source: tags/arb_5.1/HELP_SOURCE/oldhelp/faligner.hlp

Last change on this file was 5485, checked in by westram, 16 years ago
  • Summary: - moved common family find awars and their GUI elements to global functions

in awtc_next_neighbours

  • Integrated Aligners: . shortened several function interfaces by using structs . use custom family find parameters . store how many base positions of which relative have been used for

alignment (in field 'used_rels'). Do not store relatives of which
no base positions were used.

. respect sort order of relatives given by PT server (dont sort self, just test)
. documented field 'used_rels'
. linked family settings help with aligner help
. added 'Settings'-subdialog to aligner-settings (family_settings.fig)
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 4.3 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_edit.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7#SUB    subtopic.hlp
8
9# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
10
11#************* Title of helpfile !! and start of real helpfile ********
12TITLE           The integrated aligners
13
14OCCURRENCE      ARB_NT/ARB_EDIT/EDIT/Integrated Aligners
15
16DESCRIPTION     Choose the 'Integrated aligners' item from the 'ARB_EDIT/Edit'
17                menu to display the 'Integrated aligners' window.
18
19                Currently there are two integrated aligners:
20
21                          1. Fast Aligner
22
23                          2. Island Hopper (see Subtopic)
24
25                The following adjustments and features should apply to both aligners.
26
27                We did not test everything yet with island hopper, so some of them are broken.
28                Please mail to LINK{devel@arb-home.de} if you find something.
29
30
31SECTION         ADJUSTMENTS
32
33                Align
34
35                                Align selected or all marked sequences.
36                                If you type 'Ctrl-A' in the main editor window
37                                this option is set to selected species.
38
39                Reference
40
41                                The aligner needs a sequence as reference.
42                                You can either select a fixed species, the
43                                consensus of the group containing the species
44                                or the next relative found by the selected
45                                PT-Server.
46
47                                If you choose 'Auto search by pt_server', the
48                                aligner will use the next relative to align.
49                                If the nearest relative has gaps where the sequence
50                                to align has bases, the aligner will use the 2nd nearest
51                                relative or if that one has gaps too, the 3rd nearest, etc.
52                                You can define the maximum number of relatives.
53
54                                All used relatives and the number of base positions used from each relative,
55                                will be written into the field 'used_rels'.
56
57                                Press 'Settings' to define how relative search works
58                                in detail. See LINK{next_neighbours_common.hlp}
59
60                Range
61
62                                Align only a part or whole sequence.
63                                If you align only a part of the sequence, then
64                                you have to enter the number of columns around
65                                the cursor.
66
67                                Example: If you align 10 columns around
68                                position 100 then columns 90-110 get aligned.
69
70                Turn check
71
72                                The aligner is able to detect sequences which
73                                were entered in the wrong direction. With this
74                                switch you can select, if you like the aligner
75                                to turn such sequences and if it should ask you.
76
77                                NOTE: In two cases turn checking isn't
78                                reasonable:
79
80                                If you align only a part of a sequence or if you
81                                do not search Reference via pt_server. In both
82                                cases turn checking will be disabled.
83
84                Report
85
86                                The aligner can generate reports for the aligned
87                                sequence and for the reference sequence. These
88                                reports can be viewed with EDIT4, if you choose
89                                File/Load Configuration/DEFAULT_CONFIGURATION
90
91                                The report for the reference sequence (AMI)
92                                contains a '>' for every position were the aligner
93                                needed an insert in the reference sequence.
94
95                                The report for the aligned sequence (ASC) contains
96                                the following characters:
97
98                                    '-' for matching positions
99
100                                    '+' for inserts (in aligned sequence and in reference sequence)
101
102                                    '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
103
104                                    '#' for mismatching positions
105
106NOTES           This aligner knows about and uses all extended base characters
107                (ACGTUMRWSYKVHDN) for the alignment.
108                In other words: M aligned to R costs no penalty.
109
110EXAMPLES        None
111
112WARNINGS        None
113
114BUGS            If you select the menu entry 'remove all aligner entries' ARB_EDIT4
115                crashes in most cases.
116
117                Workaround:
118
119                        1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
120                        2. Remove all aligner entries
121                        3. Reload configuration
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