imrpove api, add hashCode and equals to most settings objects

src/main/java/org/micromanager/lightsheetmanager/api/AcquisitionSettings.java

@@ -115,5 +115,5 @@ interface Builder<T extends Builder<T>>  {
      *
      * @return the autofocus settings
      */
-    DefaultAutofocusSettings autofocusSettings();
+    DefaultAutofocusSettings autofocus();
 }

src/main/java/org/micromanager/lightsheetmanager/api/AcquisitionSettingsDispim.java

@@ -27,7 +27,7 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      *
      * @return immutable DefaultChannelSettings instance.
      */
-    DefaultChannelSettings channels();
+    ChannelSettings channels();
 
     /**
      * Returns the immutable DefaultTimingSettings instance.
@@ -100,13 +100,6 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      */
     boolean isUsingTimePoints();
 
-    /**
-     * Returns true if using autofocus.
-     *
-     * @return true if using autofocus.
-     */
-    boolean isUsingAutofocus();
-
     /**
      * Returns true if using multiple positions.
      *
@@ -121,13 +114,6 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      */
     boolean isUsingHardwareTimePoints();
 
-    /**
-     * Returns true if using stage scanning.
-     *
-     * @return true if using stage scanning.
-     */
-    boolean isUsingStageScanning();
-
     /**
      * Returns true if using advanced timing settings.
      *
@@ -184,14 +170,6 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T useTimePoints(final boolean state);
 
-        /**
-         * Sets the acquisition to use autofocus.
-         *
-         * @param state true to use autofocus
-         * @return {@code this} builder
-         */
-        T useAutofocus(final boolean state);
-
         /**
          * Sets the acquisition to use multiple positions.
          *
@@ -208,14 +186,6 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T useHardwareTimePoints(final boolean state);
 
-        /**
-         * Sets the acquisition to use stage scanning.
-         *
-         * @param state true to use stage scanning
-         * @return {@code this} builder
-         */
-        T useStageScanning(final boolean state);
-
         /**
          * Sets the acquisition to use advanced timing settings.
          *

src/main/java/org/micromanager/lightsheetmanager/api/AcquisitionSettingsScape.java

@@ -3,7 +3,6 @@
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
-import org.micromanager.lightsheetmanager.api.internal.DefaultChannelSettings;
 import org.micromanager.lightsheetmanager.api.internal.DefaultSheetCalibration;
 import org.micromanager.lightsheetmanager.api.internal.DefaultSliceCalibration;
 import org.micromanager.lightsheetmanager.api.internal.DefaultSliceSettings;
@@ -27,7 +26,7 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      *
      * @return immutable DefaultChannelSettings instance.
      */
-    DefaultChannelSettings channels();
+    ChannelSettings channels();
 
     /**
      * Returns the immutable DefaultTimingSettings instance.
@@ -62,14 +61,14 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      *
      * @return immutable DefaultSheetCalibration instance.
      */
-    DefaultSheetCalibration sheetCalibration(final int view);
+    DefaultSheetCalibration sheetCalibration();
 
     /**
      * Returns the immutable DefaultSliceCalibration instance.
      *
      * @return immutable DefaultSliceCalibration instance.
      */
-    DefaultSliceCalibration sliceCalibration(final int view);
+    DefaultSliceCalibration sliceCalibration();
 
     /**
      * Returns the acquisition mode.
@@ -99,13 +98,6 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      */
     boolean isUsingTimePoints();
 
-    /**
-     * Returns true if using autofocus.
-     *
-     * @return true if using autofocus.
-     */
-    boolean isUsingAutofocus();
-
     /**
      * Returns true if using multiple positions.
      *
@@ -120,13 +112,6 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      */
     boolean isUsingHardwareTimePoints();
 
-    /**
-     * Returns true if using stage scanning.
-     *
-     * @return true if using stage scanning.
-     */
-    boolean isUsingStageScanning();
-
     /**
      * Returns true if using advanced timing settings.
      *
@@ -160,26 +145,26 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
         /**
          * Sets the acquisition mode.
          *
-         * @param acqMode the acquisition mode
+         * @param mode the acquisition mode
          * @return {@code this} builder
          */
-        T acquisitionMode(final AcquisitionMode acqMode);
+        T acquisitionMode(final AcquisitionMode mode);
 
