From 96b7fff67970caeaee73f49d57d28081354aa612 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 19 Oct 2010 07:58:25 +0000
Subject: [PATCH] PhiX-Lane is now also parsed in and available as column. More
XML Elements are read in and can be used for further processing if needed.
SVN: 18338
---
.../dsu/dss/plugins/ChipResultsSummary.java | 23 ++-
.../cisd/dsu/dss/plugins/ChipSummary.java | 72 +++++++
.../ethz/bsse/cisd/dsu/dss/plugins/Date.java | 38 ++++
.../cisd/dsu/dss/plugins/IlluminaSummary.java | 67 +++++-
.../IlluminaSummaryReportingPlugin.java | 109 +++++-----
.../ethz/bsse/cisd/dsu/dss/plugins/Lane.java | 191 ++++++++++++++++++
.../dsu/dss/plugins/LaneResultsSummary.java | 91 ++-------
.../ethz/bsse/cisd/dsu/dss/plugins/Read.java | 66 ++++++
.../cisd/dsu/dss/plugins/doubleStats.java | 71 +++++++
.../ethz/bsse/cisd/dsu/dss/plugins/stats.java | 71 +++++++
10 files changed, 652 insertions(+), 147 deletions(-)
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipSummary.java
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Date.java
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Lane.java
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Read.java
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/doubleStats.java
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/stats.java
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java
index d96c5c46b21..b9a7dfa481e 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java
@@ -23,13 +23,15 @@ import javax.xml.bind.annotation.XmlElement;
* <ChipResultsSummary>
* <clusterCountPF>98792458</clusterCountPF>
* <clusterCountRaw>158466917</clusterCountRaw>
+ * <densityRatio>3556528488</densityRatio>
* <yield>3556528488</yield>
* </ChipResultsSummary>
- * <Software>CASAVA-1.6.0</Software>
+ * <Software>CASAVA-1.7.0</Software>
* </pre>
*
* @author Manuel Kohler
*/
+
class ChipResultsSummary
{
private Long clusterCountPF;
@@ -38,7 +40,9 @@ class ChipResultsSummary
private Long yield;
- @XmlElement
+ private Double densityRatio;
+
+ @XmlElement(name = "clusterCountPF")
public Long getClusterCountPF()
{
return clusterCountPF;
@@ -49,7 +53,7 @@ class ChipResultsSummary
this.clusterCountPF = clusterCountPF;
}
- @XmlElement
+ @XmlElement(name = "clusterCountRaw")
public Long getClusterCountRaw()
{
return clusterCountRaw;
@@ -60,7 +64,7 @@ class ChipResultsSummary
this.clusterCountRaw = clusterCountRaw;
}
- @XmlElement
+ @XmlElement(name = "yield")
public Long getYield()
{
return yield;
@@ -71,4 +75,15 @@ class ChipResultsSummary
this.yield = yield;
}
+ @XmlElement(name = "densityRatio")
+ public Double getDensityRatio()
+ {
+ return densityRatio;
+ }
+
+ public void setDensityRatio(Double densityRatio)
+ {
+ this.densityRatio = densityRatio;
+ }
+
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipSummary.java
new file mode 100644
index 00000000000..f79b6819a06
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipSummary.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <ChipSummary>
+ * <ChipID>708KLAAXX</ChipID>
+ * <Machine>BS-DSU_ELLAC</Machine>
+ * <RunFolder>101006_708KLAAXX</RunFolder>
+ * </ChipSummary>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+class ChipSummary
+{
+ private String chipID;
+
+ private String machine;
+
+ private String runFolder;
+
+ @XmlElement (name = "ChipID")
+ public String getChipID()
+ {
+ return chipID;
+ }
+
+ public void setChipID(String chipID)
+ {
+ this.chipID = chipID;
+ }
+
+ @XmlElement (name = "Machine")
+ public String getMachine()
+ {
+ return machine;
+ }
+
+ public void setMachine(String machine)
+ {
+ this.machine = machine;
+ }
+
+ @XmlElement (name = "RunFolder")
+ public String getRunFolder()
+ {
+ return runFolder;
+ }
+
+ public void setRunFolder(String runFolder)
+ {
+ this.runFolder = runFolder;
+ }
+}
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Date.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Date.java
new file mode 100644
index 00000000000..959689d5a08
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Date.java
@@ -0,0 +1,38 @@
+/* Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/*
+ * @author Manuel Kohler
+ */
+class Date
+{
+ private String Date;
+
+ @XmlElement
+ public String getDate()
+ {
+ return Date;
+ }
+
+ public void setDate(String date)
+ {
+ this.Date = date;
+ }
+
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
index b75d90f40e1..22813be1f80 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
@@ -20,21 +20,50 @@ import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
/**
+ * Note: Not all XML Elements are read in
+ *
* <pre>
* <Summary>
* <ChipResultsSummary>
- * <clusterCountPF>98792458</clusterCountPF>
- * <clusterCountRaw>158466917</clusterCountRaw>
- * <yield>3556528488</yield>
+ * ...
