Fixes #39 - duplicate names bug related to switch to case-insensitive spot names. (#40)

* fixes #39

Author: bowring

common.gradle

@@ -6,7 +6,7 @@ apply plugin: 'java'
 apply plugin: 'maven'
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '0.1.6'
+String mavenVersion = '0.1.7'
 
 
 sourceCompatibility = '1.8'

squidApp/src/main/java/org/cirdles/squid/gui/SpotManagerController.java

@@ -276,6 +276,9 @@ private void saveSpotNameAction(ActionEvent event) {
             squidProject.generatePrefixTreeFromSpotNames();
             shrimpFractionList.refresh();
             shrimpRefMatList.refresh();
+            
+            // refresh textbox in case "DUP" is removed or created
+            selectedSpotNameText.setText(((PrawnFile.Run) saveSpotNameButton.getUserData()).getPar().get(0).getValue());            
         }
     }
 }

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

@@ -7,14 +7,14 @@
 <?import javafx.scene.control.Tooltip?>
 <?import javafx.scene.layout.AnchorPane?>
 
-<AnchorPane fx:id="spotManagerPane" prefHeight="616.0" prefWidth="925.0" styleClass="backgroundCalamari" stylesheets="@css/projectManager.css" xmlns="http://javafx.com/javafx/8.0.111" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.SpotManagerController">
+<AnchorPane fx:id="spotManagerPane" prefHeight="616.0" prefWidth="925.0" styleClass="backgroundCalamari" stylesheets="@css/projectManager.css" xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.SpotManagerController">
    <children>
       <ListView fx:id="shrimpFractionList" layoutX="15.0" layoutY="83.0" prefHeight="468.0" prefWidth="435.0">
          <tooltip>
             <Tooltip text="Right-click spot for removal menu." />
          </tooltip>
       </ListView>
-      <TextField fx:id="selectedSpotNameText" layoutX="142.0" layoutY="583.0" prefHeight="27.0" prefWidth="130.0" promptText="no spot selected" />
+      <TextField fx:id="selectedSpotNameText" layoutX="142.0" layoutY="583.0" prefHeight="27.0" prefWidth="167.0" promptText="no spot selected" />
       <Label fx:id="headerLabel" layoutX="21.0" layoutY="60.0" prefHeight="17.0" prefWidth="428.0" text="Header label" />
       <Label layoutX="21.0" layoutY="33.0" text="Filter by typing spot prefix:" />
       <TextField fx:id="filterSpotNameText" layoutX="237.0" layoutY="34.0" onKeyReleased="#filterSpotNameKeyReleased" prefHeight="27.0" prefWidth="68.0" promptText="type here" />
@@ -23,7 +23,7 @@
       <Button fx:id="setFilteredSpotsAsRefMatButton" layoutX="475.0" layoutY="581.0" mnemonicParsing="false" onAction="#setFilteredSpotsToRefMatAction" prefHeight="31.0" prefWidth="435.0" text="Copy Filtered Spots to be Reference Material spots." />
       <Label fx:id="headerLabelRefMat" layoutX="481.0" layoutY="60.0" prefHeight="17.0" prefWidth="428.0" text="Header label" />
       <Label layoutX="16.0" layoutY="583.0" text="Edit Spot Name:" />
-      <Button fx:id="saveSpotNameButton" layoutX="288.0" layoutY="581.0" mnemonicParsing="false" onAction="#saveSpotNameAction" text="Save Spot Name" />
+      <Button fx:id="saveSpotNameButton" contentDisplay="CENTER" graphicTextGap="0.0" layoutX="312.0" layoutY="581.0" mnemonicParsing="false" onAction="#saveSpotNameAction" prefHeight="31.0" prefWidth="130.0" text="Save Name" />
       <Label layoutX="460.0" layoutY="3.0" prefHeight="20.0" prefWidth="366.0" text="Reference Material (RM) Spots for this Project:" />
       <Label layoutX="17.0" layoutY="562.0" style="-fx-font-size: 11;" text="Hint: To remove a spot or split session, right mouse-click on spot for menu." />
       <Label layoutX="5.0" layoutY="3.0" text="All Spots:" />

squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java

@@ -21,6 +21,7 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.concurrent.CopyOnWriteArrayList;
 import javax.xml.bind.JAXBException;
@@ -246,20 +247,22 @@ public void processPrawnSessionForDuplicateSpotNames() {
         List<Run> runs = prawnFile.getRun();
         Map<String, Integer> spotNameCountMap = new HashMap<>();
         for (int i = 0; i < runs.size(); i++) {
-            String spotName = runs.get(i).getPar().get(0).getValue();
+            String spotName = runs.get(i).getPar().get(0).getValue().trim();
+            String spotNameKey = spotName.toUpperCase(Locale.US);
             // remove existing duplicate label in case editing occurred
             int indexDUP = spotName.indexOf("-DUP");
             if (indexDUP > 0) {
                 runs.get(i).getPar().get(0).setValue(spotName.substring(0, spotName.indexOf("-DUP")));
                 spotName = runs.get(i).getPar().get(0).getValue();
+                spotNameKey = spotName.toUpperCase(Locale.US);
             }
-            if (spotNameCountMap.containsKey(spotName)) {
-                int count = spotNameCountMap.get(spotName);
+            if (spotNameCountMap.containsKey(spotNameKey)) {
+                int count = spotNameCountMap.get(spotNameKey);
                 count++;
-                spotNameCountMap.put(spotName, count);
+                spotNameCountMap.put(spotNameKey, count);
                 runs.get(i).getPar().get(0).setValue(spotName + "-DUP-" + count);
             } else {
-                spotNameCountMap.put(spotName, 0);
+                spotNameCountMap.put(spotNameKey, 0);
             }
         }
     }