finished hooking up saving and loading of analysis settings

src/main/java/com/bwc/ora/OraUtils.java

@@ -43,7 +43,8 @@ public class OraUtils {
     public static final ActionListener testAnalysisActionListener = evt -> {
         try {
             //read in image and ready for analysis
-            OraUtils.loadOctFromTiffFile(new File(OraUtils.class.getClassLoader().getResource("KS_10238_OS_L_7_90_05_529disp_reg_fr1-25_AL21p35.tif").toURI()), Oct.getInstance());
+            OraUtils.loadOctFromTiffFile(new File(OraUtils.class.getClassLoader().getResource("KS_10238_OS_L_7_90_05_529disp_reg_fr1-25_AL21p35.tif").toURI()),
+                    Oct.getInstance());
             Collections.getInstance().resetCollectionsForNewAnalysis();
             ModelsCollection.getInstance().resetSettingsToDefault();
         } catch (IOException | URISyntaxException ex) {
@@ -56,7 +57,7 @@ public class OraUtils {
     public static final ActionListener newAnalysisActionListener = evt -> {
         try {
             //read in image and ready for analysis
-            File tiffFile = OraUtils.selectFile(null, JFileChooser.FILES_ONLY, "Log OCT", "TIFF file", "tiff", "tif");
+            File tiffFile = OraUtils.selectFile(true, null, JFileChooser.FILES_ONLY, "Log OCT", "TIFF file", "tiff", "tif");
             if (tiffFile != null) {
                 OraUtils.loadOctFromTiffFile(tiffFile, Oct.getInstance());
                 Collections.getInstance().resetCollectionsForNewAnalysis();
@@ -71,7 +72,7 @@ public class OraUtils {
     public static final ActionListener exportAnalysisActionListener = evt -> {
         try {
             //read in image and ready for analysis
-            File exportDir = OraUtils.selectFile(null, JFileChooser.DIRECTORIES_ONLY, "Analysis export directory", null);
+            File exportDir = OraUtils.selectFile(true, null, JFileChooser.DIRECTORIES_ONLY, "Analysis export directory", null);
             if (exportDir != null) {
                 ExportWriter.exportAnalysis(exportDir);
             }
@@ -87,7 +88,8 @@ public static void loadOctFromTiffFile(File octFile, Oct oct) throws IOException
         oct.setLogOctImage(TiffReader.readTiffImage(octFile));
     }
 
-    public static File selectFile(Component parent, int selectorType, String selectDescription, String extensionDescription, String... extentions) {
+    public static File selectFile(boolean openDialog, Component parent, int selectorType, String selectDescription, String extensionDescription,
+            String... extentions) {
         File prevLocation = fc.getSelectedFile() != null ? fc.getSelectedFile().getParentFile() : null;
 
         fc = new JFileChooser(prevLocation);
@@ -99,13 +101,11 @@ public static File selectFile(Component parent, int selectorType, String selectD
         fc.setAcceptAllFileFilterUsed(false);
         fc.setApproveButtonText("Select");
         fc.setDialogTitle("Select " + selectDescription + "...");
-        if (fc.getSelectedFile() != null && fc.getSelectedFile().isFile()) {
-            fc.setCurrentDirectory(fc.getSelectedFile().getParentFile());
-        }
-        int returnVal = fc.showOpenDialog(parent);
+        int returnVal = openDialog ? fc.showOpenDialog(parent) : fc.showSaveDialog(parent);
         if (returnVal == JFileChooser.APPROVE_OPTION) {
             if (selectorType == JFileChooser.FILES_ONLY) {
-                return loadFile(fc.getSelectedFile());
+                System.out.println("pwd: "+fc.getCurrentDirectory());
+                return openDialog ? loadFile(fc.getSelectedFile()) : fc.getSelectedFile();
             } else if (selectorType == JFileChooser.DIRECTORIES_ONLY) {
                 return loadDir(fc.getSelectedFile());
             } else {
@@ -117,13 +117,12 @@ public static File selectFile(Component parent, int selectorType, String selectD
     }
 
     private static File loadFile(File file) {
-        if (file.exists()) {
-            if (!file.isFile()) {
-                throw new IllegalArgumentException("Supplied input file " + file.getAbsolutePath() + " is not a file!");
-            }
-        } else {
+        if (!file.exists()) {
             throw new IllegalArgumentException("Supplied input file does not exist @ " + file.getAbsolutePath() + ".");
         }
+        if (!file.isFile()) {
+            throw new IllegalArgumentException("Supplied input file " + file.getAbsolutePath() + " is not a file!");
+        }
         return file;
     }
 
