source: tags/ms_r16q2/HELP_SOURCE/oldhelp/faligner.hlp

Last change on this file was 14613, checked in by westram, 8 years ago
  • 'Mark by reference'
    • default filter expression did only work with field content created by 'Nearest relatives of LISTED' (not with entries generated by fast-aligner)
    • added config-manager + added two predefined configs for the two use-cases
    • updated help
    • attach input- and display-fields to right window border (allows to see complete error-messages)
    • fixed problems with empty and wrapped error messages
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.7 KB
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_edit4.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7SUB     islandhopping.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_EDIT4/Edit/Integrated Aligners
15
16DESCRIPTION     Currently there are two integrated aligners:
17
18                          1. Fast Aligner
19
20                          2. Island Hopper (see Subtopic)
21
22                The following adjustments and features should apply to both aligners.
23
24                We did not test everything yet with island hopper, so some of them are broken.
25                Please mail to LINK{devel@arb-home.de} if you find something.
26
27
28SECTION         ADJUSTMENTS
29
30                Align
31
32                                Align current, marked or selected sequences.
33
34                                If you type 'CTRL-A' in the main editor window
35                                this option is set to align the current species and
36                                the aligner gets called.
37
38                Reference
39
40                                The aligner needs a sequence as reference.
41                                You can either select a fixed species, the
42                                consensus of the group containing the species
43                                or the next relative(s) found by the selected
44                                PT-Server.
45
46                                If you choose a fixed species, you may press the 'COPY' button
47                                to copy the name of the 'Current Species' to the 'Reference' species.
48                                Alternatively you may use CTRL-R while the focus is inside the sequence view
49                                (Note: CTRL-R does not work, if LINK{viewdiff.hlp} is active).
50
51                                If you choose 'Auto search by pt_server', the
52                                aligner will use the next relative(s) as reference.
53                                If the nearest relative has gaps where the sequence
54                                to align has bases, the aligner will use the 2nd nearest
55                                relative or if that one has gaps too, the 3rd nearest, etc.
56                                You can define the maximum number of relatives.
57
58                                All used relatives and the number of base positions used from each relative,
59                                will be written into the field 'used_rels' (see also LINK{markbyref.hlp}).
60
61                                If you enter '0' in 'Data from range only, plus', relative
62                                search only uses data from the aligned range. If you enter
63                                a value different from '0' the used range will be
64                                expanded (positive values) or limited (negative values).
65                                When the input field is empty, the complete sequence will be used.
66
67                                Press 'More settings' to define how relative search works
68                                in detail. See LINK{next_neighbours_common.hlp}
69
70                Range
71
72                                Align only a part of or the whole sequence.
73
74                                Several possibilities exist for aligning just a part of the sequence:
75                                - select 'Positions around cursor' and specify how many positions shall be
76                                  taken into each direction from the cursor position (Example: If you align
77                                  10 columns around position 100 then columns 90-110 will be aligned).
78                                - if you use 'Selected range' the column range of the selected block will
79                                  be used.
80                                - if you select 'Multi-Range by SAI', the specified SAI will be interpreted as
81                                  a list of ranges. A list of characters defines what is considered a range.
82                                  All ranges will be aligned.
83
84                                See also LINK{e4_modsai.hlp} for howto create suitable SAIs.
85
86                Turn check
87
88                                The aligner is able to detect sequences which
89                                were entered in the wrong direction. With this
90                                switch you can select, if you like the aligner
91                                to turn such sequences and if it should ask you.
92
93                                NOTE: In two cases turn checking isn't
94                                reasonable:
95
96                                If you align only a part of a sequence or if you
97                                do not search Reference via pt_server. In both
98                                cases turn checking will be disabled.
99
100                Report
101
102                                The aligner can generate reports for the aligned
103                                sequence and for the reference sequence. These
104                                reports can be viewed with EDIT4, if you choose
105                                File/Load Configuration/DEFAULT_CONFIGURATION
106
107                                The report for the reference sequence (AMI)
108                                contains a '>' for every position were the aligner
109                                needed an insert in the reference sequence.
110
111                                The report for the aligned sequence (ASC) contains
112                                the following characters:
113
114                                    '-' for matching positions
115
116                                    '+' for inserts (in aligned sequence and in reference sequence)
117
118                                    '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)
119
120                                    '#' for mismatching positions
121
122NOTES           This aligner knows about and uses all extended base characters
123                (ACGTUMRWSYKVHDN) for the alignment.
124                In other words: M aligned to R costs no penalty.
125
126                The config-manager icon handles the settings in the 'Integrated Aligners' window and those in
127                its subwindows 'Parameters for Island Hopping' and 'Family search parameters'.
128
129EXAMPLES        None
130
131WARNINGS        None
132
133BUGS            If you select the menu entry 'remove all aligner entries' ARB_EDIT4
134                crashes in most cases.
135
136                Workaround:
137
138                        1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
139                        2. Remove all aligner entries
140                        3. Reload configuration
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