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bowringbowring
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Fixes issue #664 and refactoring (#665)
* updates antlr * updates * fixed issue #664 and refactoring
1 parent 0850734 commit 3478f87

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+1292
-2106
lines changed

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-2106
lines changed

‎README.md

+4
Original file line numberDiff line numberDiff line change
@@ -47,6 +47,10 @@ Squid3 "jar" file can then be built:
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gradle fatappjar
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```
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***Addendum***
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Azul also provides JDKs and JREs for Java 8, 11, and 17 pre-packaged with JavaFX <a href="https://www.azul.com/downloads/?package=jdk-fx" target="_blank">here</a>.
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***Note to Users***
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Thank you for using Squid3. We depend on your feedback to keep Squid3 up-to-date and useful to you. To contribute issues and feedback, please join GitHub <a href="https://github.com/" target="_blank">here</a>. While

‎common.gradle

+1-1
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
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String mavenGroupId = 'org.cirdles'
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String mavenVersion = '1.9.0'
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String mavenVersion = '1.9.1'
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[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
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‎squidApp/src/main/java/org/cirdles/squid/gui/expressions/ExpressionBuilderController.java

+23-1
Original file line numberDiff line numberDiff line change
@@ -75,6 +75,7 @@
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import org.cirdles.squid.tasks.expressions.spots.SpotFieldNode;
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import org.cirdles.squid.tasks.expressions.spots.SpotSummaryDetails;
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import org.cirdles.squid.tasks.expressions.variables.VariableNodeForIsotopicRatios;
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import org.cirdles.squid.tasks.expressions.variables.VariableNodeForPerSpotTaskExpressions;
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import org.cirdles.squid.tasks.expressions.variables.VariableNodeForSummary;
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import org.cirdles.squid.utilities.IntuitiveStringComparator;
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@@ -2185,6 +2186,17 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
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}
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sb.append(String.format("%1$-18s", "SpotName"));
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String[][] resultLabels;
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// nov 2021 handle aliased expressions
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if (!((ExpressionTree) expTree).getChildrenET().isEmpty()
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&&
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((ExpressionTree) expTree).getChildrenET().get(0) instanceof VariableNodeForPerSpotTaskExpressions) {
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if ( expTree.getName().toUpperCase(Locale.ROOT).startsWith("TOTAL_")) {
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ExpressionTreeInterface lookupExpTree = ((ExpressionTree) expTree).getChildrenET().get(0);
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expTree = task.getExpressionByName(lookupExpTree.getName()).getExpressionTree();
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}
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}
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if (((ExpressionTree) expTree).getOperation() != null) {
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if ((((ExpressionTree) expTree).getOperation().getName().compareToIgnoreCase("Value") == 0)) {
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if (((ExpressionTree) expTree).getChildrenET().get(0) instanceof VariableNodeForSummary) {
@@ -2225,6 +2237,9 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
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} else {
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resultLabels = new String[][]{{contextAgeFieldName, "1\u03C3Abs", "1\u03C3%"}, {}};
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}
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} else if ((((ExpressionTree) expTree).getOperation().getName().compareToIgnoreCase("ValueModel") == 0)) {
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// nov 2021 handle aliased expressions
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resultLabels = new String[][]{{expTree.getName(), "1\u03C3Abs", "1\u03C3%"}, {}};
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} else {
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// some smarts
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// if only one label, keep it; if two, assume 1sigma abs
@@ -2250,7 +2265,7 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
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sb.append("\n");
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2253-
// produce values
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// produce values ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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if (((ExpressionTree) expTree).getLeftET() instanceof ShrimpSpeciesNode) {
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// Check for functions of species
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if (((ExpressionTree) expTree).getOperation() instanceof ShrimpSpeciesNodeFunction) {
@@ -2312,6 +2327,13 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
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}
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}
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} else {
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// // nov 2021
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// if (((ExpressionTree) expTree).getChildrenET().get(0) instanceof VariableNodeForPerSpotTaskExpressions) {
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// if (((ExpressionTree) expTree).getName().toUpperCase(Locale.ROOT).startsWith("TOTAL_")) {
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// ExpressionTreeInterface lookupExpTree = ((ExpressionTree) expTree).getChildrenET().get(0);
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// expTree = task.getExpressionByName(lookupExpTree.getName()).getExpressionTree();
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// }
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// }
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for (ShrimpFractionExpressionInterface spot : spots) {
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if (spot.getTaskExpressionsEvaluationsPerSpot().get(expTree) != null) {
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sb.append(String.format("%1$-18s", spot.getFractionID()));

‎squidApp/src/main/java/org/cirdles/squid/gui/squidReportTable/SquidReportSettingsController.java