@@ -168,7 +167,9 @@ public void mouseClicked(MouseEvent e) {
                         ));
                         lrpCollection.setSelectedIndex(0);
                         lrpPanel.removeMouseListener(this);
-                        if (buttonToEnable != null) buttonToEnable.setEnabled(true);
+                        if (buttonToEnable != null) {
+                            buttonToEnable.setEnabled(true);
+                        }
                     }
                 }
             });
@@ -208,8 +209,8 @@ public static void setLrpsForAnalysis() {
         }
 
         boolean illegalPositionLrps = lrps.stream()
-                .anyMatch(lrp -> lrp.getLrpCenterXPosition() - ((lrpSettings.getLrpWidth() - 1) / 2) < 0
-                        || lrp.getLrpCenterXPosition() + ((lrpSettings.getLrpWidth() - 1) / 2) >= octWidth);
+                                          .anyMatch(lrp -> lrp.getLrpCenterXPosition() - ((lrpSettings.getLrpWidth() - 1) / 2) < 0
+                                                  || lrp.getLrpCenterXPosition() + ((lrpSettings.getLrpWidth() - 1) / 2) >= octWidth);
 
         if (illegalPositionLrps) {
             throw new IllegalArgumentException("Combination of LRP width, the number of LRPs and LRP " +

src/main/java/com/bwc/ora/collections/ModelsCollection.java

@@ -15,7 +15,7 @@ public class ModelsCollection {
     private final LrpSettings lrpSettings = new LrpSettings();
     private final OctSettings octSettings = new OctSettings();
     private final DisplaySettings displaySettings = new DisplaySettings();
-    private final ScaleBar scaleBar = new ScaleBar("scale_bars", 100);
+    private transient final ScaleBar scaleBar = new ScaleBar("scale_bars", 100);
     private final AnalysisSettings analysisSettings = new AnalysisSettings();
 
     private ModelsCollection() {

src/main/java/com/bwc/ora/io/SettingsIOUtils.java

@@ -1,19 +1,60 @@
 package com.bwc.ora.io;
 
+import com.bwc.ora.OraUtils;
+import com.bwc.ora.collections.Collections;
 import com.bwc.ora.collections.ModelsCollection;
+import com.bwc.ora.models.Oct;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 
+import javax.swing.*;
+import java.awt.event.ActionListener;
 import java.io.*;
 
 public class SettingsIOUtils {
 
-    public static final String SETTINGS_FILE_EXTENSION = "oraconf";
+    public static final String ORA_ANALYSIS_SETTINGS_FILE_EXTENSION = "oasf";
+
+    public static final ActionListener loadAnalysisSettingsActionListener = evt -> {
+        try {
+            //read in settings file for analysis
+            File osfFile = OraUtils.selectFile(true, null, JFileChooser.FILES_ONLY, "ORA Analysis Settings", ORA_ANALYSIS_SETTINGS_FILE_EXTENSION + " file",
+                    ORA_ANALYSIS_SETTINGS_FILE_EXTENSION);
+            if (osfFile != null) {
+                SettingsIOUtils.loadSettings(osfFile);
+            }
+        } catch (IOException ex) {
+            JOptionPane.showMessageDialog(null, "ORA Analysis Setting loading failed,"
+                    + " reason: " + ex.getMessage(), "Loading error!", JOptionPane.ERROR_MESSAGE);
+        }
+    };
+
+    public static final ActionListener saveAnalysisSettingsActionListener = evt -> {
+        try {
+            //read in settings file for analysis
+            File osfFile = OraUtils.selectFile(false, null, JFileChooser.FILES_ONLY, "Save Analysis Settings", ORA_ANALYSIS_SETTINGS_FILE_EXTENSION + " file",
+                    ORA_ANALYSIS_SETTINGS_FILE_EXTENSION);
+            if (osfFile != null) {
+                if (!osfFile.getName().endsWith(ORA_ANALYSIS_SETTINGS_FILE_EXTENSION)) {
+                    osfFile = new File(osfFile.getParentFile(), osfFile.getName() + "." + ORA_ANALYSIS_SETTINGS_FILE_EXTENSION);
+                }
+                SettingsIOUtils.saveCurrentSettings(osfFile);
+            } else {
+                throw new IOException("No file entered");
+            }
+        } catch (IOException ex) {
+            JOptionPane.showMessageDialog(null, "ORA Analysis Setting saving failed,"
+                    + " reason: " + ex.getMessage(), "Save error!", JOptionPane.ERROR_MESSAGE);
+        }
+    };
 
