Move inner classes to independent files (#92)

.editorconfig

@@ -11,7 +11,7 @@ tab_width = 4
 ij_continuation_indent_size = 8
 ij_formatter_off_tag = @formatter:off
 ij_formatter_on_tag = @formatter:on
-ij_formatter_tags_enabled = false
+ij_formatter_tags_enabled = true
 ij_smart_tabs = false
 ij_visual_guides = none
 ij_wrap_on_typing = false
@@ -26,6 +26,7 @@ ij_java_align_multiline_array_initializer_expression = true
 ij_java_align_multiline_assignment = true
 ij_java_align_multiline_binary_operation = true
 ij_java_align_multiline_chained_methods = true
+ij_java_align_multiline_deconstruction_list_components = true
 ij_java_align_multiline_extends_list = true
 ij_java_align_multiline_for = true
 ij_java_align_multiline_method_parentheses = false
@@ -39,6 +40,7 @@ ij_java_align_multiline_text_blocks = true
 ij_java_align_multiline_throws_list = true
 ij_java_align_subsequent_simple_methods = false
 ij_java_align_throws_keyword = true
+ij_java_align_types_in_multi_catch = true
 ij_java_annotation_parameter_wrap = off
 ij_java_array_initializer_new_line_after_left_brace = false
 ij_java_array_initializer_right_brace_on_new_line = false
@@ -55,6 +57,7 @@ ij_java_blank_lines_after_package = 2
 ij_java_blank_lines_around_class = 2
 ij_java_blank_lines_around_field = 0
 ij_java_blank_lines_around_field_in_interface = 0
+ij_java_blank_lines_around_field_with_annotations = 0
 ij_java_blank_lines_around_initializer = 1
 ij_java_blank_lines_around_method = 2
 ij_java_blank_lines_around_method_in_interface = 2
@@ -63,6 +66,7 @@ ij_java_blank_lines_before_imports = 1
 ij_java_blank_lines_before_method_body = 0
 ij_java_blank_lines_before_package = 0
 ij_java_block_brace_style = end_of_line
+ij_java_block_comment_add_space = false
 ij_java_block_comment_at_first_column = true
 ij_java_call_parameters_new_line_after_left_paren = false
 ij_java_call_parameters_right_paren_on_new_line = false
@@ -71,7 +75,7 @@ ij_java_case_statement_on_separate_line = true
 ij_java_catch_on_new_line = false
 ij_java_class_annotation_wrap = split_into_lines
 ij_java_class_brace_style = end_of_line
-ij_java_class_count_to_use_import_on_demand = 20
+ij_java_class_count_to_use_import_on_demand = 30
 ij_java_class_names_in_javadoc = 1
 ij_java_do_not_indent_top_level_class_members = false
 ij_java_do_not_wrap_after_single_annotation = false
@@ -92,7 +96,7 @@ ij_java_doc_keep_empty_return_tag = true
 ij_java_doc_keep_empty_throws_tag = true
 ij_java_doc_keep_invalid_tags = true
 ij_java_doc_param_description_on_new_line = false
-ij_java_doc_preserve_line_breaks = false
+ij_java_doc_preserve_line_breaks = true
 ij_java_doc_use_throws_not_exception_tag = true
 ij_java_else_on_new_line = false
 ij_java_enum_constants_wrap = on_every_item
@@ -106,16 +110,17 @@ ij_java_for_statement_right_paren_on_new_line = false
 ij_java_for_statement_wrap = on_every_item
 ij_java_generate_final_locals = false
 ij_java_generate_final_parameters = false
+ij_java_generate_use_type_annotation_before_type = true
 ij_java_if_brace_force = always
-ij_java_imports_layout = *, |, javax.**, java.**, |, $*
+ij_java_imports_layout = *,|,javax.**,java.**,|,$*
 ij_java_indent_case_from_switch = true
 ij_java_insert_inner_class_imports = false
 ij_java_insert_override_annotation = true
 ij_java_keep_blank_lines_before_right_brace = 2
 ij_java_keep_blank_lines_between_package_declaration_and_header = 2
 ij_java_keep_blank_lines_in_code = 2
 ij_java_keep_blank_lines_in_declarations = 2
-ij_java_keep_builder_methods_indents = true
+ij_java_keep_builder_methods_indents = false
 ij_java_keep_control_statement_in_one_line = true
