Final technique for rounding of NU-switch expressions and adds PrawnFile serialization.

build.gradle

@@ -6,7 +6,7 @@ subprojects {
     apply plugin: "java"
 
     group = "org.cirdles"
-    version = "1.4.2"
+    version = "1.4.3"
 
     description = "Replacement for data reduction in Ludwig's Squid 2.50 for SHRIMP"
 

core/src/main/java/org/cirdles/calamari/core/CalamariReportsEngine.java

@@ -369,7 +369,7 @@ private void reportWithinSpotRatiosAtInterpolatedTimes(ShrimpFraction shrimpFrac
             for (TaskExpressionEvaluatedPerSpotPerScanModelInterface taskExpressionEval : taskExpressionsEvaluated) {
                 if (nDodNum < taskExpressionEval.getRatEqTime().length) {
                     dataLine.append(", ").append(String.valueOf(taskExpressionEval.getRatEqTime()[nDodNum]));
-                    dataLine.append(", ").append(Utilities.roundedToSize(taskExpressionEval.getRatEqVal()[nDodNum],12));
+                    dataLine.append(", ").append(Utilities.roundedToSize(taskExpressionEval.getRatEqVal()[nDodNum],15));
                     dataLine.append(", ").append(Utilities.roundedToSize(taskExpressionEval.getRatEqErr()[nDodNum],15));
                 } else {
                     dataLine.append(", ").append("n/a");

core/src/main/java/org/cirdles/calamari/core/PrawnFileHandler.java

@@ -44,6 +44,8 @@
 import javax.xml.XMLConstants;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.PropertyException;
 import javax.xml.bind.Unmarshaller;
 import javax.xml.validation.Schema;
 import javax.xml.validation.SchemaFactory;
@@ -62,7 +64,7 @@
 public class PrawnFileHandler {
 
     private transient Unmarshaller jaxbUnmarshaller;
-//    private transient Marshaller jaxbMarshaller;
+    private transient Marshaller jaxbMarshaller;
     private String currentPrawnFileLocation;
     private transient Consumer<Integer> progressSubscriber;
     private transient CalamariReportsEngine reportsEngine;
@@ -311,22 +313,29 @@ public PrawnFile unmarshallPrawnFileXML(String prawnFileLocation)
     }
 
     /**
+     * Deserializes xml file to a PrawnFile object.
      * @param prawnDataFile the value of prawnDataFile
      * @return the PrawnFile
      * @throws javax.xml.bind.JAXBException
      */
     private PrawnFile readRawDataFile(File prawnDataFile) throws JAXBException {
-
         PrawnFile myPrawnFile = (PrawnFile) jaxbUnmarshaller.unmarshal(prawnDataFile);
-
-//        // test writing it back out WORKS!
-//        JAXBContext jaxbContext = JAXBContext.newInstance(PrawnFile.class);
-//        jaxbMarshaller = jaxbContext.createMarshaller();
-//        jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
-//        jaxbMarshaller.marshal(myPrawnFile, new File("myPrawnFile.xml"));
-//       // jaxbMarshaller.marshal(myPrawnFile, System.out);
         return myPrawnFile;
     }
+
+    /**
+     * Serializes a PrawnFile object to xml and intended for saving edits to original data.
+     * @param prawnFile for serialization
+     * @throws PropertyException
+     * @throws JAXBException 
+     */
+    public void writeRawDataFileAsXML(PrawnFile prawnFile, String fileName)
+        throws PropertyException, JAXBException{
+        JAXBContext jaxbContext = JAXBContext.newInstance(PrawnFile.class);
+        jaxbMarshaller = jaxbContext.createMarshaller();
+        jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+        jaxbMarshaller.marshal(prawnFile, new File(fileName));
+    }
 
     public boolean currentPrawnFileLocationIsFile() {
         return new File(currentPrawnFileLocation).isFile();

core/src/main/java/org/cirdles/calamari/prawn/PrawnFileRunFractionParser.java

@@ -136,8 +136,11 @@ private void prepareRunFractionMetaData(PrawnFile.Run runFraction) {
         String[] firstIntegrations = runFraction.getSet().getScan().get(0).getMeasurement().get(0).getData().get(0).getValue().split(",");
         peakMeasurementsCount = firstIntegrations.length;
 
-        String dateTime = runFraction.getSet().getPar().get(0).getValue() + " " + runFraction.getSet().getPar().get(1).getValue();
-        SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss");
+        String dateTime = runFraction.getSet().getPar().get(0).getValue() 
+                + " " + runFraction.getSet().getPar().get(1).getValue() 
+                + (Integer.parseInt(runFraction.getSet().getPar().get(1).getValue().substring(0, 2)) < 12 ? " AM" : " PM");
+
+        SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss aa");
         try {
             dateTimeMilliseconds = dateFormat.parse(dateTime).getTime();
         } catch (ParseException parseException) {

core/src/main/java/org/cirdles/calamari/tasks/Task.java

@@ -258,8 +258,7 @@ public void evaluateTaskExpressions(List<ShrimpFractionExpressionInterface> shri
                 // documented separately, and approximate the uncertainties:
                 shrimpFraction.setPkInterpScanArray(pkInterp[scanNum]);
 
-                // April 2017 rounding per Bodorkos
-                double eqValTmp = Utilities.roundedToSize(expression.eval2Array(singleSpot)[0][0], 12);
+                double eqValTmp = expression.eval2Array(singleSpot)[0][0];
 
                 double eqFerr;
 
@@ -279,8 +278,7 @@ public void evaluateTaskExpressions(List<ShrimpFractionExpressionInterface> shri
                         perturbed[unDupPkOrd] *= 1.0001;
                         shrimpFraction.setPkInterpScanArray(perturbed);
 
-                        // April 2017 rounding per Bodorkos
-                        double pertVal = Utilities.roundedToSize(expression.eval2Array(singleSpot)[0][0], 12);
+                        double pertVal = expression.eval2Array(singleSpot)[0][0];
 
                         double fDelt = (pertVal - eqValTmp) / eqValTmp; // improvement suggested by Bodorkos
                         double tA = pkInterpFerr[scanNum][unDupPkOrd];

core/src/main/java/org/cirdles/calamari/tasks/TaskExpressionEvaluatedPerSpotPerScanModel.java

@@ -53,7 +53,8 @@ public TaskExpressionEvaluatedPerSpotPerScanModel(
         int sigDigs = 12;
 
         this.expression = expression;
-        this.ratEqVal = Utilities.roundedToSize(ratEqVal.clone(), sigDigs);
+//        this.ratEqVal = Utilities.roundedToSize(ratEqVal.clone(), sigDigs);
+        this.ratEqVal = ratEqVal.clone();
         this.ratEqTime = ratEqTime.clone();
         this.ratEqErr = ratEqErr.clone();