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Concept Index

a

  • accuracy calculation
  • Adding tags
  • allocating records
  • allocation of structures from Tcl
  • annotation allocation, Tcl
  • annotations structure, Tcl access
  • annotations, complementing
  • annotations, converting from string to values
  • annotations, converting from values to string
  • annotations, creation of
  • annotations, deletion within
  • annotations, insertion within
  • annotations, merging in consensus
  • annotations, reading and writing
  • annotations, removing
  • annotations, removing from consensus
  • annotations, removing from readings
  • annotations, searching for
  • annotations, shifting in consensus
  • annotations, splitting lists
  • annotations, type conversion
  • Annotations: editor widget
  • Argument parsing
  • Assembly, checking
  • Assembly, directed
  • Assembly, independent
  • Assembly, new contigs
  • Assembly, one contig
  • Assembly, preassembled data
  • Assembly, screen only
  • Assembly, shotgun
  • Assembly, single stranded

    • b

  • Bell, upon errors
  • Break contig

    • c

  • Cache, GReadings
  • Calculating quality
  • Callbacks, registration
  • Capturing command output
  • chain_left, db_info command
  • Check assembly
  • Check database
  • cli_arg.h
  • clone allocation, Tcl
  • clone structure, Tcl access
  • closing gap4 databases from Tcl
  • Command line arguments
  • Command registration
  • compiling
  • Complement contig
  • complementing
  • Composition Makefile
  • Composition source code
  • Composition, algorithm
  • Composition, argument parsing
  • Composition, command registration
  • Composition, GUI
  • Composition, interface
  • Composition, package
  • Composition, returning result
  • composition.c
  • composition.html
  • composition.index
  • composition.tcl
  • composition.topic
  • Config file for packages
  • Configuration: editor widget
  • Configuring menus
  • consensus calculation
  • Consensus calculation
  • consensus tags, complementing
  • consensus tags, removing
  • consensus tags, shifting
  • consensus tags, splitting in two
  • contig allocation, Tcl
  • Contig breaking
  • Contig coverage
  • Contig identifier
  • contig names, reading
  • contig numbers, from reading numbers
  • contig structure, Tcl access
  • Contig, complementing
  • Contig, deletion
  • contig, deletion of
  • Contig, editing
  • contig, finding the longest
  • Contig, joining
  • Contig, relationship lists
  • contig, total length
  • contig_reg_t structure
  • Controlling menu behaviour
  • conversion of tag formats
  • copying gap4 databases from Tcl
  • Creating menus
  • Creating Tcl commands
  • Cursor in editor widget
  • cutoff data, modifying
  • cutoff data, reading
  • Cutoffs: editor widget

    • d

  • data reading
  • data writing
  • Database access to gap4
  • Database checking
  • database information from Tcl
  • database name, db_info command
  • database structure, Tcl io
  • db_name, db_info command
  • deallocating readings
  • deallocating records
  • Default files
  • Delete contig
  • Deleting a contig
  • deleting into tags
  • Dialogue components
  • Dialogue creation
  • Directed assembly
  • Disable menu states
  • Disassemble readings
  • Double stranding
  • Dynamic libraries

    • e

  • Edit contig
  • Editing commands: editor widget
  • Editor commands
  • Editor cursor
  • Editor identifier
  • Editor units
  • Editor widget
  • Editor widget commands
  • Editor widget: annotations
  • Editor widget: configuration
  • Editor widget: cutoffs
  • Editor widget: editing commands
  • Editor widget: primer selection
  • Editor widget: searching
  • Editor widget: selections
  • Editor widget: settings
  • Editor widget: status line
  • Editor widget: superedit
  • Editor widget: toggles
  • Editor widget: trace display
  • Editor, miscellaneous commands
  • Editor, quitting
  • Enable menu states
  • Error bell
  • Error messages, outputting
  • Error output
  • Extensions, writing
  • Extract readings

    • f

  • Find internal joins
  • Find long gels
  • Find oligo
  • Find primers
  • Find probes
  • Find read pairs
  • Find repeats
  • Find taq terminators
  • flushing data
  • Format codes
  • Function group output
  • Function header output
  • Function parameters

    • g

  • Gap4
  • Gap4 database access
  • Gap4 IO
  • Gap4 main commands
  • Gap4 utitility commands
  • GapIO structure
  • gel length, maximum
  • get_contig_num, db_info command
  • get_read_num, db_info command
  • Graphical User Interface for commands
  • GReadings cache
  • Group (function) output
  • GUI for commands

    • h

  • Header text output
  • Help, writing
  • hidden data, modifying
  • hidden data, reading
  • HTML help files

    • i

  • Independent assembly
  • Index help files
  • inserting into tags
  • IO handles
  • IO introduction (C)
  • IO Primitives
  • IO, gap4 database access

    • j

  • Join contigs
  • Joining two contigs
  • Joins, finding

    • k

  • Keyed Lists
  • Keyed lists, writable strings

    • l

  • left most reading
  • Libraries, loading of
  • linking
  • Loading menu states
  • Locking
  • longest_contig, db_info

    • m

  • Makefile, composition package
  • maximum reading length
  • Menu configuration
  • Menu control
  • Menu creation
  • Menu disabling
  • Menu enabling
  • Menu, loading states
  • Menu, restoring states
  • Menu, saving states
  • Minimal coverage
  • Modules, writing