 ij_java_keep_first_column_comment = true
 ij_java_keep_indents_on_empty_lines = false
@@ -130,6 +135,7 @@ ij_java_label_indent_size = 0
 ij_java_lambda_brace_style = end_of_line
 ij_java_layout_static_imports_separately = true
 ij_java_line_comment_add_space = false
+ij_java_line_comment_add_space_on_reformat = false
 ij_java_line_comment_at_first_column = true
 ij_java_method_annotation_wrap = split_into_lines
 ij_java_method_brace_style = end_of_line
@@ -138,8 +144,12 @@ ij_java_method_parameters_new_line_after_left_paren = false
 ij_java_method_parameters_right_paren_on_new_line = false
 ij_java_method_parameters_wrap = normal
 ij_java_modifier_list_wrap = false
-ij_java_names_count_to_use_import_on_demand = 10
+ij_java_multi_catch_types_wrap = normal
+ij_java_names_count_to_use_import_on_demand = 20
+ij_java_new_line_after_lparen_in_annotation = false
+ij_java_new_line_after_lparen_in_deconstruction_pattern = true
 ij_java_new_line_after_lparen_in_record_header = false
+ij_java_new_line_when_body_is_presented = false
 ij_java_packages_to_use_import_on_demand = javax.swing.*
 ij_java_parameter_annotation_wrap = off
 ij_java_parentheses_expression_new_line_after_left_paren = false
@@ -173,6 +183,7 @@ ij_java_space_before_class_left_brace = true
 ij_java_space_before_colon = true
 ij_java_space_before_colon_in_foreach = true
 ij_java_space_before_comma = false
+ij_java_space_before_deconstruction_list = false
 ij_java_space_before_do_left_brace = true
 ij_java_space_before_else_keyword = true
 ij_java_space_before_else_left_brace = true
@@ -203,6 +214,7 @@ ij_java_space_within_empty_array_initializer_braces = false
 ij_java_space_within_empty_method_call_parentheses = false
 ij_java_space_within_empty_method_parentheses = false
 ij_java_spaces_around_additive_operators = true
+ij_java_spaces_around_annotation_eq = true
 ij_java_spaces_around_assignment_operators = true
 ij_java_spaces_around_bitwise_operators = true
 ij_java_spaces_around_equality_operators = true
@@ -214,13 +226,15 @@ ij_java_spaces_around_relational_operators = true
 ij_java_spaces_around_shift_operators = true
 ij_java_spaces_around_type_bounds_in_type_parameters = true
 ij_java_spaces_around_unary_operator = false
+ij_java_spaces_inside_block_braces_when_body_is_present = false
 ij_java_spaces_within_angle_brackets = false
 ij_java_spaces_within_annotation_parentheses = false
 ij_java_spaces_within_array_initializer_braces = false
 ij_java_spaces_within_braces = false
 ij_java_spaces_within_brackets = false
 ij_java_spaces_within_cast_parentheses = false
 ij_java_spaces_within_catch_parentheses = false
+ij_java_spaces_within_deconstruction_list = false
 ij_java_spaces_within_for_parentheses = false
 ij_java_spaces_within_if_parentheses = false
 ij_java_spaces_within_method_call_parentheses = false
@@ -233,6 +247,7 @@ ij_java_spaces_within_try_parentheses = false
 ij_java_spaces_within_while_parentheses = false
 ij_java_special_else_if_treatment = true
 ij_java_subclass_name_suffix = Impl
+ij_java_switch_expressions_wrap = normal
 ij_java_ternary_operation_signs_on_next_line = false
 ij_java_ternary_operation_wrap = normal
 ij_java_test_name_suffix = Test
@@ -249,6 +264,13 @@ ij_java_while_on_new_line = false
 ij_java_wrap_comments = true
 ij_java_wrap_first_method_in_call_chain = false
 ij_java_wrap_long_lines = false
+ij_java_wrap_semicolon_after_call_chain = false
+
+[*.properties]
+ij_properties_align_group_field_declarations = false
+ij_properties_keep_blank_lines = false
+ij_properties_key_value_delimiter = equals
+ij_properties_spaces_around_key_value_delimiter = false
 