+15
Original file line numberDiff line numberDiff line change
@@ -45,6 +45,7 @@
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import org.cirdles.squid.tasks.expressions.isotopes.ShrimpSpeciesNode;
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import org.cirdles.squid.tasks.expressions.operations.Value;
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import org.cirdles.squid.tasks.expressions.spots.SpotFieldNode;
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import org.cirdles.squid.tasks.expressions.variables.VariableNodeForPerSpotTaskExpressions;
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import org.cirdles.squid.tasks.expressions.variables.VariableNodeForSummary;
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import org.cirdles.squid.utilities.IntuitiveStringComparator;
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import org.cirdles.squid.utilities.fileUtilities.ProjectFileUtilities;
@@ -665,6 +666,17 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
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}
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sb.append(String.format("%1$-" + 18 + "s", "SpotName"));
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String[][] resultLabels;
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// nov 2021 handle aliased expressions
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if (!((ExpressionTree) expTree).getChildrenET().isEmpty()
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&&
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((ExpressionTree) expTree).getChildrenET().get(0) instanceof VariableNodeForPerSpotTaskExpressions) {
674+
if (expTree.getName().toUpperCase(Locale.ROOT).startsWith("TOTAL_")) {
675+
ExpressionTreeInterface lookupExpTree = ((ExpressionTree) expTree).getChildrenET().get(0);
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expTree = task.getExpressionByName(lookupExpTree.getName()).getExpressionTree();
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}
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}
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668680
if (((ExpressionTree) expTree).getOperation() != null) {
669681
if ((((ExpressionTree) expTree).getOperation().getName().compareToIgnoreCase("Value") == 0)) {
670682
if (((ExpressionTree) expTree).getChildrenET().get(0) instanceof VariableNodeForSummary) {
@@ -705,6 +717,9 @@ private String peekDetailsPerSpot(List<ShrimpFractionExpressionInterface> spots,
705717
} else {
706718
resultLabels = new String[][]{{contextAgeFieldName, "1\u03C3Abs", "1\u03C3%"}, {}};
707719
}
720+
} else if ((((ExpressionTree) expTree).getOperation().getName().compareToIgnoreCase("ValueModel") == 0)) {
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// nov 2021 handle aliased expressions
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resultLabels = new String[][]{{expTree.getName(), "1\u03C3Abs", "1\u03C3%"}, {}};
708723
} else {
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// some smarts
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// String[][] resultLabelsFirst = clone2dArray(((ExpressionTree) expTree).getOperation().getLabelsForOutputValues());

