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 73f9925bc63cf820f3bb1eb65d6d795134856eb7..b86216ab6fc09ad752aad81af530f48163ef5f3e 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
@@ -16,29 +16,26 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class AbundanceColumnDefinition implements Serializable, IsSerializable, Comparable<AbundanceColumnDefinition>
+public class AbundanceColumnDefinition implements ISerializable,
+ Comparable<AbundanceColumnDefinition>
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private List<Long> sampleIDs = new ArrayList<Long>(1);
-
+
private String sampleCode;
-
+
private List<Treatment> treatments;
-
+
public final long getID()
{
long id = 0;
@@ -48,7 +45,7 @@ public class AbundanceColumnDefinition implements Serializable, IsSerializable,
}
return id;
}
-
+
public final List<Long> getSampleIDs()
{
return sampleIDs;
@@ -63,7 +60,7 @@ public class AbundanceColumnDefinition implements Serializable, IsSerializable,
{
sampleIDs.add(sampleID);
}
-
+
public final String getSampleCode()
{
return sampleCode;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberProvider.java
index b98b0a029efe99868520f010c7999aed87110898..a743a02c7408b80e0692953676545f8ee75c5e6e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberProvider.java
@@ -16,25 +16,20 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class AccessionNumberProvider implements IsSerializable, Serializable
+public class AccessionNumberProvider implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private String accessionNumberType;
-
+
private String accessionNumber;
-
+
public final String getAccessionNumberType()
{
return accessionNumberType;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunction.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunction.java
index 590e5f879062f1698d3e906f9e57c44cd0144810..9fb11700426132a474207c3d1449c27818b567e5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunction.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunction.java
@@ -18,14 +18,14 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
import java.util.Arrays;
-import com.google.gwt.user.client.rpc.IsSerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
/**
* Aggregate functions.
- *
+ *
* @author Franz-Josef Elmer
*/
-public enum AggregateFunction implements IsSerializable
+public enum AggregateFunction implements ISerializable
{
MEAN("mean")
{
@@ -93,21 +93,21 @@ public enum AggregateFunction implements IsSerializable
}
},
;
-
+
private final String label;
private AggregateFunction(String label)
{
this.label = label;
}
-
+
public final String getLabel()
{
return label;
}
/**
- * Aggregates the specified array of numbers to one number.
+ * Aggregates the specified array of numbers to one number.
*
* @param values an array with at least one value.
*/
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
index 531fe9673e9ddd8d4e197d53d4f1b541bd6a6674..113d3d322b22b19303ff1142097fbf9dc2ae820f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
@@ -16,17 +16,14 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
* @author Franz-Josef Elmer
*/
-public class DataSetProtein implements IsSerializable, Serializable
+public class DataSetProtein implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Peptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Peptide.java
index 5902ce1c2a837ddd1fe7c26e18c44923c0a73dce..ea8a0d91f7182231ba1f5dc54ede806b07ec172d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Peptide.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Peptide.java
@@ -16,20 +16,18 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
* @author Tomasz Pylak
*/
-public class Peptide implements IsSerializable, Serializable
+public class Peptide implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private String sequence;
+
private int charge;
public String getSequence()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
index 694f6d867a14499d1a743190dd8f7ebc5e8b8a3b..547fb3b1772a6731944859a26f4b8e6dd13556b5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
@@ -16,27 +16,25 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
import java.util.List;
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
* @author Tomasz Pylak
*/
-public class ProteinDetails implements IsSerializable, Serializable
+public class ProteinDetails implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private String sequence;
private String databaseNameAndVersion;
-
+
private double probability;
-
+
private double coverage;
private double falseDiscoveryRate;
@@ -46,11 +44,11 @@ public class ProteinDetails implements IsSerializable, Serializable
private Long dataSetTechID;
private String dataSetTypeCode;
-
+
private TechId proteinID;
private List<Peptide> peptides;
-
+
private List<IndistinguishableProteinInfo> indistinguishableProteinInfos;
public String getSequence()
@@ -82,12 +80,12 @@ public class ProteinDetails implements IsSerializable, Serializable
