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bowringbowring
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Merge pull request #753 from bowring/cleanup
Cleanup and refine solution to issue #613
2 parents 1cab35c + e37ead5 commit efc9675

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19 files changed

+113
-86
lines changed

19 files changed

+113
-86
lines changed

‎common.gradle

+1-1
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
77

88

99
String mavenGroupId = 'org.cirdles'
10-
String mavenVersion = '2.0.1'
10+
String mavenVersion = '2.0.2'
1111

1212
[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
1313

‎squidApp/src/main/resources/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignment.fxml

+52-37
Original file line numberDiff line numberDiff line change
@@ -17,70 +17,85 @@
1717
-->
1818

1919
<?import javafx.geometry.Insets?>
20-
<?import javafx.scene.control.Button?>
21-
<?import javafx.scene.control.Label?>
22-
<?import javafx.scene.control.RadioButton?>
23-
<?import javafx.scene.control.ToggleGroup?>
24-
<?import javafx.scene.layout.AnchorPane?>
25-
<?import javafx.scene.layout.HBox?>
26-
<?import javafx.scene.layout.VBox?>
27-
28-
<VBox fx:id="vboxMaster" minHeight="660.0" minWidth="1250.0" prefHeight="660.0" prefWidth="1250.0" xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.dateInterpretations.commonLeadAssignment.CommonLeadAssignmentController">
20+
<?import javafx.scene.control.*?>
21+
<?import javafx.scene.layout.*?>
22+
<VBox xmlns:fx="http://javafx.com/fxml/1" fx:id="vboxMaster" minHeight="660.0" minWidth="1250.0" prefHeight="660.0"
23+
prefWidth="1250.0" xmlns="http://javafx.com/javafx/17"
24+
fx:controller="org.cirdles.squid.gui.dateInterpretations.commonLeadAssignment.CommonLeadAssignmentController">
2925
<children>
30-
<HBox fx:id="headerHBoxForCorrections" minHeight="50.0" prefHeight="50.0" prefWidth="1200.0" spacing="35.0" styleClass="backgroundCalamari">
26+
<HBox fx:id="headerHBoxForCorrections" minHeight="50.0" prefHeight="50.0" prefWidth="1200.0" spacing="35.0"
27+
styleClass="backgroundCalamari">
3128
<children>
32-
<VBox alignment="CENTER" prefWidth="225.0">
33-
<children>
34-
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text=" 204 Corrections:" translateY="-2.0" />
35-
<Button fx:id="viewDetailsButton" onAction="#viewDetailsOnAction" text="View Details" />
36-
</children>
37-
</VBox>
29+
<VBox alignment="CENTER" prefWidth="225.0">
30+
<children>
31+
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;"
32+
text=" 204 Corrections:" translateY="-2.0"/>
33+
<Button fx:id="viewDetailsButton" onAction="#viewDetailsOnAction" text="View Details"/>
34+
</children>
35+
</VBox>
3836
<VBox>
3937
<children>
40-
<Label prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" />
41-
<RadioButton fx:id="correctionNoneRB" mnemonicParsing="false" onAction="#correctionNoneAction" selected="true" style="-fx-text-fill: #c53d13#c53d13;" text="Original 204/206 ±1σ % ">
38+
<Label prefHeight="24.0" prefWidth="286.0"
39+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;"/>
40+
<RadioButton fx:id="correctionNoneRB" mnemonicParsing="false" onAction="#correctionNoneAction"
41+
selected="true" style="-fx-text-fill: #c53d13#c53d13;"
42+
text="Original 204/206 ±1σ % ">
4243
<toggleGroup>
43-
<ToggleGroup fx:id="correctionsToggleGroup" />
44+
<ToggleGroup fx:id="correctionsToggleGroup"/>
4445
</toggleGroup>
4546
</RadioButton>
4647
</children>
4748
</VBox>
4849
<VBox>
4950
<children>
50-
<Label fx:id="biweight207Label" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label" />
51-