* </ChipResultsSummary>
* ...
- * <Software>CASAVA-1.6.0</Software>
+ * <ChipSummary>
+ * ...
+ * </ChipSummary>
+ * ...
+ * <Date>
+ * ...
+ * </Date>
+ * ...
+ * <ExpandedLaneSummary>
+ * ...
+ * </ExpandedLaneSummary>
+ * ...
+ * <LaneParameterSummary>
+ * ...
+ * </LaneParameterSummary>
+ * ...
+ * <LaneResultsSummary>
+ * ...
+ * </LaneResultsSummary>
+ * ...
+ * <Software>CASAVA-1.7.0</Software>
+ * ...
+ * <TileErrorsByLane>
+ * ...
+ * </TileErrorsByLane>
+ * ...
+ * <TileResultsByLane>
+ * ...
+ * </TileResultsByLane>
* ...
* <Summary>
* </pre>
*
* @author Manuel Kohler
*/
+
@XmlRootElement(name = "Summary")
class IlluminaSummary
{
@@ -42,8 +71,12 @@ class IlluminaSummary
private LaneResultsSummary LaneResultsSummary;
+ private ChipSummary chipSummary;
+
private String Software;
+ private String Date;
+
@XmlElement(name = "ChipResultsSummary")
public ChipResultsSummary getChipResultsSummary()
{
@@ -63,7 +96,18 @@ class IlluminaSummary
public void setLaneResultsSummary(LaneResultsSummary laneResultsSummary)
{
- LaneResultsSummary = laneResultsSummary;
+ this.LaneResultsSummary = laneResultsSummary;
+ }
+
+ @XmlElement(name = "ChipSummary")
+ public ChipSummary getChipSummary()
+ {
+ return chipSummary;
+ }
+
+ public void setChipSummary(ChipSummary chipSummary)
+ {
+ this.chipSummary = chipSummary;
}
@XmlElement(name = "Software")
@@ -74,6 +118,17 @@ class IlluminaSummary
public void setSoftware(String software)
{
- Software = software;
+ this.Software = software;
+ }
+
+ @XmlElement(name = "Date")
+ public String getDate()
+ {
+ return Date;
+ }
+
+ public void setDate(String date)
+ {
+ this.Date = date;
}
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
index 62d2a8172eb..e66d9996558 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
@@ -39,12 +39,18 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
- * Reporting plugin which shows numbers of the Summary file generated from the Illumina Sequencer.
+ * Reporting plugin which shows numbers of the Summary.xml file generated from the Illumina
+ * Sequencer. The structure of the Summary file has changed from Casava 1.6 to 1.7 so some XML
+ * elements are not available in the old files.
