source: branches/lib/HELP_SOURCE/source/e4.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      alignment.hlp
UP      security.hlp
UP      helix.hlp
UP      ecoliref.hlp
UP      species_configs.hlp

#       sub topics:
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     arb_secedit.hlp
SUB     helixsym.hlp
SUB     pfold.hlp

# format described in ../help.readme



TITLE           ARB_EDIT4 - sequence editor

                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)