<RadioButton fx:id="correction207RB" mnemonicParsing="false" onAction="#correction207Action" style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 207 ±1σ % " toggleGroup="$correctionsToggleGroup" />
51+
<Label fx:id="biweight207Label" prefHeight="24.0" prefWidth="286.0"
52+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label"/>
53+
<RadioButton fx:id="correction207RB" mnemonicParsing="false" onAction="#correction207Action"
54+
style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 207 ±1σ % "
55+
toggleGroup="$correctionsToggleGroup"/>
5256
</children>
5357
</VBox>
5458
<VBox>
5559
<children>
56-
<Label fx:id="biweight208Label" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label" />
57-
<RadioButton fx:id="correction208RB" mnemonicParsing="false" onAction="#correction208Action" style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 208 ±1σ %" toggleGroup="$correctionsToggleGroup" />
60+
<Label fx:id="biweight208Label" prefHeight="24.0" prefWidth="286.0"
61+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label"/>
62+
<RadioButton fx:id="correction208RB" mnemonicParsing="false" onAction="#correction208Action"
63+
style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 208 ±1σ %"
64+
toggleGroup="$correctionsToggleGroup"/>
65+
</children>
66+
</VBox>
67+
<VBox layoutX="807.0" layoutY="13.0">
68+
<children>
69+
<Label fx:id="customSWAPLabel" prefHeight="24.0" prefWidth="286.0"
70+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label"/>
71+
<RadioButton fx:id="customSWAPRB" mnemonicParsing="false" onAction="#customCorrectionAction"
72+
style="-fx-text-fill: #c53d13#c53d13;" text="Custom SWAP ±1σ %"
73+
toggleGroup="$correctionsToggleGroup"/>
5874
</children>
5975
</VBox>
60-
<VBox layoutX="807.0" layoutY="13.0">
61-
<children>
62-
<Label fx:id="customSWAPLabel" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label" />
63-
<RadioButton fx:id="customSWAPRB" mnemonicParsing="false" onAction="#customCorrectionAction" style="-fx-text-fill: #c53d13#c53d13;" text="Custom SWAP ±1σ %" toggleGroup="$correctionsToggleGroup" />
64-
</children>
65-
</VBox>
6676
</children>
6777
<padding>
68-
<Insets top="3.0" />
78+
<Insets top="3.0"/>
6979
</padding>
7080
</HBox>
71-
<HBox fx:id="headerHBox" minHeight="25.0" prefHeight="25.0" prefWidth="1200.0" spacing="35.0" styleClass="backgroundCalamari">
81+
<HBox fx:id="headerHBox" minHeight="25.0" prefHeight="25.0" prefWidth="1200.0" spacing="35.0"
82+
styleClass="backgroundCalamari">
7283
<children>
73-
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text=" Common Lead Assignment:" translateY="-2.0" />
74-
<Label layoutX="10.0" layoutY="13.0" style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text="Age Type:" translateX="260.0" />
84+
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;"
85+
text=" Common Lead Assignment:" translateY="-2.0"/>
86+
<Label layoutX="10.0" layoutY="13.0"
87+
style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;"
88+
text="Age Type:" translateX="260.0"/>
7589
</children>
7690
<padding>
77-
<Insets top="3.0" />
91+
<Insets top="3.0"/>
7892
</padding>
7993
</HBox>
80-
<AnchorPane fx:id="sampleTreeAnchorPane" prefHeight="638.0" prefWidth="1200.0" />
81-
<HBox fx:id="footerHBox" layoutX="10.0" layoutY="10.0" maxHeight="30.0" minHeight="30.0" prefHeight="30.0" prefWidth="1200.0" spacing="17.0" styleClass="backgroundCalamari">
94+
<AnchorPane fx:id="sampleTreeAnchorPane" prefHeight="638.0" prefWidth="1200.0"/>
95+
<HBox fx:id="footerHBox" layoutX="10.0" layoutY="10.0" maxHeight="30.0" minHeight="30.0" prefHeight="30.0"
96+
prefWidth="1200.0" spacing="17.0" styleClass="backgroundCalamari">
8297
<padding>
83-
<Insets top="3.0" />
98+
<Insets top="3.0"/>
8499
</padding>
85100
</HBox>
86101
</children>