 [.editorconfig]
 ij_editorconfig_align_group_field_declarations = false
@@ -262,6 +284,7 @@ ij_editorconfig_spaces_around_assignment_operators = true
 ij_xml_align_attributes = true
 ij_xml_align_text = false
 ij_xml_attribute_wrap = normal
+ij_xml_block_comment_add_space = false
 ij_xml_block_comment_at_first_column = true
 ij_xml_keep_blank_lines = 2
 ij_xml_keep_indents_on_empty_lines = false
@@ -275,20 +298,34 @@ ij_xml_space_after_tag_name = false
 ij_xml_space_around_equals_in_attribute = false
 ij_xml_space_inside_empty_tag = false
 ij_xml_text_wrap = normal
-ij_xml_use_custom_settings = false
+
+[{*.bash,*.sh,*.zsh}]
+indent_size = 2
+tab_width = 2
+ij_shell_binary_ops_start_line = false
+ij_shell_keep_column_alignment_padding = false
+ij_shell_minify_program = false
+ij_shell_redirect_followed_by_space = false
+ij_shell_switch_cases_indented = false
+ij_shell_use_unix_line_separator = true
 
 [{*.markdown,*.md}]
 ij_markdown_force_one_space_after_blockquote_symbol = true
 ij_markdown_force_one_space_after_header_symbol = true
 ij_markdown_force_one_space_after_list_bullet = true
 ij_markdown_force_one_space_between_words = true
+ij_markdown_format_tables = true
+ij_markdown_insert_quote_arrows_on_wrap = true
 ij_markdown_keep_indents_on_empty_lines = false
+ij_markdown_keep_line_breaks_inside_text_blocks = true
 ij_markdown_max_lines_around_block_elements = 1
 ij_markdown_max_lines_around_header = 1
 ij_markdown_max_lines_between_paragraphs = 1
 ij_markdown_min_lines_around_block_elements = 1
 ij_markdown_min_lines_around_header = 1
 ij_markdown_min_lines_between_paragraphs = 1
+ij_markdown_wrap_text_if_long = true
+ij_markdown_wrap_text_inside_blockquotes = true
 
 [{*.yaml,*.yml}]
 indent_size = 2
@@ -298,6 +335,9 @@ ij_yaml_block_mapping_on_new_line = false
 ij_yaml_indent_sequence_value = true
 ij_yaml_keep_indents_on_empty_lines = false
 ij_yaml_keep_line_breaks = true
+ij_yaml_line_comment_add_space = false
+ij_yaml_line_comment_add_space_on_reformat = false
+ij_yaml_line_comment_at_first_column = true
 ij_yaml_sequence_on_new_line = false
 ij_yaml_space_before_colon = false
 ij_yaml_spaces_within_braces = true

src/main/java/fr/igred/omero/AnnotatableWrapper.java

@@ -28,7 +28,7 @@
 import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.RepositoryObjectWrapper.ReplacePolicy;
+import fr.igred.omero.util.ReplacePolicy;
 import omero.gateway.facility.TablesFacility;
 import omero.gateway.model.AnnotationData;
 import omero.gateway.model.DataObject;

src/main/java/fr/igred/omero/RepositoryObjectWrapper.java

@@ -78,7 +78,8 @@ protected RepositoryObjectWrapper(T o) {
      *
      * @return The list of imported pixels.
      */
-    private static List<Pixels> importCandidates(DataObject target, ImportLibrary library, ImportConfig config, ImportCandidates candidates) {
+    private static List<Pixels> importCandidates(DataObject target, ImportLibrary library, ImportConfig config,
+                                                 ImportCandidates candidates) {
         List<Pixels> pixels = new ArrayList<>(0);
 
         ExecutorService threadPool = Executors.newFixedThreadPool(config.parallelUpload.get());
@@ -250,19 +251,4 @@ public void copyAnnotationLinks(Client client, RepositoryObjectWrapper<?> object
     public abstract void reload(Browser browser)
     throws ServiceException, AccessException, ExecutionException;
 
