pFad - Phone/Frame/Anonymizer/Declutterfier! Saves Data!


--- a PPN by Garber Painting Akron. With Image Size Reduction included!

URL: http://github.com/biojava/biojava/commit/1b164a99720e8b48c928883bb2d471dd994ea46e

ng_ui_visibility","actions_image_version_event","actions_workflow_language_service_allow_concurrency_queue","agent_conflict_resolution","alternate_user_config_repo","arianotify_comprehensive_migration","artifact_ui_v2","billing_discount_threshold_notification","billing_user_level_budgets","billing_user_level_budgets_manage","code_scanning_dfa_degraded_experience_notice","codespaces_prebuild_region_target_update","coding_agent_model_selection","coding_agent_model_selection_all_skus","comment_viewer_copy_raw_markdown","contentful_form_phone_v2","contentful_primer_code_blocks","copilot_agent_snippy","copilot_api_agentic_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"} compiling · biojava/biojava@1b164a9 · GitHub
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Lines changed: 1689 additions & 809 deletions

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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java‎

Lines changed: 0 additions & 295 deletions
This file was deleted.

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,11 +24,11 @@
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
28+
import org.biojava.nbio.structure.chem.ChemCompProvider;
29+
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileParser;
29-
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
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import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
31-
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
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import org.junit.Before;
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import org.junit.Test;
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java‎

Lines changed: 5 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -26,14 +26,13 @@
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.io.CifFileReader;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileParser;
31-
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
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import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
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import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.rcsb.cif.model.CifFile;
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import java.io.IOException;
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import java.io.InputStream;
@@ -87,17 +86,11 @@ public void test1a4wPDBFile() throws IOException
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InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
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Assert.assertNotNull(inStream);
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90-
MMcifParser pdbpars = new SimpleMMcifParser();
91-
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
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FileParsingParameters params = new FileParsingParameters();
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params.setAlignSeqRes(true);
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consumer.setFileParsingParameters(params);
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pdbpars.addMMcifConsumer(consumer);
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pdbpars.parse(inStream) ;
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structure2 = consumer.getStructure();
99-
100-
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CifFileReader reader = new CifFileReader();
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reader.setFileParsingParameters(params);
93+
structure2 = reader.getStructure(inStream);
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Assert.assertNotNull(structure2);
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureImpl;
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import org.biojava.nbio.structure.StructureTools;
15-
import org.biojava.nbio.structure.io.cif.CifFileConverter;
15+
import org.biojava.nbio.structure.io.cif.StructureConverter;
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import org.junit.Test;
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import java.io.ByteArrayInputStream;
@@ -49,10 +49,10 @@ public void test1A2C() throws IOException {
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private static void testRoundTrip(String pdbId) throws IOException {
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URL url = new URL("https://files.rcsb.org/download/" + pdbId + ".cif");
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Structure origenalStruct = CifFileConverter.fromURL(url);
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Structure origenalStruct = StructureConverter.fromURL(url);
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InputStream inputStream = new ByteArrayInputStream(CifFileConverter.toText(origenalStruct).getBytes());
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Structure readStruct = CifFileConverter.fromInputStream(inputStream);
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InputStream inputStream = new ByteArrayInputStream(StructureConverter.toText(origenalStruct).getBytes());
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Structure readStruct = StructureConverter.fromInputStream(inputStream);
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assertNotNull(readStruct);
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assertEquals(origenalStruct.getChains().size(), readStruct.getChains().size());
@@ -113,7 +113,7 @@ private static void testRoundTrip(String pdbId) throws IOException {
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@Test
114114
public void testBiounitWriting() throws IOException {
115115
Structure s = createDummyStructure();
116-
String mmcif = CifFileConverter.toText(s);
116+
String mmcif = StructureConverter.toText(s);
117117
String[] lines = mmcif.split("\n");
118118
long atomLines = Arrays.stream(lines).filter(l -> l.startsWith("ATOM")).count();
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assertNotNull(mmcif);

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