Programming with Gap4

Version 0.99.2 (October 1997)

• 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