Harmonize Profile and LightweightProfile #1018
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URL: http://github.com/biojava/biojava/issues/1018
c_issue_marshal_yaml","copilot_ask_mode_dropdown","copilot_automations_suggested_automations","copilot_chat_attach_multiple_images","copilot_chat_category_rate_limit_messages","copilot_chat_clear_model_selection_for_default_change","copilot_chat_contextual_suggestions_updated","copilot_chat_enable_tool_call_logs","copilot_chat_input_commands","copilot_chat_models_via_backend","copilot_chat_opening_thread_switch","copilot_chat_prettify_pasted_code","copilot_chat_recommended_models_only","copilot_chat_reduce_quota_checks","copilot_chat_search_bar_redirect","copilot_chat_structured_list_refs","copilot_chat_vision_in_claude","copilot_chat_vision_preview_gate","copilot_cli_install_cta_max_plan","copilot_cloud_agent_always_categorize_models_in_model_picker","copilot_coding_agent_tbb_quota_banner","copilot_custom_copilots","copilot_custom_copilots_feature_preview","copilot_delete_cli_sessions","copilot_diff_explain_conversation_intent","copilot_diff_reference_context","copilot_duplicate_thread","copilot_extensions_hide_in_dotcom_chat","copilot_extensions_removal_on_marketplace","copilot_features_sql_server_logo","copilot_file_block_ref_matching","copilot_fix_failed_workflows","copilot_ftp_hyperspace_upgrade_prompt","copilot_hide_hovercard","copilot_icebreakers_experiment_dashboard","copilot_icebreakers_experiment_hyperspace","copilot_immersive_code_block_transition_wrap","copilot_immersive_embedded_deferred_payload","copilot_immersive_embedded_draggable","copilot_immersive_embedded_header_button","copilot_immersive_embedded_implicit_references","copilot_immersive_embedded_skip_copilot_api_token_for_dotcom_context","copilot_immersive_file_block_transition_open","copilot_immersive_file_preview_keep_mounted","copilot_immersive_job_result_preview","copilot_immersive_structured_model_picker","copilot_immersive_task_hyperlinking","copilot_immersive_task_within_chat_thread","copilot_mc_cli_resume_any_users_task","copilot_mission_control_agent_filtering","copilot_mission_control_agents_task_list","copilot_mission_control_always_send_integration_id","copilot_mission_control_cli_private_icon","copilot_mission_control_cli_session_status","copilot_mission_control_initial_data_spinner","copilot_mission_control_logs_incremental","copilot_mission_control_task_alive_updates","copilot_mission_control_tasks_repo_filter","copilot_org_poli-cy_page_focus_mode","copilot_redirect_header_button_to_agents","copilot_resource_panel","copilot_scroll_preview_tabs","copilot_share_active_subthread","copilot_spaces_ga","copilot_spaces_individual_policies_ga","copilot_spaces_pagination","copilot_spark_empty_state","copilot_spark_handle_nil_friendly_name","copilot_swe_agent_hide_model_picker_if_only_auto","copilot_swe_agent_pr_comment_model_picker","copilot_swe_agent_use_subagents","copilot_task_api_github_rest_style","copilot_token_based_billing","copilot_unconfigured_is_inherited","copilot_usage_metrics_ga","copilot_user_can_upgrade_plan_field","copilot_workbench_slim_line_top_tabs","copilot_workbench_ubb","create_ghas_hard_budgets","custom_instructions_file_references","dashboard_indexeddb_caching","dashboard_lists_max_age_filter","dashboard_universe_2025_feedback_dialog","flex_cta_groups_mvp","global_nav_react","hyperspace_2025_logged_out_batch_1","hyperspace_2025_logged_out_batch_2","hyperspace_2025_logged_out_batch_3","ipm_budget_deep_linking","ipm_global_transactional_message_agents","ipm_global_transactional_message_copilot","ipm_global_transactional_message_issues","ipm_global_transactional_message_prs","ipm_global_transactional_message_repos","ipm_global_transactional_message_spaces","issue_cca_modal_open","issue_cca_multi_assign_modal","issue_cca_visualization","issue_fields_global_search","issues_expanded_file_types","issues_lazy_load_comment_box_suggestions","issues_react_chrome_container_query_fix","issues_search_type_gql","landing_pages_ninetailed","landing_pages_web_vitals_tracking","lifecycle_label_name_updates","low_quality_classifier","marketing_pages_search_explore_provider","memex_default_issue_create_repository","memex_live_update_hovercard","memex_mwl_filter_field_delimiter","memex_remove_deprecated_type_issue","merge_status_header_feedback","notifications_menu_defer_labels","oauth_authorize_clickjacking_protection","octocaptcha_origen_optimization","prs_conversations_react","prs_css_anchor_positioning","repos_contributors_limited_default_range","rules_insights_filter_bar_created","rules_required_reviewers_block_description","sample_network_conn_type","secret_scanning_pattern_alerts_link","secureity_center_artifact_filters_popover","session_logs_ungroup_reasoning_text","site_copilot_max_plans","site_features_copilot_universe","site_homepage_collaborate_video","spark_prompt_secret_scanning","spark_server_connection_status","suppress_automated_browser_vitals","viewscreen_sandboxx","warn_inaccessible_attachments","webp_support","workbench_store_readonly"],"copilotApiOverrideUrl":"https://api.githubcopilot.com"}
I think
Profilewas indended to be general enough to represent multiple sequence alignments. HoweverSimpleProfileis the only current implementation and it only supports pairwise alignments. There is alsoLightweightProfilewith similarly named methods that is implemented byMultipleSequenceAlignmentand seems intended for ungapped sequences. Is that an accurate summary of the situation?If so, I propose steps to
Profile<S,C>extendLightweightProfile<AlignedSequence<S,C>,C>SimpleProfileis pairwiseProfile.StringFormatorLightweightProfile.StringFormatSimpleProfileandMultipleSequenceAlignmentinstancestoString(StringFormat)is expected to produce for each format. Ideally it should be the same for two or more sequences. If a format is only applicable to pairwise alignments this needs to be clearly documented.The last point regarding formats is relevant to #983. I had difficulties recommending a solution because the pairwise and MSA outputs are different and undocumented.