From 4dc04ddf33f1e7fe8cc09de361bcb2790053a9ee Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 7 Sep 2009 10:53:07 +0000
Subject: [PATCH] SE-137 Abundance columns sorted.
SVN: 12495
---
.../phosphonetx/server/PhosphoNetXServer.java | 6 +-
.../basic/dto/AbundanceColumnDefinition.java | 32 ++++-
.../shared/basic/dto/Treatment.java | 28 ++++-
.../dto/AbundanceColumnDefinitionTest.java | 119 ++++++++++++++++++
4 files changed, 182 insertions(+), 3 deletions(-)
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinitionTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index 0f964cb130b..b67e5efdf3b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@@ -125,7 +126,10 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
columnDefinitions.put(sampleID, columnDefinition);
}
}
- return new ArrayList<AbundanceColumnDefinition>(columnDefinitions.values());
+ List<AbundanceColumnDefinition> definitions =
+ new ArrayList<AbundanceColumnDefinition>(columnDefinitions.values());
+ Collections.sort(definitions);
+ return definitions;
} finally
{
samplePermIDs.close();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinition.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinition.java
index 19b39f9fe68..cdf41fe62d4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinition.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinition.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
import java.io.Serializable;
+import java.util.Collections;
import java.util.List;
import com.google.gwt.user.client.rpc.IsSerializable;
@@ -28,7 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
*
* @author Franz-Josef Elmer
*/
-public class AbundanceColumnDefinition implements Serializable, IsSerializable
+public class AbundanceColumnDefinition implements Serializable, IsSerializable, Comparable<AbundanceColumnDefinition>
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
@@ -67,4 +68,33 @@ public class AbundanceColumnDefinition implements Serializable, IsSerializable
{
this.treatments = treatments;
}
+
+ public int compareTo(AbundanceColumnDefinition that)
+ {
+ if (this.treatments != null && that.treatments != null)
+ {
+ int sizeDiff = this.treatments.size() - that.treatments.size();
+ if (sizeDiff != 0)
+ {
+ return sizeDiff;
+ }
+ Collections.sort(this.treatments);
+ Collections.sort(that.treatments);
+ for (int i = 0, n = treatments.size(); i < n; i++)
+ {
+ Treatment thisTreatment = this.treatments.get(i);
+ Treatment thatTreatment = that.treatments.get(i);
+ int diff = thisTreatment.compareTo(thatTreatment);
+ if (diff != 0)
+ {
+ return diff;
+ }
+ }
+ }
+ if (this.sampleCode != null && that.sampleCode != null)
+ {
+ return this.sampleCode.compareTo(that.sampleCode);
+ }
+ return 0;
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Treatment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Treatment.java
index c34f7909b28..1ad181f3068 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Treatment.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Treatment.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
*
* @author Franz-Josef Elmer
*/
-public class Treatment implements Serializable, IsSerializable
+public class Treatment implements Serializable, IsSerializable, Comparable<Treatment>
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
@@ -72,6 +72,32 @@ public class Treatment implements Serializable, IsSerializable
return value + " " + type;
}
+ public int compareTo(Treatment that)
+ {
+ if (this.type.compareTo(that.type) != 0)
+ {
+ return this.type.compareTo(that.type);
+ }
+ double thisNumber = convert(this.value);
+ double thatNumber = convert(that.value);
+ if (Double.isNaN(thisNumber) || Double.isNaN(thatNumber))
+ {
+ return this.value.compareTo(that.value);
+ }
+ return Double.compare(thisNumber, thatNumber);
+ }
+
+ private double convert(String numberOrString)
+ {
+ try
+ {
+ return Double.parseDouble(numberOrString);
+ } catch (NumberFormatException e)
+ {
+ return Double.NaN;
+ }
+ }
+
@Override
public String toString()
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinitionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinitionTest.java
new file mode 100644
index 00000000000..2baae805ce3
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinitionTest.java
@@ -0,0 +1,119 @@
+/*
+ * Copyright 2009 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.openbis.plugin.phosphonetx.shared.basic.dto;
+
+import java.util.Arrays;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class AbundanceColumnDefinitionTest extends AssertJUnit
+{
+ @Test
+ public void testCompareTwoDefinitonsWithoutTreatmentsAndSampleCodes()
+ {
+ AbundanceColumnDefinition d1 = new AbundanceColumnDefinition();
+ AbundanceColumnDefinition d2 = create(null);
+
+ assertEquals(0, d1.compareTo(d2));
+
+ d1.setSampleCode("bla");
+
+ assertEquals(0, d1.compareTo(d2));
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithoutTreatmentsButSampleCodes()
+ {
+ AbundanceColumnDefinition d1 = create("abc");
+ AbundanceColumnDefinition d2 = create("abc");
+
+ assertEquals(0, d1.compareTo(d2));
+
+ d2.setSampleCode("def");
+
+ assertEquals(true, d1.compareTo(d2) < 0);
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithDifferentNumberOfTreatments()
+ {
+ AbundanceColumnDefinition d1 = create("abc");
+ d1.setSampleCode("abc");
+ AbundanceColumnDefinition d2 = create("abc", new Treatment());
+ d2.setSampleCode("abc");
+
+ assertEquals(true, d1.compareTo(d2) < 0);
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithOneNonNumericalTreatment()
+ {
+ AbundanceColumnDefinition d1 = create("abc", treatment("light", "red"));
+ AbundanceColumnDefinition d2 = create("abc", treatment("light", "blue"));
+
+ assertEquals(true, d1.compareTo(d2) > 0);
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithOneNumericalTreatment()
+ {
+ AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.5"));
+ AbundanceColumnDefinition d2 = create("abc", treatment("pH", "9e-1"));
+
+ assertEquals(true, d1.compareTo(d2) > 0);
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithOneNumericalTreatmentButDifferentTypes()
+ {
+ AbundanceColumnDefinition d1 = create("abc", treatment("K", "7.5"));
+ AbundanceColumnDefinition d2 = create("abc", treatment("pH", "9e-1"));
+
+ assertEquals(true, d1.compareTo(d2) < 0);
+ }
+
+ @Test
+ public void testCompareTwoDefinitonsWithTwoNumericalTreatment()
+ {
+ AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.50"), treatment("T", "13"));
+ AbundanceColumnDefinition d2 = create("abc", treatment("pH", "0.75e1"), treatment("T", "8"));
+
+ assertEquals(true, d1.compareTo(d2) > 0);
+ }
+
+ private AbundanceColumnDefinition create(String sampleCode, Treatment... treatments)
+ {
+ AbundanceColumnDefinition definition = new AbundanceColumnDefinition();
+ definition.setSampleCode(sampleCode);
+ definition.setTreatments(Arrays.asList(treatments));
+ return definition;
+ }
+
+ private Treatment treatment(String type, String value)
+ {
+ Treatment treatment = new Treatment();
+ treatment.setType(type);
+ treatment.setValue(value);
+ return treatment;
+ }
+}
--
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