Updates Useries visualizations and addresses issues 182, 181, 171, 16…

…4. (#183)

* fixes alwaysinfront

* fixes bug found by Noah

* tests open-system date calculator and fixes bug in seawater models population.

* working towards open-system dates

* improves graph zooming

* adds joption pane message for exception

* provides opensystem dates and unct for default seawater model

* advances seawater assignment, fixes uri timeout bug

* completes assignment of seawater models for open-system dates

* adds seawater uncertainties to evolution plots

* refactors and addresses issue 182

* fixes misc gui bugs

* fixes issue #164 by changing the fraction mass display and entry units to micrograms and sorting the fraction names in the sample manager.

pom.xml

@@ -21,7 +21,7 @@
     <groupId>org.cirdles</groupId>
     <artifactId>ET_Redux</artifactId>
     <name>ET_Redux</name>
-    <version>3.6.84</version>
+    <version>3.6.85</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>

src/main/java/org/earthtime/UPb_Redux/ReduxConstants.java

@@ -177,7 +177,8 @@ final public class ReduxConstants {
     /**
      *
      */
-    static public int DEFAULT_MASS_DISPLAY_SCALE = 5;
+    static public int DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE = 5;
+    static public int DEFAULT_MASS_IN_MICRO_GRAMS_DISPLAY_SCALE = 3;
     /**
      *
      */

src/main/java/org/earthtime/UPb_Redux/aliquots/UPbReduxAliquot.java

@@ -215,7 +215,7 @@ public UPbReduxAliquot(
 
         setDefaultUBlankMassText(getMyReduxLabData().getDefaultAssumedUBlankMassInGrams().
                 getValue().multiply(ReduxConstants.PicoGramsPerGram).
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         setDefaultR238_235sText(getMyReduxLabData().getDefaultR238_235s()//
@@ -227,7 +227,7 @@ public UPbReduxAliquot(
                         RoundingMode.HALF_UP).toPlainString());
 
         setDefaultR18O_16OText(getMyReduxLabData().getDefaultR18O_16O()//
-                .getValue().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getValue().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         try {
@@ -244,7 +244,7 @@ public UPbReduxAliquot(
 
         setDefaultPbBlankMassText(getMyReduxLabData().getDefaultPbBlankMassInGrams().
                 getValue().multiply(ReduxConstants.PicoGramsPerGram).
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         setDefaultRTh_UmagmaText(getMyReduxLabData().getDefaultRTh_Umagma().
@@ -267,38 +267,38 @@ public UPbReduxAliquot(
 
         // uncertainties
         setDefaultTracerMassOneSigmaText(getMyReduxLabData().getDefaultTracerMass()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         setDefaultUBlankMassOneSigmaText(getMyReduxLabData().getDefaultAssumedUBlankMassInGrams()//
                 .getOneSigmaAbs().multiply(ReduxConstants.PicoGramsPerGram)//
-                .setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         setDefaultR238_235sOneSigmaText(getMyReduxLabData().getDefaultR238_235s()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         this.defaultR238_235bOneSigmaText = getMyReduxLabData().getDefaultR238_235b()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString();
 
         this.defaultPbBlankMassOneSigmaText = getMyReduxLabData().getDefaultPbBlankMassInGrams()//
                 .getOneSigmaAbs().multiply(ReduxConstants.PicoGramsPerGram).//
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString();
 
         // TODO there is some odd duplication with this getters setters
         setDefaultR18O_16OOneSigmaText(getMyReduxLabData().getDefaultR18O_16O()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         this.defaultRTh_UmagmaOneSigmaText = getMyReduxLabData().getDefaultRTh_Umagma()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString();
 
         this.defaultAr231_235sampleOneSigmaText = getMyReduxLabData().getDefaultAr231_235sample()//
-                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                .getOneSigmaAbs().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString();
 
         this.automaticDataUpdateMode = false;

src/main/java/org/earthtime/UPb_Redux/dialogs/aliquotManagers/AliquotEditorDialog.java

@@ -4079,7 +4079,7 @@ private void updateInitialPbModelChooserForRow(ETFractionInterface tempFrac, boo
                         toPlainString());
         fractionStaceyKramersCorrelationCoeffsText.get(row).setEnabled(hasStaceyKramersModel);
 
