diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index f1dab90537912830a7cb38ee7efb55c6db4d58e2..6fd8124b255111c2814e3237da66b3fb1f82f0cb 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -48,12 +48,15 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ProbabilityToFDRCalculator;
/**
* @author Franz-Josef Elmer
*/
class ResultDataSetUploader extends AbstractHandler
{
+ private static final double MAX_FALSE_DISCOVERY_RATE = 0.1;
+
static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
private final Connection connection;
@@ -214,7 +217,7 @@ class ResultDataSetUploader extends AbstractHandler
Long databaseID = dataSet.getDatabaseID();
AbundanceHandler abundanceHandler =
new AbundanceHandler(openbisService, dao, groupIdentifier, experiment);
- createProbabilityToFDRMapping(dataSetID, summary);
+ ProbabilityToFDRCalculator calculator = createProbabilityToFDRMapping(dataSetID, summary);
List<ProteinGroup> proteinGroups = summary.getProteinGroups();
for (ProteinGroup proteinGroup : proteinGroups)
{
@@ -225,7 +228,10 @@ class ResultDataSetUploader extends AbstractHandler
Protein protein = proteins.get(0);
try
{
- addProtein(protein, dataSetID, databaseID, abundanceHandler);
+ if (calculator.calculateFDR(protein.getProbability()) <= MAX_FALSE_DISCOVERY_RATE)
+ {
+ addProtein(protein, dataSetID, databaseID, abundanceHandler);
+ }
} catch (Exception e)
{
logException(e, "protein", protein.getName());
@@ -354,8 +360,9 @@ class ResultDataSetUploader extends AbstractHandler
return null;
}
- private void createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
+ private ProbabilityToFDRCalculator createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
{
+ ProbabilityToFDRCalculator calculator = new ProbabilityToFDRCalculator();
Object[] s = summary.getSummaryHeader().getProgramDetails().getSummary();
if (s != null)
{
@@ -369,9 +376,10 @@ class ResultDataSetUploader extends AbstractHandler
{
double probability = proteinSummaryDataFilter.getMinProbability();
double fdr = proteinSummaryDataFilter.getFalsePositiveErrorRate();
+ calculator.add(probability, fdr);
dao.createProbabilityToFDRMapping(dataSetID, probability, fdr);
}
- return;
+ return calculator;
}
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
index f56b067d2a5c5790ea1ff38cd26b6519bb143a47..8e0db8c265559f615adf2de9049d657fd69bb51f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
@@ -16,16 +16,14 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
-import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
-import java.util.List;
import java.util.Map;
import net.lemnik.eodsql.DataSet;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ProbabilityToFDRCalculator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
@@ -35,63 +33,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWi
*/
class ErrorModel
{
- private static final class ProbabilityToFDRCalculator
- {
- private static final class MappingEntry implements Comparable<MappingEntry>
- {
- private final double probability;
-
- private final double fdr;
-
- MappingEntry(double probability, double fdr)
- {
- this.probability = probability;
- this.fdr = fdr;
- }
-
- public int compareTo(MappingEntry that)
- {
- return probability < that.probability ? -1 : (probability > that.probability ? 1
- : 0);
- }
-
- @Override
- public String toString()
- {
- return probability + " = " + fdr;
- }
- }
-
- private final List<MappingEntry> mappingEntries = new ArrayList<MappingEntry>();
-
- void add(double probability, double falseDiscoveryRate)
- {
- mappingEntries.add(new MappingEntry(probability, falseDiscoveryRate));
- }
-
- void init()
- {
- Collections.sort(mappingEntries);
- }
-
- double calculateFDR(double probability)
- {
- int index = Collections.binarySearch(mappingEntries, new MappingEntry(probability, 0));
- if (index >= 0)
- {
- return mappingEntries.get(index).fdr;
- }
- // calculate by linear interpolation
- int index1 = -index - 1;
- int index0 = index1 - 1;
- assert index0 >= 0;
- MappingEntry m0 = mappingEntries.get(index0);
- MappingEntry m1 = mappingEntries.get(index1);
- double scale = (m1.fdr - m0.fdr) / (m1.probability - m0.probability);
- return m0.fdr + scale * (probability - m0.probability);
- }
- }
-
private final Map<Long, ProbabilityToFDRCalculator> calculators =
new HashMap<Long, ProbabilityToFDRCalculator>();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ProbabilityToFDRCalculator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ProbabilityToFDRCalculator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c443ae58ae2754f332fdaa69ee8b13264deec49c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ProbabilityToFDRCalculator.java
@@ -0,0 +1,79 @@
+/*
+ * 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;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+
+public final class ProbabilityToFDRCalculator
+{
+ private static final class MappingEntry implements Comparable<ProbabilityToFDRCalculator.MappingEntry>
+ {
+ private final double probability;
+
+ private final double fdr;
+
+ MappingEntry(double probability, double fdr)
+ {
+ this.probability = probability;
+ this.fdr = fdr;
+ }
+
+ public int compareTo(ProbabilityToFDRCalculator.MappingEntry that)
+ {
+ return probability < that.probability ? -1 : (probability > that.probability ? 1
+ : 0);
+ }
+
+ @Override
+ public String toString()
+ {
+ return probability + " = " + fdr;
+ }
+ }
+
+ private final List<ProbabilityToFDRCalculator.MappingEntry> mappingEntries = new ArrayList<ProbabilityToFDRCalculator.MappingEntry>();
+
+ public void add(double probability, double falseDiscoveryRate)
+ {
+ mappingEntries.add(new MappingEntry(probability, falseDiscoveryRate));
+ }
+
+ public void init()
+ {
+ Collections.sort(mappingEntries);
+ }
+
+ public double calculateFDR(double probability)
+ {
+ int index = Collections.binarySearch(mappingEntries, new MappingEntry(probability, 0));
+ if (index >= 0)
+ {
+ return mappingEntries.get(index).fdr;
+ }
+ // calculate by linear interpolation
+ int index1 = -index - 1;
+ int index0 = index1 - 1;
+ assert index0 >= 0;
+ ProbabilityToFDRCalculator.MappingEntry m0 = mappingEntries.get(index0);
+ ProbabilityToFDRCalculator.MappingEntry m1 = mappingEntries.get(index1);
+ double scale = (m1.fdr - m0.fdr) / (m1.probability - m0.probability);
+ return m0.fdr + scale * (probability - m0.probability);
+ }
+}
\ No newline at end of file