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

Last change on this file was 19708, checked in by westram, 3 months ago
  • update doc+gui:
    • avoid terms "ARB_NT" (=former name of main arb window), "ARB_NTREE" and similar
      • instead talk about "ARB main window"
    • correct refs to 'ARB/Probes/PT_SERVER Admin'.
    • update 'What are marked species?'.
    • update protection level documentation (parts already done with previous commit).
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 11.3 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      alignment.hlp
5UP      security.hlp
6UP      helix.hlp
7UP      ecoliref.hlp
8UP      species_configs.hlp
9
10#       sub topics:
11SUB     man_arb_edit4.hlp
12SUB     arb_edit4.hlp
13SUB     e4_search.hlp
14SUB     e4_replace.hlp
15SUB     e4_block.hlp
16SUB     nekey_map.hlp
17SUB     arb_secedit.hlp
18SUB     helixsym.hlp
19SUB     pfold.hlp
20
21# format described in ../help.readme
22
23
24
25TITLE           ARB_EDIT4 - sequence editor
26
27                Sequence primary and secondary structure editor
28
29OCCURRENCE      ARB/Sequence/Edit sequences/...
30                ARB/<editor icon>
31
32DESCRIPTION     The editor allows you to view and modify the sequences of 'marked
33                species' or 'a selection of species' and 'SAI' (sequence associated
34                information) stored in the database.
35                Potential secondary structure is automatically checked
36                and the information can be displayed with the primary structure.
37                In addition, an online column statistic may help you find
38                sequence and alignment errors.
39
40                The editor permanently communicates with the database and
41                other ARB tools. Every change made by the editor is immediately
42                exported to the database. All sequence changes made by other
43                ARB tools are exported to the editor every 5 seconds.
44
45                Multiple editors can be used synchronously.
46
47
48        Display:
49
50                        First Column:   Species ID or group name.
51                        Second C.       Protection level and subtype of sequence.
52                        Last c.         Sequence and secondary structure and more.
53
54        Cursor:
55
56                        The cursor can be moved using the mouse or the arrow
57                        keys.  The current cursor positions with respect to the
58                        alignment and the E. coli sequence (there has to be an
59                        'SAI' entry: ECOLI) are indicated after the 'Position'
60                        and 'E.coli' prompts in the upper part of the
61                        'ARB_EDIT4' window.
62
63                        These 3 positions and the IUPAC-display refer to the position
64                        RIGHT of the cursor.
65
66                        'Position' counts from 1 to "alignment length".
67
68                        The 'Ecoli'- and 'Base'-position count from zero to "number of bases".
69
70                        - Zero means your cursor is left of the first base (and not AT the first base).
71                        - X means your cursor is AT or BEHIND base number X (but in front of base number X+1)
72
73                        By changing the value of one of these fields, the cursor will
74                        be repositioned. Negative values are possible - in that case
75                        the position will be calculated from the right end (e.g. -1 in
76                        'Base' field means 'position onto base')
77
78        Moving entries:
79
80                        To move an individual entry, position the cursor on the
81                        name, keep the left mouse button pressed, move the entry
82                        to the desired position, and release the button.
83
84                        Any entry can be fixed (keeps its position while
85                        scrolling vertically) at the top of the editing area by
86                        moving it somewhere above the double line (=top area).
87
88                        You can define which entries are placed in that top area by
89                        default using LINK{ad_extended.hlp}.
90
91        Undo/Redo:
92
93                        This undoes/redoes all performed database changes (see LINK{undo.hlp}).
94
95        Jump/Get:
96
97                        see LINK{e4_get_species.hlp}.
98
99        Editing:
100
101                Protection:
102
103                        To perform editing, the protection level of the particular
104                        entry ('EDIT/Set protection of selected species') has to
105                        be set below or equal the global protection level
106                        (use the 'Protect' button on the menuboard).
107
108                        Note: There are two global protection levels: one in
109                        edit-mode and another one in align-mode.
110
111                Modes:
112
113                        ARB_EDIT4 supports 2 modes: Align-mode and Edit-mode.
114                        To toggle between these two modes use the 'Align/Edit'
115                        button on the menuboard or press CTRL-E.
116
117                        Align-mode:
118
119                                Only gap symbols can be inserted ('-', '.' or
120                                'Spc' key) or deleted ('Del' or 'Backspace' key)
121
122                                Sequence data cannot be modified - it only can be
123                                checked in this mode. Sequence check is performed
124                                by typing nucleotide (amino acid) symbols.
125                                Discrepancies between typed and existing symbols
126                                are indicated by beeping.
127
128                        Edit-mode:
129
130                                Edit-mode is divided into two submodes: Insert-mode
131                                and Replace-mode. Toggle between these submodes
132                                with the 'Insert/Replace' button on the menuboard
133                                or with CTRL-I.