-        ((JTextComponent) fractionPbBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.pbBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+        ((JTextComponent) fractionPbBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.pbBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                 RoundingMode.HALF_UP).toPlainString());
         ((UnDoAbleDocument) ((JTextComponent) fractionPbBlankMassText.get(row)).getDocument()).undo.discardAllEdits();
         fractionPbBlankMassText.get(row).setEnabled(!isZircon);
@@ -4107,12 +4107,12 @@ private void updateFractionRow(ETFractionInterface tempFrac, int row) {
         fractionTracerChoice.get(row).setEnabled(!(fraCorrU || fraCorrPb));
 
         ((JTextComponent) fractionTracerMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.tracerMassInGrams.getName()).getValue().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
         fractionTracerMassText.get(row).setEnabled(!(fraCorrU));
 
         ((JTextComponent) fractionMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.fractionMass.getName()).getValue().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
                 toPlainString());
 
         updateAlphaPbModelChooserForRow(tempFrac, ((UPbFraction) tempFrac).needsAlphaPbModel(), row);
@@ -4123,11 +4123,11 @@ private void updateFractionRow(ETFractionInterface tempFrac, int row) {
 
         updateInitialPbModelChooserForRow(tempFrac, isZircon, row);
 
-        ((JTextField) fractionPbBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.pbBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+        ((JTextField) fractionPbBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.pbBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                 RoundingMode.HALF_UP).toPlainString());
         fractionPbBlankMassText.get(row).setEnabled(!isZircon);
 
-        ((JTextField) fractionUBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.uBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+        ((JTextField) fractionUBlankMassText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.uBlankMassInGrams.getName()).getValue().multiply(ReduxConstants.PicoGramsPerGram).setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                 RoundingMode.HALF_UP).toPlainString());
         fractionUBlankMassText.get(row).setEnabled(!(fraCorrU));
 
@@ -4147,36 +4147,36 @@ private void updateFractionRow(ETFractionInterface tempFrac, int row) {
         fractionR18O_16OText.get(row).setEnabled(((UPbFraction) tempFrac).isAnOxide());
 
         ((JTextField) fractionRTh_UmagmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.rTh_Umagma.getName()).getValue().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
                 toPlainString());
         fractionRTh_UmagmaText.get(row).setEnabled(true);
 
         ((JTextField) fractionAR231_235sampleText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.ar231_235sample.getName()).getValue().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
                 toPlainString());
         fractionAR231_235sampleText.get(row).setEnabled(true);
 
         //  uncertainties
         ((JTextField) fractionTracerMassOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.tracerMassInGrams.getName()).getOneSigmaAbs().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         ((JTextField) fractionUBlankMassOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.uBlankMassInGrams.getName()).getOneSigmaAbs().//
                 multiply(ReduxConstants.PicoGramsPerGram).
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).//
                 toPlainString());
 
         ((JTextField) fractionR238_235sOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.r238_235s.getName()).getOneSigmaAbs().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         ((JTextField) fractionR238_235bOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.r238_235b.getName()).getOneSigmaAbs().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         ((JTextField) fractionPbBlankMassOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.pbBlankMassInGrams.getName()).getOneSigmaAbs().
                 multiply(ReduxConstants.PicoGramsPerGram).
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
         fractionPbBlankMassOneSigmaText.get(row).setEnabled(!isZircon);
 
@@ -4186,11 +4186,11 @@ private void updateFractionRow(ETFractionInterface tempFrac, int row) {
         fractionR18O_16OOneSigmaText.get(row).setEnabled(((UPbFraction) tempFrac).isAnOxide());
 
         ((JTextField) fractionRTh_UmagmaOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.rTh_Umagma.getName()).getOneSigmaAbs().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
         ((JTextField) fractionAr231_235sampleOneSigmaText.get(row)).setText(tempFrac.getAnalysisMeasure(AnalysisMeasures.ar231_235sample.getName()).getOneSigmaAbs().
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE,
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE,
                         RoundingMode.HALF_UP).toPlainString());
 
     }

src/main/java/org/earthtime/UPb_Redux/dialogs/fractionManagers/UPbFractionEditorDialog.form

@@ -3500,8 +3500,10 @@
                   <Font name="Tahoma" size="12" style="1"/>
                 </Property>
                 <Property name="horizontalAlignment" type="int" value="11"/>
-                <Property name="text" type="java.lang.String" value="fraction mass in g:"/>
               </Properties>
+              <AuxValues>
+                <AuxValue name="JavaCodeGenerator_CreateCodePost" type="java.lang.String" value="fractionMassInGrams_label.setText(&quot;fraction mass in \u03BCg:&quot;);&#xa;"/>
+              </AuxValues>
             </Component>
             <Component class="javax.swing.JCheckBox" name="fractionIsZircon_CheckBox">
               <Properties>

src/main/java/org/earthtime/UPb_Redux/dialogs/fractionManagers/UPbFractionEditorDialog.java

