String, Format>();
- map.put(getKey(UnknownFormat1_0.UNKNOWN_1_0), UnknownFormat1_0.UNKNOWN_1_0);
- map.put(getKey(HCSImageFormat1_0.HCS_IMAGE_1_0), HCSImageFormat1_0.HCS_IMAGE_1_0);
+ map.put(getKey(UnknownFormatV1_0.UNKNOWN_1_0), UnknownFormatV1_0.UNKNOWN_1_0);
+ map.put(getKey(HCSImageFormatV1_0.HCS_IMAGE_1_0), HCSImageFormatV1_0.HCS_IMAGE_1_0);
return map;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
index 44b6649c0c9011e1879ade85b1ee16449bf2f84d..6fb42641ad8d36a47f58cf729f51990dc56edb82 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
@@ -20,7 +20,7 @@ import java.util.HashMap;
import java.util.Map;
import ch.systemsx.cisd.bds.exception.DataStructureException;
-import ch.systemsx.cisd.bds.hcs.HCSImageFormat1_0;
+import ch.systemsx.cisd.bds.hcs.HCSImageFormatV1_0;
import ch.systemsx.cisd.bds.hcs.HCSImageFormattedData;
import ch.systemsx.cisd.bds.storage.IDirectory;
@@ -36,8 +36,8 @@ public final class FormattedDataFactory
static
{
- register(UnknownFormat1_0.UNKNOWN_1_0, NoFormattedData.class);
- register(HCSImageFormat1_0.HCS_IMAGE_1_0, HCSImageFormattedData.class);
+ register(UnknownFormatV1_0.UNKNOWN_1_0, NoFormattedData.class);
+ register(HCSImageFormatV1_0.HCS_IMAGE_1_0, HCSImageFormattedData.class);
}
private FormattedDataFactory()
diff --git a/bds/source/java/ch/systemsx/cisd/bds/NoFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/NoFormattedData.java
index 095f0194e36fb6ae6b11651d9c5b1fca80afed39..132b0b25bf9c2e619ddc3fa70f078c09998c8689 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/NoFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/NoFormattedData.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.bds;
/**
- * Most simplest implementation of {@link IFormattedData}. It is associated with {@link UnknownFormat1_0}.
+ * Most simplest implementation of {@link IFormattedData}. It is associated with {@link UnknownFormatV1_0}.
*
* @author Franz-Josef Elmer
*/
@@ -25,7 +25,7 @@ public final class NoFormattedData extends AbstractFormattedData
{
/**
* Creates a new instance for the specified context. The format has to be backward-compatible with
- * {@link UnknownFormat1_0}. The format parameters are ignored.
+ * {@link UnknownFormatV1_0}. The format parameters are ignored.
*/
public NoFormattedData(final FormattedDataContext context)
{
@@ -37,11 +37,11 @@ public final class NoFormattedData extends AbstractFormattedData
//
/**
- * Returns {@link UnknownFormat1_0#UNKNOWN_1_0}.
+ * Returns {@link UnknownFormatV1_0#UNKNOWN_1_0}.
*/
public final Format getFormat()
{
- return UnknownFormat1_0.UNKNOWN_1_0;
+ return UnknownFormatV1_0.UNKNOWN_1_0;
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
similarity index 85%
rename from bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java
rename to bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
index bbd709770df5f9cc7e698d740928322072d9585b..3f9a4e7be7663019d4baa9a8ab760d4cc17d1788 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
@@ -21,15 +21,15 @@ package ch.systemsx.cisd.bds;
*
* @author Franz-Josef Elmer
*/
-public final class UnknownFormat1_0 extends Format
+public final class UnknownFormatV1_0 extends Format
{
public static final String FORMAT_CODE = "UNKNOWN";
/**
* The one and only one instance.
