source: branches/lib/HELP_SOURCE/source/e4_options.hlp

Last change on this file was 19575, checked in by westram, 3 weeks ago
  • reintegrates 'help' into 'trunk'
    • preformatted text gets checked for width now (to enforce it fits into the arb help window).
    • fixed help following these checks, using the following steps:
      • ignore problems in foreign documentation.
      • increase default help window width.
      • introduce control comments to
        • accept oversized preformatted sections.
        • enforce preformatted style for whole sections.
        • simply define single-line preformatted sections
          Used intensive for definition of internal script languages.
    • fixed several non-related problems found in documentation.
    • minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections).
    • refactor system interface (GUI version) and use it from help module.
  • adds: log:branches/help@19532:19574
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.8 KB
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1#       main topics:
2UP      e4.hlp
3
4#       sub topics:
5#SUB     subtopic.hlp
6
7# format described in ../help.readme
8
9
10
11TITLE           ARB_EDIT4 Options
12
13OCCURRENCE      ARB_EDIT4/Properties/Options...
14
15DESCRIPTION     This window allows you to adjust some display parameters
16
17SECTION Online Sequence Compression
18
19                Online Sequence Compression (OSC) is a way to hide column positions
20                (normally: column positions containing only or many gaps) in order
21                to simplify editing of alignments with wide gaps.
22
23                OSC affects only the manner how sequences are DISPLAYED in the
24                editor and does not affect the sequences themselves.
25
26           Available modes:
27
28                Show all gaps: Nothing is hidden.
29
30                Show some gaps: For each column range (consisting of gaps only) a different
31                amount of gaps is shown, depending on the width of that column range.
32                In detail:
33
34                   sequence has less than gaps    =>    display that many gaps
35                            100                                 G/10+1
36                            1000                                G/100+1
37                            else                                G/1000+1
38
39                Hide all gaps:
40
41                     Hide no nucleotides: All column ranges consisting of gaps only are hidden.
42
43                     Hide columns with less than X% nucleotides: This mode really makes nucleotides
44                     disappear from display. Use with care!
45
46
47                Those above mentioned column values are calculated on the basis of
48                all sequences currently loaded in the editor.
49
50                Only sequence data is taken into respect while calculating gap positions.
51                It is possible, that parts of a SAI get hidden by using OSC.
52
53                You may use <CTRL-K> to toggle between 'Show all gaps' and 'Hide all gaps'
54                while the focus is inside the sequence view.
55
56SECTION Layout
57
58        Sequence-helix spacing: Extra distance between sequence data and helix display (Default=0).
59
60        Sequence-sequence spacing: Extra distance between two sequences (Default=0).
61
62        Note: You may use negative values for the above settings to get a very compact
63        display. Note that this will cause some minor drawbacks like cut-off
64        underlengths (e.g. with small 'g') and character overlapping. Additional compaction
65        is possible by switching off the helix display (see LINK{helixsym.hlp}).
66
67SECTION Scroll-Speed
68
69        Define the horizontal and vertical scroll speed for mouse scrolling (with middle mouse button).
70        The default scroll-speed is 10/10, which scrolls with same speed as the mouse is moved.
71
72        The display may also be scrolled using the mouse-wheel (optionally together with ALT/META).
73
74SECTION Editing
75
76        Gap characters: set of characters which are handled as "gaps"
77
78
79
80EXAMPLES        None
81
82WARNINGS        None
83
84BUGS            None
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