*
* @author Manuel Kohler
*/
public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingPlugin
{
+ private static final int MEGA = 1000000;
+
+ private static final int KILO = 1000;
+
private static final long serialVersionUID = 1L;
private static final String SUMMARY_FILE_NAME = "Summary.xml";
@@ -55,7 +61,7 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
private static final String[] PROPERTIES =
{ "GENOME_ANALYZER", "END_TYPE", "ILLUMINA_PIPELINE_VERSION",
- "CYCLES_REQUESTED_BY_CUSTOMER" };
+ "CYCLES_REQUESTED_BY_CUSTOMER" };
public IlluminaSummaryReportingPlugin(Properties properties, File storeRoot)
{
@@ -68,31 +74,35 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
builder.addHeader("Sample Code");
builder.addHeader("Clusters");
builder.addHeader("Clusters (PF)");
- builder.addHeader("Yield (kbases)");
+ builder.addHeader("Yield (Mbases)");
+ builder.addHeader("Density Ratio");
+ builder.addHeader("PhiX: Clusters");
+ builder.addHeader("PhiX: ClustersPF");
+ builder.addHeader("PhiX: Yield (Mbases)");
+ builder.addHeader("PhiX: % Align (PF)");
+
builder.addHeader("Software");
+ builder.addHeader("Eland finished");
for (String property : PROPERTIES)
{
builder.addHeader(property);
}
- builder.addHeader("PhiX: Clusters");
- builder.addHeader("PhiX: ClustersPF");
- builder.addHeader("PhiX: Yield (kbases)");
- builder.addHeader("PhiX: % Align (PF)");
+
for (DatasetDescription dataset : datasets)
{
File originalData = getDataSubDir(dataset);
// set the directory containing the Summary.xml
File childDirectory =
- new File(originalData, dataset.getSampleCode()
- + DATA_INTENSITIES_BASE_CALLS_PATH);
+ new File(originalData, dataset.getSampleCode()
+ + DATA_INTENSITIES_BASE_CALLS_PATH);
File[] files = childDirectory.listFiles(new FileFilter()
+ {
+ public boolean accept(File file)
{
- public boolean accept(File file)
- {
- return file.isDirectory() && file.getName().startsWith(GERALD_DIR);
- }
- });
+ return file.isDirectory() && file.getName().startsWith(GERALD_DIR);
+ }
+ });
System.out.println(files[0]);
if (files.length == 1)
@@ -103,35 +113,12 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
} else
{
// throw new EnvironmentFailureException(String.format("More than one ..."));
+ // removed because it doesn't help, so just do nothing
}
- // if (childDirectory.exists())
- // {
- // File summaryFile = extractSummaryFile(dataset, childDirectory);
- // describe(builder, dataset, summaryFile);
- // } else
- // {
- // File summaryFile = extractSummaryFile(dataset, originalData);
- // }
}
return builder.getTableModel();
}
- // private static File extractSummaryFile(DatasetDescription dataset, File originalData)
- // {
- // List<File> files = new ArrayList<File>();
- // FileUtilities.findFiles(originalData, files, createIlluminaSummaryFileFilter());
- // int size = files.size();
- // if (size == 1)
- // {
- // return files.get(0);
- // } else
- // {
- // throw new EnvironmentFailureException(String.format(
- // "%s file was found for the dataset %s (%s).", (size == 0) ? "No summary"
- // : " More than one", dataset.getDatasetCode(), dataset.getSampleCode()));
- // }
- // }
-
private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset,
File summaryFile)
{
@@ -143,6 +130,8 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
DatasetDescription dataset, IlluminaSummary summary)
{
ChipResultsSummary chipResultSummary = summary.getChipResultsSummary();
+ LaneResultsSummary laneResultSummary = summary.getLaneResultsSummary();
+ // ChipSummary chipSummary = summary.getChipSummary();
String software_version = summary.getSoftware();
if (software_version == null)
@@ -150,18 +139,29 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
software_version = "Not available";
}