*/
- public static final Format UNKNOWN_1_0 = new UnknownFormat1_0();
+ public static final Format UNKNOWN_1_0 = new UnknownFormatV1_0();
- private UnknownFormat1_0()
+ private UnknownFormatV1_0()
{
super(FORMAT_CODE, new Version(1, 0), null);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
index e33a725740a0355d2b64906e719658d63b0d9cd6..66b4518da5e1703fa6c4950e7ead79d992f31322 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
@@ -95,7 +95,7 @@ public final class FormatParameterFactory implements IFormatParameterFactory
} else if (name.equals(ChannelList.NUMBER_OF_CHANNELS))
{
return new FormatParameter(name, ChannelList.createChannelListFromString(value));
- } else if (name.equals(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA))
+ } else if (name.equals(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA))
{
return new FormatParameter(name, Boolean.valueOf(value));
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
index 7f8c409349d3110d6b92a57c5a667037a077611f..27c5c82365bcd999d4615e826a1e930d1809c318 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
@@ -130,7 +130,7 @@ public class Geometry implements IStorable
public final boolean contains(final Location location)
{
assert location != null : "Given location can not be null.";
- return location.x <= getColumns() && location.y <= getRows();
+ return location.getX() <= getColumns() && location.getY() <= getRows();
}
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
index 83982c84ad8bdc2ba359011946cba7e278fef5a3..98fb9e12798bd542cb465a14e35d05b9e30d90f1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
public class HCSImageAnnotations implements IAnnotations
{
private static final Set<Format> FORMATS =
- Collections.unmodifiableSet(new HashSet<Format>(Arrays.asList(HCSImageFormat1_0.HCS_IMAGE_1_0)));
+ Collections.unmodifiableSet(new HashSet<Format>(Arrays.asList(HCSImageFormatV1_0.HCS_IMAGE_1_0)));
private String deviceID;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormat1_0.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
similarity index 96%
rename from bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormat1_0.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
index ef7d5d79aaa56e4917fb6eefabcaf13ab965f199..c938138ad32a8bec7217fae3c2ffa0363f4fc0d8 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormat1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.bds.Version;
*
* @author Christian Ribeaud
*/
-public final class HCSImageFormat1_0 extends Format
+public final class HCSImageFormatV1_0 extends Format
{
public static final String FORMAT_CODE = "HCS_IMAGE";
@@ -56,9 +56,9 @@ public final class HCSImageFormat1_0 extends Format
/**
* The one and only one instance.
*/
- public static final Format HCS_IMAGE_1_0 = new HCSImageFormat1_0();
+ public static final Format HCS_IMAGE_1_0 = new HCSImageFormatV1_0();
- private HCSImageFormat1_0()
+ private HCSImageFormatV1_0()
{
super(FORMAT_CODE, new Version(1, 0), null);
}
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 55e29a3ae6aed36784559ca895cb6b7d171a8879..04df7cd5c085b84c7d36ddcab789787adb1ae79f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -35,7 +35,7 @@ import ch.systemsx.cisd.bds.storage.INode;
/**
* {@link IFormattedData} implementation for <i>HCS (High-Content Screening) with Images</i>. It is associated with
- * {@link HCSImageFormat1_0}.
+ * {@link HCSImageFormatV1_0}.
*
* @author Christian Ribeaud
*/
@@ -55,7 +55,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
private final boolean containsOriginalData()
{
- return (Boolean) getFormatParameters().getValue(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA);
+ return (Boolean) getFormatParameters().getValue(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA);
}
private final Geometry getWellGeometry()
@@ -105,7 +105,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
final static String createWellFileName(final Location wellLocation)
{
assert wellLocation != null : "Well location can not be null.";
- return ROW + wellLocation.y + "_" + COLUMN + wellLocation.x + ".tiff";
+ return ROW + wellLocation.getY() + "_" + COLUMN + wellLocation.getX() + ".tiff";
}
private final IDirectory getStandardDataDirectory() throws DataStructureException
@@ -120,12 +120,12 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
private final static String getPlateColumnDir(final Location plateLocation)
{
- return COLUMN + plateLocation.x;
+ return COLUMN + plateLocation.getX();
}
private final static String getPlateRowDirName(final Location plateLocation)
{
- return ROW + plateLocation.y;
+ return ROW + plateLocation.getY();
}
private final static String getChannelName(final int channel)
@@ -235,7 +235,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
public final Format getFormat()
{
- return HCSImageFormat1_0.HCS_IMAGE_1_0;
+ return HCSImageFormatV1_0.HCS_IMAGE_1_0;
}
@Override
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 7e42df5d01e144a124c10525cb541a2237a1e8f1..3af684d35e576abb3a49855e38313119fd527b7f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -61,9 +61,9 @@ public interface IHCSImageFormattedData extends IFormattedData
public final static class NodePath
{
- public final INode node;
+ private final INode node;
- public final String path;
+ private final String path;
public NodePath(final INode node, final String path)
{
@@ -72,5 +72,15 @@ public interface IHCSImageFormattedData extends IFormattedData
this.node = node;
this.path = path;
}
+
+ public INode getNode()
+ {
+ return node;
+ }
+
+ public String getPath()
+ {
+ return path;
+ }
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
index b110adec65631ea3e4e1d61756405736c1924a7c..648248d159330cb27a8ae8d1e8af0e9641ac8a4f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
@@ -30,12 +30,12 @@ public final class Location
/**
* The <i>x</i> (or <i>column</i>) coordinate.
