initialize variables with zero or an empty string to be more robust against missing values

SVN: 18415

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()

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;

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()

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)

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;
 

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()

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()