+ // TODO : Cover Paired end runs
+
List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
row.add(new StringTableCell(dataset.getSampleCode()));
row.add(new IntegerTableCell(chipResultSummary.getClusterCountRaw()));
row.add(new IntegerTableCell(chipResultSummary.getClusterCountPF()));
- row.add(new IntegerTableCell(chipResultSummary.getYield() / 1000));
+ row.add(new IntegerTableCell(chipResultSummary.getYield() / MEGA));
+ row.add(new DoubleTableCell(chipResultSummary.getDensityRatio()));
+
+ // PhiX Lane
+ row.add(new IntegerTableCell(laneResultSummary.getRead().getLanes().get(4)
+ .getClusterCountRaw().getMean()));
+ row.add(new IntegerTableCell(laneResultSummary.getRead().getLanes().get(4)
+ .getClusterCountPF().getMean()));
+ row.add(new IntegerTableCell(laneResultSummary.getRead().getLanes().get(4).getLaneYield()
+ / KILO));
+ row.add(new DoubleTableCell(laneResultSummary.getRead().getLanes().get(4)
+ .getPercentUniquelyAlignedPF().getMean()));
+
row.add(new StringTableCell(software_version));
+ row.add(new StringTableCell(summary.getDate()));
addPropertyColumnValues(dataset, row);
- // just dummies
- row.add(new IntegerTableCell(1));
- row.add(new IntegerTableCell(1));
- row.add(new IntegerTableCell(1));
- row.add(new DoubleTableCell(1.0));
+
builder.addRow(row);
}
@@ -194,10 +194,10 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
String sampleCode = dataset.getSampleCode();
String databaseInstanceCode = dataset.getDatabaseInstanceCode();
SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new SpaceIdentifier(databaseInstanceCode, spaceCode),
- sampleCode);
+ new SampleIdentifier(new SpaceIdentifier(databaseInstanceCode, spaceCode),
+ sampleCode);
Sample sampleOrNull =
- ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
+ ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
if (sampleOrNull == null)
{
throw new EnvironmentFailureException(String.format(
@@ -207,23 +207,12 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
return sampleOrNull;
}
- // private static FileFilter createIlluminaSummaryFileFilter()
- // {
- // return new FileFilter()
- // {
- // public boolean accept(File file)
- // {
- // return file.isFile() && file.getName().equals(SUMMARY_FILE_NAME);
- // }
- // };
- // }
-
/**
* Loader of Illumina summary XML file.
* <p>
* NOTE: This is not thread safe as it holds {@link JaxbXmlParser} singleton. As long as it is
* used only by {@link IlluminaSummaryReportingPlugin} it will work correctly because we only
- * use a singleto of each reporting plugin.
+ * use a singleton of each reporting plugin.
*
* @author Piotr Buczek
*/
@@ -231,7 +220,7 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
{
// we use one instance
private static JaxbXmlParser<IlluminaSummary> PARSER_INSTANCE =
- new JaxbXmlParser<IlluminaSummary>(IlluminaSummary.class, false);
+ new JaxbXmlParser<IlluminaSummary>(IlluminaSummary.class, false);
public static IlluminaSummary readSummaryXML(File summaryXml)
{
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Lane.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Lane.java
new file mode 100644
index 00000000000..f221cc5ec2c
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Lane.java
@@ -0,0 +1,191 @@
+/*
+ * Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <Lane>
+ * <laneNumber>1</laneNumber>
+ * <averageAlignScorePF>
+ * ...
+ * </averageAlignScorePF>
+ * <clusterCountPF>
+ * ...
+ * </clusterCountPF>
+ * <clusterCountRaw>
+ * ...
+ * </clusterCountRaw>
+ * <errorPF>
+ * ...
+ * </errorPF>
+ * <laneYield>2290093</laneYield>
+ * <oneSig>
+ * ...
+ * </oneSig>
+ * <percentClustersPF>
+ * ...
+ * </percentClustersPF>
+ * <percentUniquelyAlignedPF>
+ * ...
+ * </percentUniquelyAlignedPF>
+ * <signal20AsPctOf1>
+ * ...