{
return probability;
}
-
+
public void setProbability(double probability)
{
this.probability = probability;
}
-
+
public void setCoverage(double coverage)
{
this.coverage = coverage;
@@ -97,7 +95,7 @@ public class ProteinDetails implements IsSerializable, Serializable
{
return coverage;
}
-
+
public void setFalseDiscoveryRate(double falseDiscoveryRate)
{
this.falseDiscoveryRate = falseDiscoveryRate;
@@ -153,7 +151,8 @@ public class ProteinDetails implements IsSerializable, Serializable
this.dataSetTypeCode = dataSetTypeCode;
}
- public void setIndistinguishableProteinInfos(List<IndistinguishableProteinInfo> indistinguishableProteinInfos)
+ public void setIndistinguishableProteinInfos(
+ List<IndistinguishableProteinInfo> indistinguishableProteinInfos)
{
this.indistinguishableProteinInfos = indistinguishableProteinInfos;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
index f53b613680e3e7be880ca03ac94ee8f52edc08bc..caa912d5bb0c786210768cc5e33eab0d97b4d77c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
@@ -16,35 +16,31 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
import java.util.Map;
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class ProteinInfo implements Serializable, IsSerializable
+public class ProteinInfo implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private TechId id;
-
+
private String accessionNumber;
-
+
private TechId experimentID;
-
+
private String dataSetPermID;
-
+
private String description;
-
+
private double coverage;
-
+
private Map<Long, Double> abundances;
public final TechId getId()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
index 188adbd03d7fa83bdf415ca76ce9b7049a1419b5..389a34403842feaedea53705e4d064d733c7a07a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
@@ -16,30 +16,25 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class ProteinSequence implements IsSerializable, Serializable
+public class ProteinSequence implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private String shortName;
-
+
private TechId id;
-
+
private TechId databaseID;
-
+
private String sequence;
-
+
private String databaseNameAndVersion;
public final String getShortName()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
index a6bba8abacc1dd6cd272ecf31c0602a8bba23231..a6bd43170ad0ac0c38236e4c455c919fd29fca6f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
@@ -16,24 +16,20 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class ProteinSummary implements Serializable, IsSerializable
+public class ProteinSummary implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
private double fdr;
-
+
private int proteinCount;
-
+
private int peptideCount;
public double getFDR()
@@ -65,5 +61,5 @@ public class ProteinSummary implements Serializable, IsSerializable
{
this.peptideCount = peptideCount;
}
-
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/SampleWithPropertiesAndAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/SampleWithPropertiesAndAbundance.java
index 4ff79d8f09f2988b7e54dbc5a460a0b3e347af96..1465f6a0faf877fbfa26df1ee3af1568d81e7d89 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/SampleWithPropertiesAndAbundance.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/SampleWithPropertiesAndAbundance.java
@@ -16,12 +16,10 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
import java.util.List;
-import com.google.gwt.user.client.rpc.IsSerializable;
-
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
@@ -32,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
* @author Franz-Josef Elmer
*/
-public class SampleWithPropertiesAndAbundance implements IsSerializable, Serializable,
+public class SampleWithPropertiesAndAbundance implements ISerializable,
IEntityInformationHolderWithPermId, IEntityPropertiesHolder
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
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 00872995fbfb229e4753f113b50f57d2db883da0..33c730e0510f249bfcb82923c587fa135ab3678a 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
@@ -16,27 +16,22 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class Treatment implements Serializable, IsSerializable, Comparable<Treatment>
+public class Treatment implements ISerializable, Comparable<Treatment>
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private String value;
-
+
private String type;
-
+
private String typeCode;
-
+
private String valueType;
public final String getValue()
@@ -68,7 +63,7 @@ public class Treatment implements Serializable, IsSerializable, Comparable<Treat
{
this.type = type;
}
-
+
public final String getTypeCode()
{
return typeCode;
@@ -99,7 +94,7 @@ public class Treatment implements Serializable, IsSerializable, Comparable<Treat
}
return Double.compare(thisNumber, thatNumber);
}
-
+
private double convert(String numberOrString)
{
try
@@ -116,6 +111,5 @@ public class Treatment implements Serializable, IsSerializable, Comparable<Treat
{
return getLabel();
}
-
-
+
}