‎squidApp/src/main/resources/org/cirdles/squid/gui/AboutSquid.fxml

+24-35
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!--
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Copyright 2018 James F. Bowring and CIRDLES.org.
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@@ -15,53 +16,41 @@
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limitations under the License.
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-->
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<?import javafx.scene.control.*?>
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<?import javafx.scene.image.*?>
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<?import javafx.scene.layout.Pane?>
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<?import java.lang.String?>
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<Pane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="700.0"
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prefWidth="550.0" styleClass="main-Pain" stylesheets="@css/about.css" xmlns="http://javafx.com/javafx/10.0.1"
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xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.AboutSquidController">
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<?import javafx.scene.control.Hyperlink?>
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<?import javafx.scene.control.Label?>
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<?import javafx.scene.image.Image?>
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<?import javafx.scene.image.ImageView?>
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<?import javafx.scene.layout.Pane?>
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<Pane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="700.0" prefWidth="550.0" styleClass="main-Pain" stylesheets="@css/about.css" xmlns="http://javafx.com/javafx/17" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.AboutSquidController">
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<children>
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<Label fx:id="versionText" alignment="CENTER" contentDisplay="CENTER" graphicTextGap="0.0" layoutX="94.0"
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layoutY="206.0" prefHeight="45.0" prefWidth="360.0" text="Squid V 0.0.1" textAlignment="CENTER">
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<Label fx:id="versionText" alignment="CENTER" contentDisplay="CENTER" graphicTextGap="0.0" layoutX="94.0" layoutY="206.0" prefHeight="45.0" prefWidth="360.0" text="Squid V 0.0.1" textAlignment="CENTER">
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<styleClass>
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<String fx:value="project-Title"/>
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<String fx:value="main-Text-Color"/>
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<String fx:value="project-Title" />
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<String fx:value="main-Text-Color" />
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</styleClass>
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</Label>
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<ImageView fitHeight="75.0" fitWidth="156.0" layoutX="304.0" layoutY="603.0" pickOnBounds="true"
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preserveRatio="true" scaleX="0.75" scaleY="0.75">
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<ImageView fitHeight="75.0" fitWidth="156.0" layoutX="304.0" layoutY="603.0" pickOnBounds="true" preserveRatio="true" scaleX="0.75" scaleY="0.75">
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<image>
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<Image url="@images/cirdles-logov2.png"/>
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<Image url="@images/cirdles-logov2.png" />
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</image>
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</ImageView>
39-
<Hyperlink layoutX="326.0" layoutY="669.0" onAction="#visitSquidOnCirdlesAction" styleClass="links"
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text="A CIRDLES Project" textAlignment="CENTER"/>
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<Hyperlink layoutX="102.0" layoutY="669.0" onAction="#visitUsOnGithubAction" styleClass="links"
42-
text="Visit Us on GitHub!" textAlignment="CENTER"/>
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<ImageView fitHeight="91.0" fitWidth="62.0" layoutX="127.0" layoutY="606.0" pickOnBounds="true"
44-
preserveRatio="true">
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<Hyperlink layoutX="326.0" layoutY="669.0" onAction="#visitSquidOnCirdlesAction" styleClass="links" text="A CIRDLES Project" textAlignment="CENTER" />
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<Hyperlink layoutX="102.0" layoutY="669.0" onAction="#visitUsOnGithubAction" styleClass="links" text="Visit Us on GitHub!" textAlignment="CENTER" />
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<ImageView fitHeight="91.0" fitWidth="62.0" layoutX="127.0" layoutY="606.0" pickOnBounds="true" preserveRatio="true">
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<image>
46-
<Image url="@images/githubBluesqueLogo.png"/>
43+
<Image url="@images/githubBluesqueLogo.png" />
4744
</image>
4845
</ImageView>
49-
<Label fx:id="aboutDetailsLabel" alignment="TOP_CENTER" contentDisplay="TOP" layoutX="25.0" layoutY="270.0"
50-
prefHeight="80.0" prefWidth="500.0" styleClass="description-Text"
51-
text="Developed by the CIRDLES team at the College of Charleston." textAlignment="JUSTIFY"
52-
wrapText="true"/>
53-
<Label fx:id="buildDate" alignment="CENTER" contentDisplay="CENTER" graphicTextGap="0.0" layoutX="94.0"
54-
layoutY="251.0" prefHeight="17.0" prefWidth="360.0" styleClass="main-Text-Color"
55-
stylesheets="@css/about.css" text="Build Date: mm/dd/yyyy" textAlignment="CENTER"/>
56-
<ImageView fitHeight="300.0" fitWidth="400.0" layoutX="124.0" layoutY="-41.0" pickOnBounds="true"
57-
preserveRatio="true" styleClass="logo">
46+
<Label fx:id="aboutDetailsLabel" alignment="TOP_CENTER" contentDisplay="TOP" layoutX="25.0" layoutY="270.0" prefHeight="80.0" prefWidth="500.0" styleClass="description-Text" text="Developed by the CIRDLES team at the College of Charleston." textAlignment="JUSTIFY" wrapText="true" />
47+
<Label fx:id="buildDate" alignment="CENTER" contentDisplay="CENTER" graphicTextGap="0.0" layoutX="94.0" layoutY="251.0" prefHeight="17.0" prefWidth="360.0" styleClass="main-Text-Color" stylesheets="@css/about.css" text="Build Date: mm/dd/yyyy" textAlignment="CENTER" />
48+
<ImageView fitHeight="300.0" fitWidth="400.0" layoutX="124.0" layoutY="-41.0" pickOnBounds="true" preserveRatio="true" styleClass="logo">
5849
<image>
59-
<Image url="@images/SquidLogoSansBg.png"/>
50+
<Image url="@images/SquidLogoSansBg.png" />
6051
</image>
6152
</ImageView>
62-
<Label fx:id="contributorsLabel" layoutX="25.0" layoutY="350.0" prefHeight="100.0" prefWidth="500.0"
63-
styleClass="description-Text" text="Contributors" textAlignment="JUSTIFY" wrapText="true"/>
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<Label fx:id="supportersLabel" layoutX="25.0" layoutY="451.0" prefHeight="150.0" prefWidth="500.0"
65-
styleClass="description-Text" text="Supporters" textAlignment="JUSTIFY" wrapText="true"/>
53+
<Label fx:id="contributorsLabel" layoutX="25.0" layoutY="350.0" prefHeight="100.0" prefWidth="500.0" styleClass="description-Text" text="Contributors" textAlignment="JUSTIFY" wrapText="true" />
54+
<Label fx:id="supportersLabel" layoutX="25.0" layoutY="451.0" prefHeight="150.0" prefWidth="500.0" styleClass="description-Text" text="Supporters" textAlignment="JUSTIFY" wrapText="true" />
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</children>
67-
</Pane>
56+
</Pane>

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