From 59d8bbeab3d7f15c4631be3a4a5a64b92a8cdd7f Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Fri, 22 Oct 2010 13:01:50 +0000
Subject: [PATCH] initialize variables with zero or an empty string to be more
robust against missing values
SVN: 18415
---
.../cisd/dsu/dss/plugins/ChipResultsSummary.java | 8 ++++----
.../ethz/bsse/cisd/dsu/dss/plugins/ChipSummary.java | 12 ++++++------
.../bsse/cisd/dsu/dss/plugins/IlluminaSummary.java | 4 ++--
.../dss/plugins/IlluminaSummaryReportingPlugin.java | 10 ++++++++--
.../java/ch/ethz/bsse/cisd/dsu/dss/plugins/Lane.java | 4 ++--
.../ethz/bsse/cisd/dsu/dss/plugins/doubleStats.java | 6 +++---
.../ch/ethz/bsse/cisd/dsu/dss/plugins/stats.java | 6 +++---
7 files changed, 28 insertions(+), 22 deletions(-)
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 b9a7dfa481e..eadc082e447 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
@@ -34,13 +34,13 @@ import javax.xml.bind.annotation.XmlElement;
class ChipResultsSummary
{
- private Long clusterCountPF;
+ private Long clusterCountPF = 0L;
- private Long clusterCountRaw;
+ private Long clusterCountRaw = 0L;
- private Long yield;
+ private Long yield = 0L;
- private Double densityRatio;
+ private Double densityRatio = 0.0;
@XmlElement(name = "clusterCountPF")
public Long getClusterCountPF()
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
index f79b6819a06..f749f17e926 100644
--- 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
@@ -31,13 +31,13 @@ import javax.xml.bind.annotation.XmlElement;
*/
class ChipSummary
{
- private String chipID;
+ private String chipID = "";
- private String machine;
+ private String machine = "";
- private String runFolder;
+ private String runFolder = "";
- @XmlElement (name = "ChipID")
+ @XmlElement(name = "ChipID")
public String getChipID()
{
return chipID;
@@ -48,7 +48,7 @@ class ChipSummary
this.chipID = chipID;
}
- @XmlElement (name = "Machine")
+ @XmlElement(name = "Machine")
public String getMachine()
{
return machine;
@@ -59,7 +59,7 @@ class ChipSummary
this.machine = machine;
}
- @XmlElement (name = "RunFolder")
+ @XmlElement(name = "RunFolder")
public String getRunFolder()
{
return runFolder;
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 22813be1f80..9226df41972 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
@@ -73,9 +73,9 @@ class IlluminaSummary
private ChipSummary chipSummary;
- private String Software;
+ private String Software = "";
- private String Date;
+ private String Date = "";
@XmlElement(name = "ChipResultsSummary")
public ChipResultsSummary getChipResultsSummary()
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 5e576669063..929cd0714c7 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
@@ -132,14 +132,20 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
software_version = "Not available";
}
- // TODO : Cover Paired end runs
+ Double densityRatio = chipResultSummary.getDensityRatio();
+ // if (densityRatio == null)
+ // {
+ // // densityRatio = 0.0;
+ // }
+
+ // TODO 2010-10-20, Manuel Kohler : 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() / MEGA));
- row.add(new DoubleTableCell(chipResultSummary.getDensityRatio()));
+ row.add(new DoubleTableCell(densityRatio));
// PhiX Lane
row.add(new IntegerTableCell(laneResultSummary.getRead().getLanes().get(4)
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
index f221cc5ec2c..42af59dde95 100644
--- 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
@@ -55,7 +55,7 @@ import javax.xml.bind.annotation.XmlElement;
class Lane
{
- private Integer laneNumber;
+ private Integer laneNumber = 0;
// since Casava 1.7 available
private doubleStats averageAlignScorePF;
@@ -67,7 +67,7 @@ class Lane
// since Casava 1.7 available
private doubleStats errorPF;
- private Integer laneYield;
+ private Integer laneYield = 0;
private stats oneSig;
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
index d45ae2c7b7e..0d21e99a72c 100644
--- 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
@@ -30,11 +30,11 @@ import javax.xml.bind.annotation.XmlElement;
public class doubleStats
{
- private double mean;
+ private double mean = 0.0;
- private double stdev;
+ private double stdev = 0.0;
- private double sumsq;
+ private double sumsq = 0.0;
@XmlElement(name = "mean")
public double getMean()
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
index 205a0d7939e..11717aacc51 100644
--- 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
@@ -30,11 +30,11 @@ import javax.xml.bind.annotation.XmlElement;
public class stats
{
- private Long mean;
+ private Long mean = 0L;
- private Long stdev;
+ private Long stdev = 0L;
- private Long sumsq;
+ private Long sumsq = 0L;
@XmlElement(name = "mean")
public Long getMean()
--
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