+ * </signal20AsPctOf1>
+ * </Lane>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+
+class Lane
+{
+ private Integer laneNumber;
+
+ // since Casava 1.7 available
+ private doubleStats averageAlignScorePF;
+
+ private stats clusterCountPF;
+
+ private stats clusterCountRaw;
+
+ // since Casava 1.7 available
+ private doubleStats errorPF;
+
+ private Integer laneYield;
+
+ private stats oneSig;
+
+ private doubleStats percentClustersPF;
+
+ // since Casava 1.7 available
+ private doubleStats percentUniquelyAlignedPF;
+
+ private doubleStats signal20AsPctOf1;
+
+ @XmlElement(name = "laneNumber")
+ public Integer getLaneNumber()
+ {
+ return laneNumber;
+ }
+
+ public void setLaneNumber(Integer laneNumber)
+ {
+ this.laneNumber = laneNumber;
+ }
+
+ @XmlElement(name = "averageAlignScorePF")
+ public doubleStats getAverageAlignScorePF()
+ {
+ return averageAlignScorePF;
+ }
+
+ public void setAverageAlignScorePF(doubleStats averageAlignScorePF)
+ {
+ this.averageAlignScorePF = averageAlignScorePF;
+ }
+
+ @XmlElement(name = "clusterCountPF")
+ public stats getClusterCountPF()
+ {
+ return clusterCountPF;
+ }
+
+ public void setClusterCountPF(stats clusterCountPF)
+ {
+ this.clusterCountPF = clusterCountPF;
+ }
+
+ @XmlElement(name = "clusterCountRaw")
+ public stats getClusterCountRaw()
+ {
+ return clusterCountRaw;
+ }
+
+ public void setClusterCountRaw(stats clusterCountRaw)
+ {
+ this.clusterCountRaw = clusterCountRaw;
+ }
+
+ @XmlElement(name = "errorPF")
+ public doubleStats getErrorPF()
+ {
+ return errorPF;
+ }
+
+ public void setErrorPF(doubleStats errorPF)
+ {
+ this.errorPF = errorPF;
+ }
+
+ @XmlElement(name = "laneYield")
+ public Integer getLaneYield()
+ {
+ return laneYield;
+ }
+
+ public void setLaneYield(Integer laneYield)
+ {
+ this.laneYield = laneYield;
+ }
+
+ @XmlElement(name = "oneSig")
+ public stats getOneSig()
+ {
+ return oneSig;
+ }
+
+ public void setOneSig(stats oneSig)
+ {
+ this.oneSig = oneSig;
+ }
+
+ @XmlElement(name = "percentClustersPF")
+ public doubleStats getPercentClustersPF()
+ {
+ return percentClustersPF;
+ }
+
+ public void setPercentClustersPF(doubleStats percentClustersPF)
+ {
+ this.percentClustersPF = percentClustersPF;
+ }
+
+ @XmlElement(name = "percentUniquelyAlignedPF")
+ public doubleStats getPercentUniquelyAlignedPF()
+ {
+ return percentUniquelyAlignedPF;
+ }
+
+ public void setPercentUniquelyAlignedPF(doubleStats percentUniquelyAlignedPF)
+ {
+ this.percentUniquelyAlignedPF = percentUniquelyAlignedPF;
+ }
+
+ @XmlElement(name = "signal20AsPctOf1")
+ public doubleStats getSignal20AsPctOf1()
+ {
+ return signal20AsPctOf1;
+ }
+
+ public void setSignal20AsPctOf1(doubleStats signal20AsPctOf1)
+ {
+ this.signal20AsPctOf1 = signal20AsPctOf1;
+ }
+
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
index 7f6865e89ec..50c3538b359 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/LaneResultsSummary.java
@@ -16,94 +16,31 @@
package ch.ethz.bsse.cisd.dsu.dss.plugins;
+import javax.xml.bind.annotation.XmlElement;
+
/**
* <pre>
- * <LaneResultsSummary>
- * <Read>
- * <readNumber>1</readNumber>
- * <Lane>
- * <laneNumber>1</laneNumber>
- * <clusterCountPF>
- * <mean>251107</mean>
- * <stdev>9934</stdev>
- * <sumsq>11841370000</sumsq>
- * </clusterCountPF>
- * <clusterCountRaw>
- * <mean>290967</mean>
- * <stdev>12357</stdev>
- * <sumsq>18322720000</sumsq>
- * </clusterCountRaw>
- * <laneYield>2290093</laneYield>
- * <oneSig>
- * <mean>497</mean>
- * <stdev>61</stdev>
- * <sumsq>447654</sumsq>
- * </oneSig>
- * <percentClustersPF>
- * <mean>86.32</mean>
- * <stdev>1.66</stdev>
- * <sumsq>331.22</sumsq>
- * </percentClustersPF>
- * <signal20AsPctOf1>
- * <mean>81.60</mean>
- * <stdev>6.26</stdev>
- * <sumsq>4700.89</sumsq>
- * </signal20AsPctOf1>
- * </Lane>
- * ...
