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

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
File size: 2.0 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           View differences to selected
12
13OCCURRENCE      ARB_EDIT4/View/View differences ...
14
15DESCRIPTION     Select a species, SAI or group consensus by clicking into its sequence data.
16
17                Then check 'Selected' or press 'SET' to restrict the sequence display
18                of all other sequences (i.e. all but the selected sequence) to
19                show only the differences to the selected sequence (aka reference sequence).
20
21                Checking 'Follow cursor' will instantly set a new reference sequence,
22                as soon as you set the cursor into a new sequence.
23
24                To revert display to standard mode, select 'None'.
25
26                Key bindings:
27
28                    * CTRL-D: toggles "View differences" mode
29                    * CTRL-R: sets reference sequence to the cursor terminal (this only
30                      works if "View differences" mode is active, otherwise CTRL-R sets
31                      the aligner reference species; see LINK{faligner.hlp})
32
33                You may define the character used for positions where the displayed
34                sequence does NOT differ from the reference sequence.
35                Default is to display a space, other recommended values
36                are '|' (esp. w/o helix display and smaller seq-spacing),
37                '_', '~', ':' or single quotes.
38
39                If 'Mind case?' is checked, characters only differing in case are displayed as
40                differences.
41
42                If 'Mind gap type?' is checked, different gaps are displayed as "differences".
43                What is regarded as "gap" may be defined in the text field behind the toggle.
44
45NOTES           Useful to manually correct alignments.
46
47                The IUPAC field in the top area can be used to guess the sequence
48                data at cursor position.
49
50EXAMPLES        None
51
52WARNINGS        Editing works as usual, even if you do not see what you edit.
53
54BUGS            No bugs known
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