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 page is maintained by
James Bonfield
. Last generated on 21 January 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/scripting_219.html