         /**
          * Sets the camera mode.
          *
-         * @param cameraMode the camera mode.
+         * @param mode the camera mode.
          * @return {@code this} builder
          */
-        T cameraMode(final CameraMode cameraMode);
+        T cameraMode(final CameraMode mode);
 
         /**
          * Sets the imaging camera order.
          *
-         * @param cameraOrder the imaging camera order
+         * @param order the imaging camera order
          * @return {@code this} builder
          */
-        T imagingCameraOrder(final CameraData[] cameraOrder);
+        T imagingCameraOrder(final CameraData[] order);
 
         /**
          * Sets the acquisition to use time points.
@@ -189,14 +174,6 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T useTimePoints(final boolean state);
 
-        /**
-         * Sets the acquisition to use autofocus.
-         *
-         * @param state true to use autofocus
-         * @return {@code this} builder
-         */
-        T useAutofocus(final boolean state);
-
         /**
          * Sets the acquisition to use multiple positions.
          *

src/main/java/org/micromanager/lightsheetmanager/api/AutofocusSettings.java

@@ -1,17 +1,22 @@
 package org.micromanager.lightsheetmanager.api;
 
-
 import org.micromanager.lightsheetmanager.api.data.AutofocusMode;
 import org.micromanager.lightsheetmanager.api.data.AutofocusType;
 
 /**
  * Autofocus settings.
- *
  */
 public interface AutofocusSettings {
 
     interface Builder {
 
+        /**
+         * Return true if channels are enabled.
+         *
+         * @param state true if channels are enabled
+         */
+        Builder enabled(final boolean state);
+
         /**
          * Sets the number of images to capture in the autofocus routine.
          *
@@ -106,6 +111,13 @@ interface Builder {
      */
     Builder copyBuilder();
 
+    /**
+     * Return true if channels are enabled.
+     *
+     * @return true if channels are enabled
+     */
+    boolean enabled();
+
     /**
      * Returns the number of images used in for autofocus routine.
      *

src/main/java/org/micromanager/lightsheetmanager/api/ChannelSettings.java

@@ -3,8 +3,12 @@
 import org.micromanager.lightsheetmanager.api.data.ChannelMode;
 import org.micromanager.lightsheetmanager.model.channels.ChannelSpec;
 
+import java.util.Map;
+
 public interface ChannelSettings {
 
+    Builder copyBuilder();
+
     boolean enabled();
 
     int count();
@@ -21,6 +25,13 @@ public interface ChannelSettings {
 
     ChannelSpec[] data();
 
+    /**
+     * Returns an immutable shallow copy of the map.
+     *
+     * @return an immutable shallow copy of the map
+     */
+    Map<String, ChannelSpec[]> groups();
+
     interface Builder {
 
         Builder enabled(final boolean state);

src/main/java/org/micromanager/lightsheetmanager/api/SliceSettings.java

@@ -8,7 +8,7 @@ interface Builder {
          *
          * @param slicePeriodMs the slice period in milliseconds
          */
-        Builder slicePeriod(final double slicePeriodMs);
+        Builder period(final double slicePeriodMs);
 
         /**
          * Sets the sample exposure time in milliseconds.
@@ -22,7 +22,7 @@ interface Builder {
          *
          * @param state true to minimize the slice period
          */
-        Builder minimizeSlicePeriod(final boolean state);
+        Builder minimizePeriod(final boolean state);
 
         /**
          * Creates an immutable instance of SliceSettings
@@ -44,7 +44,7 @@ interface Builder {
      *
      * @return the slice period in milliseconds
      */
-    double slicePeriod();
+    double period();
 
     /**
      * Returns the sample exposure time in milliseconds.
@@ -58,5 +58,5 @@ interface Builder {
      *
      * @return true if slice period is minimized
      */
-    boolean isSlicePeriodMinimized();
+    boolean periodMinimized();
 }

src/main/java/org/micromanager/lightsheetmanager/api/StageScanSettings.java

@@ -16,6 +16,13 @@ public interface StageScanSettings {
      */
     Builder copyBuilder();
 
