From 8a06ce3bcf22b44e94e4b691e5fc07d445d58ae4 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 18 May 2011 11:54:42 +0000
Subject: [PATCH] LMS-2256 display the number of genes in the assay in the gene
summary view
SVN: 21370
---
.../server/FeatureVectorSummaryProvider.java | 4 ++--
.../MaterialReplicaFeatureSummaryProvider.java | 3 ++-
.../MaterialFeatureVectorSummaryLoader.java | 7 ++++++-
.../logic/WellReplicaSummaryCalculator.java | 17 +++++++++--------
.../basic/dto/MaterialFeatureVectorSummary.java | 11 ++++++++++-
.../MaterialReplicaFeatureSummaryResult.java | 9 ++++++++-
.../FeatureVectorSummaryGridColumnIDs.java | 2 +-
7 files changed, 38 insertions(+), 15 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/FeatureVectorSummaryProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/FeatureVectorSummaryProvider.java
index a06bbb354c8..4d664115a3e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/FeatureVectorSummaryProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/FeatureVectorSummaryProvider.java
@@ -43,7 +43,7 @@ class FeatureVectorSummaryProvider extends AbstractTableModelProvider<MaterialFe
{
private static final String SHOW_DETAILS_MSG = "Show details";
- private static final String RANK_COLUMN_TITLE_SUFFIX_MSG = " rank";
+ private static final String RANK_COLUMN_MSG = " Rank";
private static final String MATERIAL_PROPS_GROUP = "MATERIAL_PROP-";
@@ -89,7 +89,7 @@ class FeatureVectorSummaryProvider extends AbstractTableModelProvider<MaterialFe
featureColumnIds.add(featureColumnId);
String rankColumnId = getRankColumnId(featureCode);
- String rankTitle = featureLabel + RANK_COLUMN_TITLE_SUFFIX_MSG;
+ String rankTitle = RANK_COLUMN_MSG;
builder.addColumn(rankColumnId).withTitle(rankTitle).withDataType(DataTypeCode.INTEGER);
rankColumnIds.add(rankColumnId);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
index bcd8e51afe5..3ab37d858d3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
@@ -73,7 +73,8 @@ class MaterialReplicaFeatureSummaryProvider extends
builder.addColumn(FEATURE);
builder.addColumn(MEDIAN).withDataType(DataTypeCode.REAL);
builder.addColumn(DEVIATION).withDataType(DataTypeCode.REAL);
- builder.addColumn(RANK).withDataType(DataTypeCode.INTEGER);
+ String rankTitle = "Rank (" + replicaResult.getNumberOfMaterialsInExperiment() + ")";
+ builder.addColumn(RANK).withDataType(DataTypeCode.INTEGER).withTitle(rankTitle);
List<MaterialReplicaFeatureSummary> rows = replicaResult.getFeatureSummaries();
List<String> subgroupLabels = replicaResult.getSubgroupLabels();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index 672cee58449..6b6d025c2ae 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -66,7 +66,12 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
List<MaterialReplicaFeatureSummary> replicaRows = convertToFeatureRows(resultOrNull);
List<String> subgroupLabels = tryGetSubgroupLabels(resultOrNull);
- return new MaterialReplicaFeatureSummaryResult(subgroupLabels, replicaRows);
+
+ int materialsInExperiment =
+ (resultOrNull != null ? resultOrNull.getGeneralSummary()
+ .getNumberOfMaterialsInExperiment() : 0);
+ return new MaterialReplicaFeatureSummaryResult(subgroupLabels, replicaRows,
+ materialsInExperiment);
}
private static List<MaterialReplicaFeatureSummary> convertToFeatureRows(
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
index 3739e11f46c..66b586a140d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
@@ -35,8 +35,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialFeatur
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
/**
- * Calculates summaries and ranks for each group of well replicas. Usually a replica is determined
- * by the material in the well, e.g. gene or compound.
+ * Calculates summaries and ranks for each group of well replicas (biological or technical). Usually
+ * a replica is determined by the material in the well, e.g. gene or compound.