@@ -1440,8 +1440,9 @@ private void showSavedData(ETFractionInterface myFraction) {
 
         fractionIsZircon_CheckBox.setSelected(((FractionI)myFraction).isZircon());
 
+        // july 2019 issue 164 - switching to micrograms       
         fractionMass_text.setText(myFraction.getAnalysisMeasure(AnalysisMeasures.fractionMass.getName()).//
-                getValue().setScale(ReduxConstants.DEFAULT_PARAMETERS_SCALE, RoundingMode.HALF_UP).toPlainString());
+                getValue().movePointRight(6).setScale(ReduxConstants.DEFAULT_MASS_IN_MICRO_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).toPlainString());
 
         // Pb tab **************************************************************
         r206_204_text.setText(myFraction.getMeasuredRatioByName(MeasuredRatios.r206_204m.getName()).//
@@ -1554,14 +1555,14 @@ private void showSavedData(ETFractionInterface myFraction) {
 
         inputAlphaUOneSigmaAbs_text.setText(((UPbFraction) myFraction).getInputAlphaU().getOneSigmaAbs().//
                 movePointRight(2).//
-                setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).toPlainString());
+                setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).toPlainString());
 
         // tracer tab **********************************************************
         tracerMassOneSigmaAbs_label.setText("<html><u>1\u03C3 ABS:</u></html>");
         tracerMass_text.setText(myFraction.getAnalysisMeasure(AnalysisMeasures.tracerMassInGrams.getName()).//
                 getValue().setScale(ReduxConstants.DEFAULT_PARAMETERS_SCALE, RoundingMode.HALF_UP).toPlainString());
         tracerMassOneSigmaAbs_text.setText(myFraction.getAnalysisMeasure(AnalysisMeasures.tracerMassInGrams.getName()).//
-                getOneSigma().setScale(ReduxConstants.DEFAULT_MASS_DISPLAY_SCALE, RoundingMode.HALF_UP).toPlainString());
+                getOneSigma().setScale(ReduxConstants.DEFAULT_MASS_IN_GRAMS_DISPLAY_SCALE, RoundingMode.HALF_UP).toPlainString());
 
         // set up Tracer chooser modified June 2012
         ItemListener[] tracerActionListeners = tracerChooser.getItemListeners();
@@ -2004,8 +2005,9 @@ private void save(ETFractionInterface myFraction)
         }
 
         try {
+            // july 2019 issue 164 switch to micrograms display
             myFraction.getAnalysisMeasure(AnalysisMeasures.fractionMass.getName()).
-                    setValue(new BigDecimal(fractionMass_text.getText()));
+                    setValue(new BigDecimal(fractionMass_text.getText()).movePointLeft(6));
 
             // Pb tab
             myFraction.getMeasuredRatioByName(MeasuredRatios.r206_204m.getName()).setValue(new BigDecimal(r206_204_text.getText()));
@@ -2475,6 +2477,7 @@ private void initComponents() {
         fractionMass_text = new javax.swing.JTextField();
         fractionID_text = new javax.swing.JTextField();
         fractionMassInGrams_label = new javax.swing.JLabel();
+        fractionMassInGrams_label.setText("fraction mass in \u03BCg:");
         fractionIsZircon_CheckBox = new javax.swing.JCheckBox();
         fraction_Chooser = new javax.swing.JComboBox<>();
         fractionID_label1 = new javax.swing.JLabel();
@@ -4142,7 +4145,6 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
 
         fractionMassInGrams_label.setFont(new java.awt.Font("Tahoma", 1, 12)); // NOI18N
         fractionMassInGrams_label.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
-        fractionMassInGrams_label.setText("fraction mass in g:");
 
         fractionIsZircon_CheckBox.setFont(new java.awt.Font("Tahoma", 1, 12)); // NOI18N
         fractionIsZircon_CheckBox.setText("No InitialPb");

src/main/java/org/earthtime/UPb_Redux/dialogs/sampleManagers/analysisManagers/SampleAnalysisWorkflowManagerIDTIMS.form

@@ -416,9 +416,6 @@
             </Property>
             <Property name="text" type="java.lang.String" value="Set Physical Constants:"/>
           </Properties>
-          <AccessibilityProperties>
-            <Property name="AccessibleContext.accessibleName" type="java.lang.String" value="Set Physical Constants:"/>
-          </AccessibilityProperties>
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
               <AbsoluteConstraints x="670" y="30" width="140" height="30"/>