-
-    /**
-     * Policy to specify how to handle objects when they are replaced.
-     */
-    public enum ReplacePolicy {
-        /** Unlink objects only */
-        UNLINK,
-
-        /** Delete all objects */
-        DELETE,
-
-        /** Delete orphaned objects */
-        DELETE_ORPHANED
-    }
-
 }

src/main/java/fr/igred/omero/annotations/AnnotationWrapper.java

@@ -18,16 +18,16 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
-import fr.igred.omero.exception.AccessException;
-import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.containers.DatasetWrapper;
 import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.exception.AccessException;
+import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.screen.PlateAcquisitionWrapper;
 import fr.igred.omero.screen.PlateWrapper;
-import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.screen.ScreenWrapper;
 import fr.igred.omero.screen.WellWrapper;
 import omero.RLong;

src/main/java/fr/igred/omero/client/Browser.java

@@ -22,14 +22,14 @@
 import fr.igred.omero.annotations.AnnotationWrapper;
 import fr.igred.omero.annotations.MapAnnotationWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
-import fr.igred.omero.exception.AccessException;
-import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.meta.ExperimenterWrapper;
 import fr.igred.omero.containers.DatasetWrapper;
 import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.exception.AccessException;
+import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.meta.ExperimenterWrapper;
 import fr.igred.omero.screen.PlateWrapper;
-import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.screen.ScreenWrapper;
 import fr.igred.omero.screen.WellWrapper;
 import omero.RLong;

src/main/java/fr/igred/omero/client/Client.java

@@ -21,14 +21,14 @@
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.annotations.AnnotationWrapper;
 import fr.igred.omero.annotations.TableWrapper;
+import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
+import fr.igred.omero.core.ImageWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.meta.ExperimenterWrapper;
 import fr.igred.omero.meta.GroupWrapper;
-import fr.igred.omero.containers.FolderWrapper;
-import fr.igred.omero.core.ImageWrapper;
-import fr.igred.omero.containers.ProjectWrapper;
 import omero.ApiUsageException;
 import omero.gateway.Gateway;
 import omero.gateway.SecurityContext;

src/main/java/fr/igred/omero/client/package-info.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2020-2023 GReD
+ *  Copyright (C) 2020-2024 GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software

src/main/java/fr/igred/omero/containers/DatasetWrapper.java

@@ -18,15 +18,16 @@
 package fr.igred.omero.containers;
 
 
-import fr.igred.omero.client.Browser;
-import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
+import fr.igred.omero.core.ImageWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.core.ImageWrapper;
-import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.roi.ROIWrapper;
+import fr.igred.omero.util.ReplacePolicy;
 import omero.RLong;
 import omero.gateway.model.DatasetData;
 import omero.gateway.model.ImageData;

src/main/java/fr/igred/omero/containers/FolderWrapper.java

@@ -18,14 +18,14 @@
 package fr.igred.omero.containers;
 
 
+import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.client.Browser;
 import fr.igred.omero.client.Client;
-import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.core.ImageWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.core.ImageWrapper;
-import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import omero.gateway.facility.ROIFacility;
 import omero.gateway.model.AnnotationData;

src/main/java/fr/igred/omero/containers/ProjectWrapper.java

@@ -18,14 +18,14 @@
 package fr.igred.omero.containers;
 
 
-import fr.igred.omero.client.Browser;
-import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
+import fr.igred.omero.core.ImageWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.core.ImageWrapper;
-import fr.igred.omero.RepositoryObjectWrapper;
 import omero.gateway.model.ImageData;
 import omero.gateway.model.ProjectData;
 import omero.model.ProjectDatasetLink;

src/main/java/fr/igred/omero/core/ImageWrapper.java

@@ -18,23 +18,23 @@
 package fr.igred.omero.core;
 
 
+import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.client.Browser;
 import fr.igred.omero.client.Client;
-import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.containers.DatasetWrapper;
 import fr.igred.omero.containers.FolderWrapper;
 import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.core.PixelsWrapper.Bounds;
-import fr.igred.omero.core.PixelsWrapper.Coordinates;
+import fr.igred.omero.roi.ROIWrapper;
 import fr.igred.omero.screen.PlateAcquisitionWrapper;
 import fr.igred.omero.screen.PlateWrapper;
-import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.screen.ScreenWrapper;
 import fr.igred.omero.screen.WellSampleWrapper;
 import fr.igred.omero.screen.WellWrapper;
-import fr.igred.omero.roi.ROIWrapper;
+import fr.igred.omero.util.Bounds;
+import fr.igred.omero.util.Coordinates;
 import ij.CompositeImage;
 import ij.IJ;
 import ij.ImagePlus;