     public static void saveCurrentSettings(File analysisSettingsFile) throws IOException {
-        try (PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(analysisSettingsFile)))) {
+        System.out.println("Saving to " + analysisSettingsFile.getAbsolutePath());
+        try (PrintWriter pw = new PrintWriter(analysisSettingsFile)) {
             Gson jsonFormatter = new GsonBuilder().setPrettyPrinting().create();
-            pw.print(jsonFormatter.toJson(ModelsCollection.getInstance()));
+            String json = jsonFormatter.toJson(ModelsCollection.getInstance());
+            System.out.println("Settings JSON:\n" + json);
+            pw.println(json);
         }
     }
 

src/main/java/com/bwc/ora/models/LrpSettings.java

@@ -21,8 +21,8 @@ public class LrpSettings {
 
     private transient final PropertyChangeSupport propertyChangeSupport = new PropertyChangeSupport(this);
 
-    private final Integer[] lrpWidthOptions = new Integer[] { 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25 };
-    private final int[] lrpSmoothingRange = new int[] { 0, 49 };
+    private transient final Integer[] lrpWidthOptions = new Integer[] { 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25 };
+    private transient final int[] lrpSmoothingRange = new int[] { 0, 49 };
     private int lrpWidth = 5;
     public static final String PROP_LRP_WIDTH = "lrpWidth";
     private int lrpHeight = 300;

src/main/java/com/bwc/ora/views/menus/SettingsMenu.java

@@ -1,6 +1,7 @@
 package com.bwc.ora.views.menus;
 
 import com.bwc.ora.collections.ModelsCollection;
+import com.bwc.ora.io.SettingsIOUtils;
 import com.bwc.ora.models.DisplaySettings;
 
 import javax.swing.*;
@@ -14,6 +15,8 @@ public class SettingsMenu extends JMenu {
     private JCheckBoxMenuItem displayFileNameCheckBox = new JCheckBoxMenuItem("Display OCT File Name", true);
     private JCheckBoxMenuItem displayLrpPeaksCheckBox = new JCheckBoxMenuItem("Display LRP Peaks", true);
     private JCheckBoxMenuItem showFwhmCheckBox = new JCheckBoxMenuItem("Display FWHM on LRP", false);
+    private JMenuItem loadAnalysisSettingsMenuItem = new JMenuItem("Load Analysis Settings");
+    private JMenuItem saveAnalysisSettingsMenuItem = new JMenuItem("Save Analysis Settings");
 
     public SettingsMenu() {
         setText("Settings");
@@ -30,8 +33,17 @@ private void initSettingsMenu() {
         add(displayScaleBarsCheckBox);
         add(displayLrpPeaksCheckBox);
         add(showFwhmCheckBox);
+        addSeparator();
+        add(saveAnalysisSettingsMenuItem);
+        add(loadAnalysisSettingsMenuItem);
 
         connectSettingsToModel();
+        registerItemListeners();
+    }
+
+    private void registerItemListeners() {
+        saveAnalysisSettingsMenuItem.addActionListener(SettingsIOUtils.saveAnalysisSettingsActionListener);
+        loadAnalysisSettingsMenuItem.addActionListener(SettingsIOUtils.loadAnalysisSettingsActionListener);
     }
 
     private void connectSettingsToModel() {