‎squidApp/src/main/resources/org/cirdles/squid/gui/dateInterpretations/countCorrections/CountCorrections.fxml

+44-31
Original file line numberDiff line numberDiff line change
@@ -17,57 +17,70 @@
1717
-->
1818

1919
<?import javafx.geometry.Insets?>
20-
<?import javafx.scene.control.Button?>
21-
<?import javafx.scene.control.Label?>
22-
<?import javafx.scene.control.RadioButton?>
23-
<?import javafx.scene.control.ToggleGroup?>
24-
<?import javafx.scene.layout.AnchorPane?>
25-
<?import javafx.scene.layout.HBox?>
26-
<?import javafx.scene.layout.VBox?>
27-
28-
<VBox fx:id="vboxMaster" minHeight="660.0" minWidth="1250.0" prefHeight="660.0" prefWidth="1250.0" stylesheets="@../../css/projectManager.css" xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.dateInterpretations.countCorrections.CountCorrectionsController">
20+
<?import javafx.scene.control.*?>
21+
<?import javafx.scene.layout.*?>
22+
<VBox xmlns:fx="http://javafx.com/fxml/1" fx:id="vboxMaster" minHeight="660.0" minWidth="1250.0" prefHeight="660.0"
23+
prefWidth="1250.0" stylesheets="@../../css/projectManager.css"
24+
xmlns="http://javafx.com/javafx/17"
25+
fx:controller="org.cirdles.squid.gui.dateInterpretations.countCorrections.CountCorrectionsController">
2926
<children>
30-
<HBox fx:id="headerHBox" minHeight="50.0" prefHeight="50.0" prefWidth="1200.0" spacing="35.0" styleClass="backgroundCalamari">
27+
<HBox fx:id="headerHBox" minHeight="50.0" prefHeight="50.0" prefWidth="1200.0" spacing="35.0"
28+
styleClass="backgroundCalamari">
3129
<children>
32-
<VBox alignment="CENTER" prefWidth="225.0">
33-
<children>
34-
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;" text=" 204 Corrections:" translateY="-2.0" />
35-
<Button fx:id="returnToCommonLeadButton" onAction="#returnOnAction" text="Return" />
36-
</children>
37-
</VBox>
30+
<VBox alignment="CENTER" prefWidth="225.0">
31+
<children>
32+
<Label style="-fx-font-family: SansSerif; -fx-font-size: 14; -fx-text-fill: #c53d13; -fx-font-weight: bold;"
33+
text=" 204 Corrections:" translateY="-2.0"/>
34+
<Button fx:id="returnToCommonLeadButton" onAction="#returnOnAction" text="Return"/>
35+
</children>
36+
</VBox>
3837
<VBox>
3938
<children>
40-
<Label prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" />
41-
<RadioButton fx:id="correctionNoneRB" mnemonicParsing="false" onAction="#correctionNoneAction" selected="true" style="-fx-text-fill: #c53d13#c53d13;" text="Original 204/206 ±1σ % ">
39+
<Label prefHeight="24.0" prefWidth="286.0"
40+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;"/>
41+
<RadioButton fx:id="correctionNoneRB" mnemonicParsing="false" onAction="#correctionNoneAction"
42+
selected="true" style="-fx-text-fill: #c53d13#c53d13;"
43+
text="Original 204/206 ±1σ % ">
4244
<toggleGroup>
43-
<ToggleGroup fx:id="correctionsToggleGroup" />
45+
<ToggleGroup fx:id="correctionsToggleGroup"/>
4446
</toggleGroup>
4547
</RadioButton>
4648
</children>
4749
</VBox>
4850
<VBox>
4951
<children>
50-
<Label fx:id="biweight207Label" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label" />
51-
<RadioButton fx:id="correction207RB" mnemonicParsing="false" onAction="#correction207Action" style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 207 ±1σ % " toggleGroup="$correctionsToggleGroup" />
52+
<Label fx:id="biweight207Label" prefHeight="24.0" prefWidth="286.0"
53+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label"/>
54+
<RadioButton fx:id="correction207RB" mnemonicParsing="false" onAction="#correction207Action"
55+
style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 207 ±1σ % "
56+
toggleGroup="$correctionsToggleGroup"/>
5257
</children>
5358
</VBox>
5459
<VBox>
5560
<children>
56-
<Label fx:id="biweight208Label" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label" />
57-
<RadioButton fx:id="correction208RB" mnemonicParsing="false" onAction="#correction208Action" style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 208 ±1σ %" toggleGroup="$correctionsToggleGroup" />
61+
<Label fx:id="biweight208Label" prefHeight="24.0" prefWidth="286.0"
62+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="Label"/>
63+
<RadioButton fx:id="correction208RB" mnemonicParsing="false" onAction="#correction208Action"
64+
style="-fx-text-fill: #c53d13#c53d13;" text="Corrected from 208 ±1σ %"
65+
toggleGroup="$correctionsToggleGroup"/>
66+
</children>
67+
</VBox>
68+
<VBox layoutX="814.0" layoutY="13.0">
69+
<children>
70+
<Label fx:id="customSwapLabel" prefHeight="24.0" prefWidth="286.0"
71+
style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;"
72+
text="SWAPCustomCorrection204"/>
73+
<RadioButton fx:id="customSWAPRB" mnemonicParsing="false" onAction="#customCorrectionAction"
74+
style="-fx-text-fill: #c53d13#c53d13;" text="Custom SWAP ±1σ %"
75+
toggleGroup="$correctionsToggleGroup"/>
5876
</children>
5977
</VBox>
60-
<VBox layoutX="814.0" layoutY="13.0">
61-
<children>
62-
<Label fx:id="customSwapLabel" prefHeight="24.0" prefWidth="286.0" style="-fx-text-fill: #c53d13#c53d13 #c53d13; -fx-font-size: 13;" text="SWAPCustomCorrection204" />
63-
<RadioButton fx:id="customSWAPRB" mnemonicParsing="false" onAction="#customCorrectionAction" style="-fx-text-fill: #c53d13#c53d13;" text="Custom SWAP ±1σ %" toggleGroup="$correctionsToggleGroup" />
64-
</children>
65-
</VBox>
6678
</children>
6779
<padding>
68-
<Insets top="3.0" />
80+
<Insets top="3.0"/>
6981
</padding>
7082
</HBox>
71-
<AnchorPane fx:id="sampleTreeAnchorPane" prefHeight="638.0" prefWidth="1200.0" stylesheets="@../../css/projectManager.css" />
83+
<AnchorPane fx:id="sampleTreeAnchorPane" prefHeight="638.0" prefWidth="1200.0"
84+
stylesheets="@../../css/projectManager.css"/>
7285
</children>
7386
</VBox>