- * </Read>
- * </LaneResultsSummary>
+ * <ExpandedLaneSummary>
+ * <Read>
+ * </Read>
+ * </ExpandedLaneSummary>
* </pre>
*
* @author Manuel Kohler
*/
-public class LaneResultsSummary
+class LaneResultsSummary
{
- private String Read;
-
- private Long clusterCountPF;
-
- private Long clusterCountRaw;
-
- private Long laneyield;
-
- public String getRead()
- {
- return Read;
- }
-
- public void setRead(String read)
- {
- Read = read;
- }
- public Long getClusterCountPF()
- {
- return clusterCountPF;
- }
-
- public void setClusterCountPF(Long clusterCountPF)
- {
- this.clusterCountPF = clusterCountPF;
- }
-
- public Long getClusterCountRaw()
- {
- return clusterCountRaw;
- }
-
- public void setClusterCountRaw(Long clusterCountRaw)
- {
- this.clusterCountRaw = clusterCountRaw;
- }
+ private Read read;
- public Long getLaneyield()
+ @XmlElement(name = "Read")
+ public Read getRead()
{
- return laneyield;
+ return read;
}
- public void setLaneyield(Long laneyield)
+ public void setRead(Read read)
{
- this.laneyield = laneyield;
+ this.read = read;
}
-}
\ No newline at end of file
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Read.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Read.java
new file mode 100644
index 00000000000..18dcee10c78
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/Read.java
@@ -0,0 +1,66 @@
+/* Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <Read>
+ * <readNumber>1</readNumber>
+ * <Lane>
+ * ...
+ * </Lane>
+ * ...
+ * </Read>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+
+class Read
+{
+ private List<Integer> readNumber = new ArrayList<Integer>();
+
+ private List<Lane> lanes;
+
+ @XmlElement (name = "readNumber")
+ public List<Integer> getReadNumbers()
+ {
+ return readNumber;
+ }
+
+ public void setReadNumbers(List<Integer> readNumber)
+ {
+ this.readNumber = readNumber;
+ }
+
+ @XmlElement (name = "Lane")
+ public List<Lane> getLanes()
+ {
+ return lanes;
+ }
+
+ public void setLanes(List<Lane> lanes)
+ {
+ this.lanes = lanes;
+ }
+
+
+}
+
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/doubleStats.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/doubleStats.java
new file mode 100644
index 00000000000..d45ae2c7b7e
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/doubleStats.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <mean>277736.1</mean>
+ * <stdev>11981.2</stdev>
+ * <sumsq>17.3</sumsq>
+ * </pre>
+ *
+ * @author kohleman
+ */
+
+public class doubleStats
+{
+ private double mean;
+
+ private double stdev;
+
+ private double sumsq;
+
+ @XmlElement(name = "mean")
+ public double getMean()
+ {
+ return mean;
+ }
+
+ public void setMean(double mean)
+ {
+ this.mean = mean;
+ }
+
+ @XmlElement(name = "stdev")
+ public double getStdev()
+ {
+ return stdev;
+ }
+
+ public void setStdev(double stdev)
+ {
+ this.stdev = stdev;
+ }
+
+ @XmlElement(name = "sumsq")
+ public double getSumsq()
+ {
+ return sumsq;
+ }
+
+ public void setSumsq(double sumsq)
+ {
+ this.sumsq = sumsq;
+ }
+}
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/stats.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/stats.java
new file mode 100644
index 00000000000..205a0d7939e
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/stats.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <mean>277736</mean>
+ * <stdev>11981</stdev>
+ * <sumsq>17224950000</sumsq>
+ * </pre>
+ *
+ * @author kohleman
+ */
+
+public class stats
+{
+ private Long mean;
+
+ private Long stdev;
+
+ private Long sumsq;
+
+ @XmlElement(name = "mean")
+ public Long getMean()
+ {
+ return mean;
+ }
+
+ public void setMean(Long mean)
+ {
+ this.mean = mean;
+ }
+
+ @XmlElement(name = "stdev")
+ public Long getStdev()
+ {
+ return stdev;
+ }
+
+ public void setStdev(Long stdev)
+ {
+ this.stdev = stdev;
+ }
+
+ @XmlElement(name = "sumsq")
+ public Long getSumsq()
+ {
+ return sumsq;
+ }
+
+ public void setSumsq(Long sumsq)
+ {
+ this.sumsq = sumsq;
+ }
+}
--
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