*/
- public final int x;
+ private final int x;
/**
* The <i>y</i> (or <i>row</i>) coordinate.
*/
- public final int y;
+ private final int y;
public Location(final int x, final int y)
{
@@ -127,4 +127,20 @@ public final class Location
{
return "[x=" + x + ",y=" + y + "]";
}
+
+ /**
+ * Returns the <i>x</i> (or <i>column</i>) coordinate.
+ */
+ public int getX()
+ {
+ return x;
+ }
+
+ /**
+ * Returns the <i>y</i> (or <i>row</i>) coordinate.
+ */
+ public int getY()
+ {
+ return y;
+ }
}
\ No newline at end of file
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java b/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
index edfb370d2a52a3bfe90d8db7ba7040cfab6a7ef6..966673912ec603ebab6870b7e465cbf0d8036995 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
@@ -87,23 +87,28 @@ public final class NodeFilters
public final boolean accept(final INode node)
{
assert node != null : "Given node can not be null.";
- String name = node.getName();
- if (ignoreCase)
- {
- name = name.toLowerCase();
- }
- for (String suffix : suffixes)
+ final String nameWithRightCase = toRightCase(node.getName());
+ for (final String suffix : suffixes)
{
- if (ignoreCase)
- {
- suffix = suffix.toLowerCase();
- }
- if (name.endsWith(suffix))
+ final String suffixWithRightCase = toRightCase(suffix);
+ if (nameWithRightCase.endsWith(suffixWithRightCase))
{
return true;
}
}
return false;
}
+
+ private final String toRightCase(String s)
+ {
+ if (ignoreCase)
+ {
+ return s.toLowerCase();
+ } else
+ {
+ return s;
+ }
+ }
}
+
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
index 93a0ddaef881e6e99f503bb929a364de6649578b..5212ea8a7967a8dd4bc35cd6c39a367472ff1ed0 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
@@ -42,7 +42,7 @@ public final class DataStructureLoaderTest extends AbstractFileSystemTestCase
DataStructureV1_0 dataStructure = new DataStructureV1_0(new FileStorage(dir));
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(experimentIdentifier);
ExperimentRegistrator experimentRegistrator = new ExperimentRegistrator("john", "doe", "j@doe");
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
similarity index 92%
rename from bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
rename to bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
index f6dcfb905218b1214026dca715ad77c7a87beb96..9f347c32fec5c09bdee5371aacfd5fd254d17f00 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
*
* @author Franz-Josef Elmer
*/
-public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
+public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
{
private static void assertPartOfString(String part, String string)
{
@@ -81,10 +81,10 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
public void testGetFormattedData()
{
dataStructure.create();
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
IFormattedData formattedData = dataStructure.getFormattedData();
assertTrue(formattedData instanceof NoFormattedData);
- assertEquals(UnknownFormat1_0.UNKNOWN_1_0, formattedData.getFormat());
+ assertEquals(UnknownFormatV1_0.UNKNOWN_1_0, formattedData.getFormat());
}
@Test
@@ -261,7 +261,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
try
{
dataStructure.close();
@@ -277,7 +277,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("g", "p", "e"));
dataStructure.setExperimentRegistrationDate(new ExperimentRegistratorDate(new Date(0)));
try
@@ -295,7 +295,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("g", "p", "e"));
dataStructure.setExperimentRegistrator(new ExperimentRegistrator("g", "p", "g@p"));
try
@@ -313,7 +313,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("g", "p", "e"));
dataStructure.setExperimentRegistrator(new ExperimentRegistrator("g", "p", "g@p"));
dataStructure.setExperimentRegistrationDate(new ExperimentRegistratorDate(new Date(0)));
@@ -332,7 +332,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
dataStructure.setExperimentIdentifier(new ExperimentIdentifier("g", "p", "e"));
dataStructure.setExperimentRegistrator(new ExperimentRegistrator("g", "p", "g@p"));
dataStructure.setExperimentRegistrationDate(new ExperimentRegistratorDate(new Date(0)));
@@ -352,7 +352,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
dataStructure.create();
dataStructure.getOriginalData().addKeyValuePair("answer", "42");