    • n

  • New contigs assembly
  • Notification tasks
  • Notification, sending
  • Notifications, registration
  • num_contigs, db_info command
  • num_readings, db_info command

    • o

  • Oligos, finding
  • One contig assembly
  • Online help
  • opening gap4 databases from Tcl
  • Option parsing
  • Output buffering, start_message
  • Output of text messages
  • output: saving
  • Overview of Gap4 IO (C)

    • p

  • Package config file
  • Packages, writing
  • Parameters, text output
  • Parsing arguments
  • Path expansion
  • Piping output to commands
  • Pitfalls, in setting Tcl results
  • Plugins, writing
  • Primer selection in editor widget
  • Primers, finding
  • Primers, suggesting
  • Probes, finding

    • q

  • Quality calculation
  • quality calculation
  • Quality codes
  • Quitting the editor

    • r

  • rc files
  • reading allocation, Tcl
  • reading data records
  • Reading identifier
  • Reading identifiers, getting
  • reading length, maximum
  • Reading name cache
  • reading name, Tcl access
  • Reading names, getting
  • reading names, reading
  • reading names, writing
  • Reading pairs, finding
  • Reading sequences
  • reading structure, Tcl access
  • reading tags, removing
  • reading text records
  • Reading, disassembly
  • readings, deallocating
  • Readings, extracting
  • Readings, finding unattached
  • Readings, long runs
  • Readings, shifting
  • Redirecting output
  • REG_ANNO
  • REG_BUFFER_END
  • REG_BUFFER_START
  • REG_COMPLEMENT
  • REG_CURSOR_NOTIFY
  • reg_data structure
  • REG_DELETE
  • REG_DEREGISTER
  • REG_GENERIC
  • REG_GET_LOCK
  • REG_GET_OPS
  • REG_HIGHLIGHT_READ
  • REG_INVOKE_OP
  • REG_JOIN_TO
  • REG_LENGTH
  • REG_NUMBER_CHANGE
  • REG_ORDER
  • REG_PARAMS
  • REG_QUERY_NAME
  • REG_QUIT
  • REG_REGISTER
  • Registering a command
  • Registration callbacks
  • Registration introduction
  • Registration notifications
  • Registration of data
  • Registration structures
  • Registration types
  • removing readings
  • removing records
  • Repeats, finding
  • Restoring menu states
  • Results, returning to Tcl
  • Returning results to Tcl
  • Runtime libraries

    • s

  • Saving menu states
  • Screen-only assembly
  • Scrolling on output
  • Searching in the editor widget
  • Selections: editor widget
  • Sending a notification
  • Sequence, reading
  • Sequence, writing
  • Settings: editor widget
  • Shift readings
  • Shotgun assembly
  • Show relationships
  • Single stranded assembly
  • stash
  • Status line in editor widget
  • Strands
  • Strings, making writable
  • structure allocation from Tcl
  • Superedit: editor widget

    • t

  • t_contig_length, db_info command
  • tag structure, Tcl access
  • tag, creation of
  • tag, deletion within
  • tag, insertion within
  • tag, searching for
  • Tags, adding
  • tags, complementing
  • tags, converting from string to values
  • tags, converting from values to string
  • tags, merging in consensus
  • tags, reading and writing
  • tags, removing
  • tags, removing from consensus
  • tags, removing from readings
  • tags, shifting in consensus
  • tags, splitting lists
  • tags, type conversion
  • Taq terminators, suggesting
  • TASK_CANVAS_CURSOR_DELETE
  • TASK_CANVAS_CURSOR_X
  • TASK_CANVAS_CURSOR_Y
  • TASK_CANVAS_REDRAW
  • TASK_CANVAS_RESIZE
  • TASK_CANVAS_SCROLLX
  • TASK_CANVAS_SCROLLY
  • TASK_CANVAS_WORLD
  • TASK_CANVAS_ZOOM
  • TASK_CANVAS_ZOOMBACK
  • TASK_CS_REDRAW
  • TASK_DISPLAY_RULER
  • TASK_DISPLAY_TICKS
  • TASK_EDITOR_GETCON
  • TASK_RENZ_INFO
  • TASK_TEMPLATE_REDRAW
  • TASK_WINDOW_ADD
  • TASK_WINDOW_DELETE
  • Tasks, notification
  • Tcl commands, creating
  • Tcl results
  • Tcl_DStringAppend; varargs version
  • Tcl_SetResult; varargs version
  • Tcl_SetVar, writable strings
  • tclIndex file
  • TclX
  • template allocation, Tcl
  • template structure, Tcl access
  • Terminator reactions, suggesting
  • Texinfo
  • Text buffering, start_message
  • Text output
  • text reading
  • text writing
  • Tilde expansion
  • time stamps
  • Tk, initialising
  • Tk_utils library
  • Tkutils library
  • Toggles: editor widget
  • Topic help files
  • trace data, reading and writing
  • Trace display in editor widget
  • Types, registration scheme

    • u

  • Unattached readings
  • Units in editor widget

    • v

  • vector allocation, Tcl
  • vector structure, Tcl access

    • w

  • Writable strings
  • writing data records
  • Writing help
  • Writing packages
  • Writing sequences
  • writing text records

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    This page is maintained by staden-package. Last generated on 1 March 2001.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/scripting_219.html