source: branches/lib/HELP_SOURCE/source/e4_search.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
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 4.6 KB
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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           Search and highlight sequence patterns
12
13OCCURRENCE      ARB_EDIT4/View/Search
14                ARB_EDIT4/<extended top area>/<search fields and buttons>
15
16DESCRIPTION     ARB_EDIT4 supports searching and highlighting sequence patterns.
17
18                It supports 9 different pattern types, which will each be displayed
19                in it's own color. Pattern types are e.g. "User1", "Probe",
20                "Primer (global)", ...
21
22                Basic controls for each search pattern are available in the
23                extended top-area of ARB_EDIT4 (to extend the top-area click the
24                'MORE' button): there you may jump to the next/previous occurrence of
25                each pattern type, toggle pattern type display and open the detailed
26                search parameter dialog for each pattern type.
27
28SECTION         Detailed search parameters (one window for each pattern type)
29
30                Search patterns
31
32                        In the text field you can enter multiple search patterns.
33                        Different patterns are separated by newlines or commas.
34
35                        '?' is treated as single letter wildcard
36
37                        '#' is an end-of-line comment
38
39                                Text written behind # will not be used for search.
40                                Instead this text will be displayed in the message
41                                window when you position your cursor on a found
42                                pattern.
43
44                Mark species with matches
45
46                        Marks all species that match any of the current search patterns
47                        (does not change marks of any other species).
48
49                Last/Next
50
51                        Jumps to the last/next occurrence of any of the given patterns.
52                        You can repeat your last search by pressing <CTRL-S> while focus
53                        is inside sequence view.
54
55                        In the extended top-area of ARB_EDIT4 there are global NEXT/LAST
56                        buttons. They jump to the next match of ANY of all 9 pattern types.
57
58                Show?
59
60                        If checked, the found parts are shown in different
61                        background colors (defined at Properties/Data Search)
62
63                        See NOTES below for overlap priority.
64
65                Open folded?
66
67                        If checked, the Last/Next-Button will open folded groups,
68                        to jump to the next occurrence. Otherwise search will jump
69                        over folded groups.
70
71                Auto jump?
72
73                        If checked, the cursor will automatically jump to the
74                        nearest occurrence, if you change the search pattern or
75                        other search parameters.
76
77                Ignore gaps in sequence?
78
79                        If checked, gaps in sequence will be ignored.
80                        (ACGU will find A-CG-U, AC---GU, ...)
81
82                Ignore gaps in pattern?
83
84                        If checked, gaps in the search pattern will be ignored.
85                        (A-CG-U, AC---GU, ... will find ACGU)
86
87                Treat T and U as match?
88
89                        If checked, T and U will be treated as equal.
90                        (ACGU will find ACGT and vice versa)
91
92                Ignore case?
93
94                        If checked, a and A, c and C, ... are treated as
95                        equal (aCGu will find ACGU, AcgU, acgu, ...)
96
97                Search for complement?
98
99                        If checked, search will go as well for complemented
100                        patterns.
101
102                Search for reverse?
103
104                        If checked, search will go as well for reversed patterns.
105
106                Exact!
107
108                        If checked, search will only go for the given combination
109                        of 'complement' and 'reverse'.
110
111                        Example: If 'Exact', 'complement' and 'reverse' are checked,
112                                 search will go only for complemented AND reversed
113                                 patterns.
114
115                Allowed mismatches
116
117                        Defines the minimum and maximum allowed number of
118                        non-matching base characters.
119
120SECTION         Store/restore search patterns
121
122                There are two ways to store/restore search patterns:
123
124                      * using the LINK{prop_configs.hlp} icon
125                      * using the SAVE and LOAD buttons
126
127                The latter is obsoleted and is only supported for compatibility.
128
129                Both store/restore all search parameters described above and
130                both provide the possibility to exchange the search parameters between
131                databases/users by saving/loading them to/from files and to move
132                search parameters between different pattern types.
133
134NOTES           Highlighted search patterns are drawn on top of
135                other conditions determining background color (see LINK{e4_background_priority.hlp}).
136
137                If the results from different pattern types overlap, patterns are
138                prioritized as listed in the 'View/Search' submenu,
139                i.e. "User1" is painted above "Primer (global)" and hence parts of
140                the latter may be invisible.
141
142                The hits may also be highlighted in ARB_SECEDIT (see LINK{sec_display.hlp}).
143
144EXAMPLES        None
145
146WARNINGS        None
147
148BUGS            No bugs known
149
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