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	Tehdyt toimenpiteet Programming with Gap4 - Table of Contents Programming with Gap4 Version 0.99.2 (October 1997) James Bonfield Preface Conventions Used in This Manual Tk_utils Library Keyed Lists Runtime Loading of Libraries load_package Default Files set_def set_defx Specifying Menu Configurations set_menu add_menu add_cascade add_command add_separator add_radio add_check Controlling Menu Behaviour create_menus menu_state_on menu_state_off menu_state_set menu_state_save menu_state_restore Common Dialogue Components Text Output and Errors tout_init tout_create_wins tout_set_scroll tout_set_redir tout_pipe error_bell vmessage verror vfuncheader vfuncgroup vfuncparams start_message and end_message Other Utility Commands tkinit capture expandpath vTcl_SetResult vTcl_DStringAppend w and vw Tcl Scripting of Gap4 Introduction Low-level IO Access Introduction IO Primitives io_read_text and io_write_text io_read_data and io_write_data Flushing data Low-level IO Commands Opening, Closing and Copying Databases io_read_database io_read_reading io_read_contig io_read_annotation io_read_vector io_read_template io_read_clone io_read_reading_name and io_write_reading_name io_add_* commands and io_allocate Utility Commands db_info edid_to_editor add_tags get_read_names contig_order_to_number reset_contig_order flush_contig_order remove_contig_duplicates get_tag_array Main Commands assemble_direct assemble... commands break_contig TODO: calc_quality check_assembly check_database complement_contig delete_contig disassemble_readings double_strand edit_contig enter_tags extract_readings find_long_gels find_oligo find_primers find_probes find_read_pairs find_repeats find_taq_terminator find_internal_joins get_consensus join_contig minimal_coverage pre_assemble shift_readings show_relationships unattached_readings The Editor Widget Introduction Configuration Options Widget Commands Units and Coordinates The Editing Cursor The Selection Cutoff Adjustments Annotations Editing Commands Editing Toggles and Settings Searching Primer Selection The Status Line The Trace Display Miscellaneous Commands Quitting the Widget The EdNames Widget Database I/O in C Introduction and Overview "g" Level - Raw Database Access "Communication" Level - Interfaces to the "g" Level Basic Gap4 I/O Other I/O Functions Compiling and Linking with Other Programs Database Structures The GDatabase Structure The GReadings Structure The GContigs Structure The GAnnotations Structure The GVectors Structure The GTemplates Structure The GClones Structure The GapIO Structure IO.h Macros Basic Gap4 I/O GT_Write, GT_Write_cached, TextWrite, DataWrite, ArrayWrite, BitmapWrite io_handle and handle_io io_read_seq io_write_seq get_read_info, get_vector_info, get_clone_info and get_subclone_info io_init_reading, io_init_contig and io_init_annotations io_read_annotation and io_write_annotation allocate deallocate io_deallocate_reading io_read_rd and io_write_rd open_db close_db del_db flush2t get_gel_num and get_contig_num lget_gel_num and lget_contig_num to_contigs_only chain_left rnumtocnum Other I/O functions io_get_extension io_mod_extension io_insert_base, io_modify_base and io_delete_base io_delete_contig write_rname get_read_name, get_contig_name, get_vector_name, get_template_name, and get_clone_name Sequence Editing Functions in C io_complement_seq io_insert_seq io_delete_seq io_replace_seq pad_consensus calc_consensus calc_quality Annotation Functions in C shift_contig_tags merge_contig_tags complement_contig_tags split_contig_tags remove_contig_tags remove_contig_tags rmanno tag2values values2tag rmanno_list insert_NEW_tag create_tag_for_gel ctagget and vtagget tag_shift_for_insert tag_shift_for_delete type2str and str2type Contig Registration Scheme Introduction Data Structures Registering a Piece of Data The Callback Function The Notifications Available REG_GENERIC REG_NUMBER_CHANGE REG_JOIN_TO REG_ORDER REG_LENGTH REG_QUERY_NAME REG_DELETE REG_GET_LOCK and REG_SET_LOCK REG_COMPLEMENT REG_PARAMS REG_QUIT REG_CURSOR_NOTIFY REG_GET_OPS REG_INVOKE_OP REG_ANNO REG_REGISTER and REG_DEREGISTER REG_HIGHLIGHT_READ REG_BUFFER_START and REG_BUFFER_END Sending a Notification Specific Notification Tasks TASK_EDITOR_GETCON TASK_CANVAS_SCROLLX TASK_CANVAS_SCROLLY TASK_CANVAS_ZOOMBACK TASK_CANVAS_ZOOM TASK_CANVAS_CURSOR_X TASK_CANVAS_CURSOR_Y TASK_CANVAS_CURSOR_DELETE TASK_CANVAS_RESIZE TASK_CANVAS_REDRAW TASK_CANVAS_WORLD TASK_WINDOW_ADD TASK_WINDOW_DELETE TASK_CS_REDRAW TASK_RENZ_INFO TASK_TEMPLATE_REDRAW TASK_DISPLAY_RULER TASK_DISPLAY_TICKS C Functions Available contig_register_init register_id contig_register contig_deregister contig_notify contig_register_join result_to_regs result_names result_time result_notify result_data type_to_result type_notify type_contig_notify Locking Mechanisms Examples of Specific Functions Deleting a contig Joining two contigs Tcl Interfaces clear_cp clear_template register_id result_names result_time result_delete result_quit reg_get_ops reg_invoke_op reg_notify_update reg_notify_highlight quit_displays Future Enhancements Writing Packages Creating a New Tcl Command Registering the Command Parsing the Arguments Returning a Result Writing the Code Itself Adding a GUI to the Command The Dialogue Creation Calling the New Command The tclIndex file Creating the Config File Writing the Online Help Wrapping it all up Composition Package Makefile composition.c composition.tcl Function Index Variable and Type Index Concept Index This document was generated on 25 April 2003 using the texi2html translator version 1.39 (with local modifications) This page is maintained by staden-package. Last generated on 25 April 2003. URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/scripting_219.html