*
* @author Tomasz Pylak
*/
@@ -50,13 +50,13 @@ public class WellReplicaSummaryCalculator
.calculateReplicasFeatureVectorSummaries();
}
- public static float[] calculateSummaryFeatureVector(List<IWellData> oneReplicaWells,
+ public static float[] calculateSummaryFeatureVector(List<IWellData> techicalReplicaWells,
MaterialReplicaSummaryAggregationType aggregationType)
{
- validate(oneReplicaWells);
- int numberOfFeatures = getNumberOfFeatures(oneReplicaWells);
- return calculateSummaryFeatureVector(oneReplicaWells, aggregationType, numberOfFeatures)
- .getAggregates();
+ validate(techicalReplicaWells);
+ int numberOfFeatures = getNumberOfFeatures(techicalReplicaWells);
+ return calculateSummaryFeatureVector(techicalReplicaWells, aggregationType,
+ numberOfFeatures).getAggregates();
}
private static void validate(List<IWellData> wellDataList)
@@ -112,6 +112,7 @@ public class WellReplicaSummaryCalculator
List<MaterialFeatureVectorSummary> summaries =
new ArrayList<MaterialFeatureVectorSummary>();
Set<Long> replicaIds = replicaToWellDataMap.getKeys();
+ int numberOfReplicas = replicaIds.size();
for (Long replicaId : replicaIds)
{
List<IWellData> replicaWells = replicaToWellDataMap.getOrDie(replicaId);
@@ -120,7 +121,7 @@ public class WellReplicaSummaryCalculator
Material material = replicaWells.get(0).getMaterial();
MaterialFeatureVectorSummary summary =
new MaterialFeatureVectorSummary(material, summaryFeatures.getAggregates(),
- summaryFeatures.getDeviation(), ranks.get(replicaId));
+ summaryFeatures.getDeviation(), ranks.get(replicaId), numberOfReplicas);
summaries.add(summary);
}
return summaries;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
index 1830116e17b..69656ef667b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
@@ -37,6 +37,8 @@ public class MaterialFeatureVectorSummary implements ISerializable
private int[] featureVectorRanks;
+ private int numberOfMaterialsInExperiment;
+
// GTW
@SuppressWarnings("unused")
private MaterialFeatureVectorSummary()
@@ -44,12 +46,14 @@ public class MaterialFeatureVectorSummary implements ISerializable
}
public MaterialFeatureVectorSummary(Material material, float[] featureVectorSummary,
- float[] featureVectorDeviations, int[] featureVectorRanks)
+ float[] featureVectorDeviations, int[] featureVectorRanks,
+ int numberOfMaterialsInExperiment)
{
this.material = material;
this.featureVectorSummary = featureVectorSummary;
this.featureVectorDeviations = featureVectorDeviations;
this.featureVectorRanks = featureVectorRanks;
+ this.numberOfMaterialsInExperiment = numberOfMaterialsInExperiment;
}
public Material getMaterial()
@@ -71,4 +75,9 @@ public class MaterialFeatureVectorSummary implements ISerializable
{
return featureVectorRanks;
}
+
+ public int getNumberOfMaterialsInExperiment()
+ {
+ return numberOfMaterialsInExperiment;
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummaryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummaryResult.java
index 5ed046fb71b..4dbb554f836 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummaryResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummaryResult.java
@@ -36,11 +36,14 @@ public class MaterialReplicaFeatureSummaryResult implements ISerializable
// represents a single row in the table
private final List<MaterialReplicaFeatureSummary> replicaSummaries;
+ private final int numberOfMaterialsInExperiment;
+
public MaterialReplicaFeatureSummaryResult(List<String> subgroupLabels,
- List<MaterialReplicaFeatureSummary> replicaSummaries)
+ List<MaterialReplicaFeatureSummary> replicaSummaries, int numberOfMaterialsInExperiment)
{
this.subgroupLabels = Collections.unmodifiableList(subgroupLabels);
this.replicaSummaries = Collections.unmodifiableList(replicaSummaries);
+ this.numberOfMaterialsInExperiment = numberOfMaterialsInExperiment;
}
public List<String> getSubgroupLabels()
@@ -54,4 +57,8 @@ public class MaterialReplicaFeatureSummaryResult implements ISerializable
return replicaSummaries;
}
+ public int getNumberOfMaterialsInExperiment()
+ {
+ return numberOfMaterialsInExperiment;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/FeatureVectorSummaryGridColumnIDs.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/FeatureVectorSummaryGridColumnIDs.java
index e0c05a93868..7c920a3dfa5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/FeatureVectorSummaryGridColumnIDs.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/FeatureVectorSummaryGridColumnIDs.java
@@ -25,6 +25,6 @@ public class FeatureVectorSummaryGridColumnIDs
public static final String DETAILS = "details";
- public static final String RANK_PREFIX = "RANK-";
+ public static final String RANK_PREFIX = "RANK";
}
--
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