‎squidCore/src/main/java/org/cirdles/squid/core/PrawnXMLFileHandler.java

+1-1
Original file line numberDiff line numberDiff line change
@@ -56,9 +56,9 @@ public class PrawnXMLFileHandler implements Serializable {
5656
private static final long serialVersionUID = -581339876224458493L;
5757
private static final PrawnFileRunFractionParser PRAWN_FILE_RUN_FRACTION_PARSER
5858
= new PrawnFileRunFractionParser();
59+
private final SquidProject squidProject;
5960
private transient Unmarshaller jaxbUnmarshaller;
6061
private transient Marshaller jaxbMarshaller;
61-
private final SquidProject squidProject;
6262
private CalamariReportsEngine reportsEngine;
6363
private String currentPrawnSourceFileLocation;
6464

‎squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFraction.java

+3
Original file line numberDiff line numberDiff line change
@@ -1000,6 +1000,9 @@ public String getOverCtCorr() {
10001000
case PB_208:
10011001
retVal.append("Corrected from 208");
10021002
break;
1003+
case CUSTOM:
1004+
retVal.append("SWAPCustomCorrection204");
1005+
break;
10031006
}
10041007
return retVal.toString();
10051008
}

‎squidCore/src/main/java/org/cirdles/squid/shrimp/SquidRatiosModel.java

+1-3
Original file line numberDiff line numberDiff line change
@@ -29,12 +29,10 @@
2929
public class SquidRatiosModel implements Serializable, Comparable<SquidRatiosModel> {
3030

3131
private static final long serialVersionUID = -2944080263487487243L;
32-
32+
private final int reportingOrderIndex;
3333
private String ratioName;
3434
private SquidSpeciesModel numerator;
3535
private SquidSpeciesModel denominator;
36-
private final int reportingOrderIndex;
37-
3836
private List<Double> ratEqTime;
3937
private List<Double> ratEqVal;
4038
// one sigma absolute uncertainties for ratEqVal

‎squidCore/src/main/java/org/cirdles/squid/shrimp/SquidSessionModel.java

+1-2
Original file line numberDiff line numberDiff line change
@@ -24,15 +24,14 @@
2424
public class SquidSessionModel implements Serializable {
2525

2626
private static final long serialVersionUID = -2969849117024998190L;
27-
27+
private final Map<String, Integer> filtersForUnknownNames;
2828
private List<SquidSpeciesModel> squidSpeciesModelList;
2929
private List<SquidRatiosModel> squidRatiosModelList;
3030
private boolean useSBM;
3131
private boolean userLinFits;
3232
private int indexOfBackgroundSpecies;
3333
private String referenceMaterialNameFilter;
3434
private String concentrationReferenceMaterialNameFilter;
35-
private final Map<String, Integer> filtersForUnknownNames;
3635

3736
public SquidSessionModel(
3837
List<SquidSpeciesModel> squidSpeciesSpecsList,

‎squidCore/src/main/java/org/cirdles/squid/shrimp/SquidSpeciesModel.java

+1-2
Original file line numberDiff line numberDiff line change
@@ -31,11 +31,10 @@ public class SquidSpeciesModel implements
3131
XMLSerializerInterface {
3232

3333
private static final long serialVersionUID = 3001823455775925098L;
34-
34+
private final String prawnFileIsotopeName;
3535
private int massStationIndex;
3636
private String massStationSpeciesName;
3737
private String isotopeName;
38-
private final String prawnFileIsotopeName;
3938
private String elementName;
4039
private boolean isBackground;
4140
private String uThBearingName;

‎squidCore/src/main/java/org/cirdles/squid/squidReports/squidReportColumns/SquidReportColumn.java

+1-4
Original file line numberDiff line numberDiff line change
@@ -44,15 +44,12 @@
4444
public class SquidReportColumn implements Serializable, SquidReportColumnInterface {
4545

4646
private static final long serialVersionUID = -4256285353332428810L;
47-
47+
private final String expressionName;
4848
// source of spot-specific data for this column
4949
private transient ExpressionTreeInterface expTree;
5050
private transient boolean amIsotopicRatio;
5151
// provides for multi-row column headers
5252
private transient String[] columnHeaders;
53-
54-
private final String expressionName;
55-
5653
// used to calculate shiftPointRightCount = Squid3Constants.getUnitConversionMoveCount(units)
5754
private String units;
5855

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