- dataStructure.setFormat(UnknownFormat1_0.UNKNOWN_1_0);
+ dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(experimentIdentifier);
ExperimentRegistratorDate experimentRegistratorDate = new ExperimentRegistratorDate(new Date(4711L * 4711000L));
@@ -394,9 +394,8 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
IDirectory metaDataDir = Utilities.getSubDirectory(root, DIR_METADATA);
IDirectory checksumDir = Utilities.getSubDirectory(metaDataDir, ChecksumHandler.CHECKSUM_DIRECTORY);
- assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n" +
- "d41d8cd98f00b204e9800998ecf8427e origFile1\n" +
- "d41d8cd98f00b204e9800998ecf8427e origFile2\n", Utilities.getString(checksumDir,
+ assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n" + "d41d8cd98f00b204e9800998ecf8427e origFile1\n"
+ + "d41d8cd98f00b204e9800998ecf8427e origFile2\n", Utilities.getString(checksumDir,
DataStructureV1_0.DIR_ORIGINAL));
}
@@ -409,7 +408,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
private void checkFormattedData(IFormattedData formattedData)
{
- assertEquals(UnknownFormat1_0.UNKNOWN_1_0, formattedData.getFormat());
+ assertEquals(UnknownFormatV1_0.UNKNOWN_1_0, formattedData.getFormat());
IFormatParameters formatParameters = formattedData.getFormatParameters();
Iterator<FormatParameter> iterator = formatParameters.iterator();
assertTrue(iterator.hasNext());
@@ -445,7 +444,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
}
@Test
- public void testOpenVersion1_1()
+ public void testOpenVersionV1_1()
{
createExampleDataStructure();
storage.mount();
@@ -456,7 +455,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
}
@Test
- public void testOpenVersion2_0()
+ public void testOpenVersionV2_0()
{
createExampleDataStructure();
storage.mount();
@@ -475,26 +474,26 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
}
@Test
- public void testOpenWithUnknownFormat1_1()
+ public void testOpenWithUnknownFormatV1_1()
{
createExampleDataStructure();
storage.mount();
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(1, 1), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(1, 1), null).saveTo(metaData);
storage.unmount();
dataStructure.open();
- assertEquals(UnknownFormat1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
+ assertEquals(UnknownFormatV1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
}
@Test
- public void testOpenWithUnknownFormat2_0()
+ public void testOpenWithUnknownFormatV2_0()
{
createExampleDataStructure();
storage.mount();
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
storage.unmount();
dataStructure.open();
try
@@ -517,7 +516,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
new Format("another format", new Version(1, 1), null).saveTo(metaData);
storage.unmount();
dataStructure.open();
- assertEquals(UnknownFormat1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
+ assertEquals(UnknownFormatV1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
}
private final void createExampleDataStructure()
@@ -534,7 +533,7 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
IDirectory originalDataDir = data.makeDirectory(DataStructureV1_0.DIR_ORIGINAL);
originalDataDir.addKeyValuePair("file1", "This is my first file.");
IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormat1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
new ExperimentIdentifier("g", "p", "e").saveTo(metaData);
new ExperimentRegistratorDate(new Date(0)).saveTo(metaData);
new ExperimentRegistrator("john", "doe", "j@doe").saveTo(metaData);
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
similarity index 90%
rename from bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
rename to bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
index 0c7821adcbc84bda5e53e99eb658d611bd86bb76..d0b8b6bc0446e45ecac4fb6fe3a3b9ef1c8a60f8 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
@@ -30,7 +30,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.DataStructureLoader;
import ch.systemsx.cisd.bds.DataStructureV1_0;
-import ch.systemsx.cisd.bds.DataStructureV1_0Test;
+import ch.systemsx.cisd.bds.DataStructureTestV1_0;
import ch.systemsx.cisd.bds.Format;
import ch.systemsx.cisd.bds.FormatParameter;
import ch.systemsx.cisd.bds.IDataStructure;
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
*
* @author Christian Ribeaud
*/