+    /**
+     * Returns true if the autofocus settings are enabled.
+     *
+     * @return true if the autofocus settings are enabled
+     */
+    boolean enabled();
+
     /**
      * Returns the acceleration factor.
      *
@@ -67,6 +74,14 @@ public interface StageScanSettings {
 
     interface Builder {
 
+        /**
+         * Enable or disable the autofocus settings.
+         *
+         * @param state true to enable stage scanning
+         * @return {@code this} builder
+         */
+        Builder enabled(final boolean state);
+
         /**
          * Sets the acceleration factor.
          * <p>

src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java

@@ -2,7 +2,9 @@
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import com.google.gson.JsonDeserializer;
 import org.micromanager.lightsheetmanager.api.AcquisitionSettings;
+import org.micromanager.lightsheetmanager.api.ChannelSettings;
 import org.micromanager.lightsheetmanager.api.StageScanSettings;
 import org.micromanager.lightsheetmanager.model.DataStorage;
 
@@ -24,13 +26,13 @@ public abstract static class Builder<T extends Builder<T>> implements Acquisitio
         public Builder() {
         }
 
-        public Builder(final BaseAcquisitionSettings settings) {
-            saveDirectory_ = settings.saveDirectory_;
-            saveNamePrefix_ = settings.saveNamePrefix_;
-            saveDuringAcq_ = settings.saveDuringAcq_;
-            demoMode_ = settings.demoMode_;
-            saveMode_ = settings.saveMode_;
-            afBuilder_ = settings.autofocusSettings_.copyBuilder();
+        public Builder(final AcquisitionSettings settings) {
+            saveDirectory_ = settings.saveDirectory();
+            saveNamePrefix_ = settings.saveNamePrefix();
+            saveDuringAcq_ = settings.isSavingImagesDuringAcquisition();
+            demoMode_ = settings.demoMode();
+            saveMode_ = settings.saveMode();
+            afBuilder_ = settings.autofocus().copyBuilder();
         }
 
         /**
@@ -122,7 +124,7 @@ public DefaultAutofocusSettings.Builder autofocusSettingsBuilder() {
     private final boolean demoMode_;
     private final DataStorage.SaveMode saveMode_;
 
-    private final DefaultAutofocusSettings autofocusSettings_;
+    private final DefaultAutofocusSettings autofocus_;
 
 //    public DefaultAcquisitionSettings() {
 //        saveNamePrefix_ = "";
@@ -136,7 +138,7 @@ protected BaseAcquisitionSettings(Builder<?> builder) {
         saveDuringAcq_ = builder.saveDuringAcq_;
         demoMode_ = builder.demoMode_;
         saveMode_ = builder.saveMode_;
-        autofocusSettings_ = builder.afBuilder_.build();
+        autofocus_ = builder.afBuilder_.build();
     }
 
     /**
@@ -195,8 +197,8 @@ public DataStorage.SaveMode saveMode() {
      * @return the autofocus settings
      */
     @Override
-    public DefaultAutofocusSettings autofocusSettings() {
-        return autofocusSettings_;
+    public DefaultAutofocusSettings autofocus() {
+        return autofocus_;
     }
 
     @Override
@@ -218,11 +220,16 @@ public String toPrettyJson() {
 
     public static <T extends AcquisitionSettings> T fromJson(final String json, final Class<T> cls) {
         Gson gson = new GsonBuilder()
-                .registerTypeAdapter(StageScanSettings.class, (com.google.gson.JsonDeserializer<StageScanSettings>)
+                .registerTypeAdapter(StageScanSettings.class, (JsonDeserializer<StageScanSettings>)
                         (jsonElement, typeOfT, context) -> {
                             // This forces Gson to use the concrete implementation class
                             return context.deserialize(jsonElement, DefaultStageScanSettings.class);
                         })
+                .registerTypeAdapter(ChannelSettings.class, (JsonDeserializer<ChannelSettings>)
+                        (jsonElement, typeOfT, context) -> {
+                            // This forces Gson to use the concrete implementation class
+                            return context.deserialize(jsonElement, DefaultChannelSettings.class);
+                        })
                 .create();
         return gson.fromJson(json, cls);
     }