134
135                                In Replace-mode inserted Nucleotides/gaps overwrite
136                                existing Nucleotides/gaps.
137                                In Insert-mode inserted Nucleotides/gaps do not
138                                overwrite, instead the whole sequence is shifted.
139
140                Direction:
141
142                        ARB_EDIT4 should perform any editing function into both
143                        directions - forward and backward. To toggle the editing
144                        direction use the "5'->3'" button on the menuboard.
145
146                Repeat editing functions:
147
148                        Nearly every editing function can be performed repeatedly
149                        by typing some digits before you perform the editing
150                        function.
151
152                                Example:  '9-' inserts nine '-'
153
154                        If you need to insert digits, use the toggle in
155                        'Properties/Options'.
156
157                Key mapping:
158
159                        Nucleotide (amino acid) and gap symbols can be assigned
160                        to any of the letter and symbol keys
161                        using 'Properties/Key mappings'.
162
163                Moving nucleotide (amino acid) symbols:
164
165                        SHIFT + LEFT/RIGHT
166
167                                Push or pull a coherent sequence stretch next
168                                to the cursor.
169
170                        ALT + LEFT/RIGHT
171
172                                Move a single nucleotide (amino acid) symbol.
173
174                                If you move your cursor towards a gap, the next
175                                nucleotide (amino acid) symbol in movement
176                                direction is fetched and moved to the actual
177                                position.
178
179                                If you move your cursor towards a nucleotide
180                                (amino acid) symbol, it will jump aside the next
181                                nucleotide (amino acid) symbol.
182
183                                Alternate keys are: CTRL-O and CTRL-P
184
185                Change gap type
186
187                       Consecutive runs of gaps can be set to
188
189                       CTRL-'-'         minus sign (normal gaps)
190                       CTRL-'.'         dots (recommended at both sequence ends)
191                       CTRL-SPACE       toggles between both gap types
192
193                       These gap types have different meanings:
194
195                       '-'        is only used for aligning
196                       '.'        marks potentially missing bases
197
198
199                Other keys:
200
201                        CTRL+LEFT/RIGHT
202
203                                Jumps to the start of the next gap-region or non-gap-region.
204                                You may configure whether it always jumps over gap-regions.
205
206                        CTRL+UP/DOWN
207
208                                Like CTRL-LEFT/RIGHT, but vertical.
209
210                        HOME/END
211
212                                Jumps to the start/end of sequence.
213
214                        CTRL+HOME/END
215
216                                Jumps to the first/last sequence.
217
218                        ENTER
219
220                                Fold/unfold group
221
222                        ALT+UP/DOWN
223
224                                Jump to previous/next group consensus
225
226                        PAGE-UP/DOWN
227
228                                Scroll down/up the sequence display w/o changing the cursor position
229                                (Hint: use a simple cursor movement to move display back to the cursors position).
230
231                        ALT+PAGE-UP/DOWN
232
233                                Like PAGE-UP/DOWN, but scroll right/left.
234
235                        CTRL-A
236
237                                Call Aligner with current settings (see LINK{faligner.hlp}).
238
239                        CTRL-D
240
241                                Toggle "view differences" mode (see LINK{viewdiff.hlp}).
242
243                        CTRL-E
244
245                                Toggle EDIT/ALIGN mode (see above).
246
247                        CTRL-I
248
249                                Toggle INSERT/REPLACE mode (see above).
250
251                        CTRL-J
252
253                                Jump to opposite helix position.
254
255                        CTRL-L
256
257                                Move cursor into view and refresh display.
258
259                        CTRL-M
260
261                                Toggle mark of species/group.
262
263                        CTRL-R
264
265                                Shared key:
266                                  * sets reference sequence for "view differences" (only if active; see LINK{viewdiff.hlp})
267                                  * otherwise sets aligner reference species (see LINK{faligner.hlp})
268
269                        CTRL-S
270
271                                Repeat last search (see LINK{e4_search.hlp}).
272
273        Messages:
274
275                Many (less serious) errors will not be announced by a popup
276                window. Instead they appear at the small text window in the
277                upper-right corner of the editor window.
278
279                You can press one of the small buttons at the left side of this
280                text window:
281
282                        - press the small lens to see more errors
283                        - press the small X to get rid of all errors
284
285EXAMPLES        None
286
287NOTES           You may use the META key instead of ALT (especially if there is no ALT key :)
288
289WARNINGS        The key mappings may conflict with some window managers
290                (eg. olvwm). Disable the CTRL-LEFT/RIGHT keys of the window
291                manager.
292
293                If you perform major database modifications such as
294
295                        - adding new SAIs
296
297                you have to QUIT and restart the editor.
298
299BUGS
300
301                - sometimes the editor crashes after aligning
302                - some update problems (please report system and circumstances)
303                  (workaround: resize the editor window)
304
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