-public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
+public final class HCSDataStructureTestV1_0 extends AbstractFileSystemTestCase
{
private FileStorage storage;
@@ -60,9 +60,9 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
private final void setFormatAndFormatParameters()
{
- dataStructure.setFormat(HCSImageFormat1_0.HCS_IMAGE_1_0);
- dataStructure.addFormatParameter(new FormatParameter(HCSImageFormat1_0.DEVICE_ID, "M1"));
- dataStructure.addFormatParameter(new FormatParameter(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA, Boolean.TRUE));
+ dataStructure.setFormat(HCSImageFormatV1_0.HCS_IMAGE_1_0);
+ dataStructure.addFormatParameter(new FormatParameter(HCSImageFormatV1_0.DEVICE_ID, "M1"));
+ dataStructure.addFormatParameter(new FormatParameter(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA, Boolean.TRUE));
dataStructure.addFormatParameter(new FormatParameter(ChannelList.NUMBER_OF_CHANNELS, createChannelList()));
dataStructure.addFormatParameter(new FormatParameter(PlateGeometry.PLATE_GEOMETRY, new PlateGeometry(2, 3)));
dataStructure.addFormatParameter(new FormatParameter(WellGeometry.WELL_GEOMETRY, new WellGeometry(7, 5)));
@@ -85,7 +85,7 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
public void testGetFormattedData()
{
dataStructure.create();
- final Format format = HCSImageFormat1_0.HCS_IMAGE_1_0;
+ final Format format = HCSImageFormatV1_0.HCS_IMAGE_1_0;
try
{
dataStructure.getFormattedData();
@@ -105,7 +105,7 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
{
// Creating...
dataStructure.create();
- DataStructureV1_0Test.createExampleDataStructure(storage);
+ DataStructureTestV1_0.createExampleDataStructure(storage);
setFormatAndFormatParameters();
dataStructure.close();
// And loading...
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
index a5b54ec75bb9e8fd8aa63019943fba03628ac931..e868022dd465c8f370c5b611705c17be5e16cf16 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
@@ -82,7 +82,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
{
directory = context.mock(IDirectory.class);
formatParameters = context.mock(IFormatParameters.class);
- final Format format = HCSImageFormat1_0.HCS_IMAGE_1_0;
+ final Format format = HCSImageFormatV1_0.HCS_IMAGE_1_0;
context.checking(new Expectations()
{
{
@@ -188,7 +188,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
@Test
public final void testGetFormat()
{
- assertEquals(HCSImageFormat1_0.HCS_IMAGE_1_0, formattedData.getFormat());
+ assertEquals(HCSImageFormatV1_0.HCS_IMAGE_1_0, formattedData.getFormat());
context.assertIsSatisfied();
}
@@ -208,7 +208,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
one(directory).tryGetNode(DataStructureV1_0.DIR_ORIGINAL);
will(returnValue(originalNode));
- one(formatParameters).getValue(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA);
+ one(formatParameters).getValue(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA);
will(returnValue(Boolean.TRUE));
}
});
@@ -217,8 +217,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
assertNotNull(nodePath);
- assertTrue(nodePath.node instanceof ILink);
- assertEquals(standardFileName, nodePath.node.getName());
+ assertTrue(nodePath.getNode() instanceof ILink);
+ assertEquals(standardFileName, nodePath.getNode().getName());
// Look at the standard leaf directory if the node is there as well.
final INode standardFile = standardLeafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);
@@ -242,7 +242,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
exactly(2).of(directory).tryGetNode(DataStructureV1_0.DIR_STANDARD);
will(returnValue(standardNode));
- one(formatParameters).getValue(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA);
+ one(formatParameters).getValue(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA);
will(returnValue(Boolean.FALSE));
}
});
@@ -251,8 +251,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
assertNotNull(nodePath);
- assertTrue(nodePath.node instanceof IFile);
- assertEquals(standardFileName, nodePath.node.getName());
+ assertTrue(nodePath.getNode() instanceof IFile);
+ assertEquals(standardFileName, nodePath.getNode().getName());
// Look at the standard leaf directory if the node is there as well.
final INode standardFile = standardLeafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);