#Please insert up references in the next lines (line starts with keyword UP)
UP arb.hlp
UP glossary.hlp
UP alignment.hlp
UP security.hlp
UP helix.hlp
UP ecoliref.hlp
UP species_configs.hlp
#Please insert subtopic references (line starts with keyword SUB)
SUB man_arb_edit4.hlp
SUB arb_edit4.hlp
SUB e4_search.hlp
SUB e4_replace.hlp
SUB e4_block.hlp
SUB nekey_map.hlp
SUB helixsym.hlp
SUB pfold.hlp
# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
#************* Title of helpfile !! and start of real helpfile ********
TITLE ARB_EDIT4 - Sequence primary and secondary structure editor
OCCURRENCE ARB_NT/Sequence/Edit marked sequences
DESCRIPTION The editor allows you to view and modify the sequences of 'marked
species' or 'a selection of species' and 'SAI' (sequence associated
information) stored in the database.
Potential secondary structure is automatically checked
and the information can be displayed with the primary structure.
In addition, an online column statistic may help you find
sequence and alignment errors.
The editor permanently communicates with the database and
other ARB tools. Every change made by the editor is immediately
exported to the database. All sequence changes made by other
ARB tools are exported to the editor every 5 seconds.
Multiple editors can be used synchronously.
Display:
First Column: Species ID or group name.
Second C. Protection level and subtype of sequence.
Last c. Sequence and secondary structure and more.
Cursor:
The cursor can be moved using the mouse or the arrow
keys. The current cursor positions with respect to the
alignment and the E. coli sequence (there has to be an
'SAI' entry: ECOLI) are indicated after the 'Position'
and 'E.coli' prompts in the upper part of the
'ARB_EDIT4' window.
These 3 positions and the IUPAC-display refer to the position
RIGHT of the cursor.
'Position' counts from 1 to "alignment length".
The 'Ecoli'- and 'Base'-position count from zero to "number of bases".
- Zero means your cursor is left of the first base (and not AT the first base).
- X means your cursor is AT or BEHIND base number X (but in front of base number X+1)
By changing the value of one of these fields, the cursor will
be repositioned. Negative values are possible - in that case
the position will be calculated from the right end (e.g. -1 in
'Base' field means 'position onto base')
Moving entries:
To move an individual entry, position the cursor on the
name, keep the left mouse button pressed, move the entry
to the desired position, and release the button.
Any entry can be fixed (keeps its position while
scrolling vertically) at the top of the editing area by
moving it somewhere above the double line (=top area).
You can define which entries are placed in that top area by
default using LINK{ad_extended.hlp}.
Undo/Redo:
This undoes/redoes all performed database changes (see LINK{undo.hlp}).
Jump/Get:
see LINK{e4_get_species.hlp}.
Editing:
Protection:
To perform editing, the protection level of the particular
entry ('EDIT/Set protection of selected species') has to
be set below or equal the global protection level
(use the 'Protect' button on the menuboard).
Note: There are two global protection levels: one in
edit-mode and another one in align-mode.
Modes:
ARB_EDIT4 supports 2 modes: Align-mode and Edit-mode.
To toggle between these two modes use the 'Align/Edit'
button on the menuboard or press CTRL-E.
Align-mode:
Only gap symbols can be inserted ('-', '.' or
'Spc' key) or deleted ('Del' or 'Backspace' key)
Sequence data cannot be modified - it only can be
checked in this mode. Sequence check is performed
by typing nucleotide (amino acid) symbols.
Discrepancies between typed and existing symbols
are indicated by beeping.
Edit-mode:
Edit-mode is divided into two submodes: Insert-mode
and Replace-mode. Toggle between these submodes
with the 'Insert/Replace' button on the menuboard
or with CTRL-I.
In Replace-mode inserted Nucleotides/gaps overwrite
existing Nucleotides/gaps.
In Insert-mode inserted Nucleotides/gaps do not
overwrite, instead the whole sequence is shifted.
Direction:
ARB_EDIT4 should perform any editing function into both
directions - forward and backward. To toggle the editing
direction use the "5'->3'" button on the menuboard.
Repeat editing functions:
Nearly every editing function can be performed repeatedly
by typing some digits before you perform the editing
function.
Example: '9-' inserts nine '-'
If you need to insert digits, use the toggle in
'Properties/Options'.
Key mapping:
Nucleotide (amino acid) and gap symbols can be assigned
to any of the letter and symbol keys
using 'Properties/Key mappings'.
Moving nucleotide (amino acid) symbols:
SHIFT + LEFT/RIGHT
Push or pull a coherent sequence stretch next
to the cursor.
ALT + LEFT/RIGHT
Move a single nucleotide (amino acid) symbol.
If you move your cursor towards a gap, the next
nucleotide (amino acid) symbol in movement
direction is fetched and moved to the actual
position.
If you move your cursor towards a nucleotide
(amino acid) symbol, it will jump aside the next
nucleotide (amino acid) symbol.
Alternate keys are: CTRL-O and CTRL-P
Change gap type
Consecutive runs of gaps can be set to
CTRL-'-' minus sign (normal gaps)
CTRL-'.' dots (recommended at both sequence ends)
CTRL-SPACE toggles between both gap types
These gap types have different meanings:
'-' is only used for aligning
'.' marks potentially missing bases
Other keys:
CTRL+LEFT/RIGHT
Jumps to the start of the next gap-region or non-gap-region.
You may configure whether it always jumps over gap-regions.
CTRL+UP/DOWN
Like CTRL-LEFT/RIGHT, but vertical.
HOME/END
Jumps to the start/end of sequence.
CTRL+HOME/END
Jumps to the first/last sequence.
ENTER
Fold/unfold group
ALT+UP/DOWN
Jump to previous/next group consensus
PAGE-UP/DOWN
Scroll down/up the sequence display w/o changing the cursor position
(Hint: use a simple cursor movement to move display back to the cursors position).
ALT+PAGE-UP/DOWN
Like PAGE-UP/DOWN, but scroll right/left.
CTRL-A
Call Aligner with current settings (see LINK{faligner.hlp}).
CTRL-D
Toggle "view differences" mode (see LINK{viewdiff.hlp}).
CTRL-E
Toggle EDIT/ALIGN mode (see above).
CTRL-I
Toggle INSERT/REPLACE mode (see above).
CTRL-J
Jump to opposite helix position.
CTRL-L
Move cursor into view and refresh display.
CTRL-M
Toggle mark of species/group.
CTRL-R
Shared key:
* sets reference sequence for "view differences" (only if active; see LINK{viewdiff.hlp})
* otherwise sets aligner reference species (see LINK{faligner.hlp})
CTRL-S
Repeat last search (see LINK{e4_search.hlp}).
Messages:
Many (less serious) errors will not be announced by a popup
window. Instead they appear at the small text window in the
upper-right corner of the editor window.
You can press one of the small buttons at the left side of this
text window:
- press the small lens to see more errors
- press the small X to get rid of all errors
EXAMPLES None
NOTES You may use the META key instead of ALT (especially if there is no ALT key :)
WARNINGS The key mappings may conflict with some window managers
(eg. olvwm). Disable the CTRL-LEFT/RIGHT keys of the window
manager.
If you perform major database modifications such as
- adding new SAIs
you have to QUIT and restart the editor.
BUGS
- sometimes the editor crashes after aligning
- some update problems (please report system and circumstances)
(workaround: resize the editor window)