1 | #Please insert up references in the next lines (line starts with keyword UP) |
---|
2 | UP arb.hlp |
---|
3 | UP glossary.hlp |
---|
4 | UP arb_merge_workflow.hlp |
---|
5 | |
---|
6 | #Please insert subtopic references (line starts with keyword SUB) |
---|
7 | SUB del_list.hlp |
---|
8 | SUB write_field_list.hlp |
---|
9 | SUB mod_field_list.hlp |
---|
10 | |
---|
11 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
---|
12 | |
---|
13 | #************* Title of helpfile !! and start of real helpfile ******** |
---|
14 | TITLE Compare and Transfer Species Entries |
---|
15 | |
---|
16 | OCCURRENCE ARB_MERGE/Transfer species |
---|
17 | |
---|
18 | DESCRIPTION Allows |
---|
19 | * database searching, |
---|
20 | * comparison of the two databases, |
---|
21 | * transferring data from left to right |
---|
22 | * realigning sequences to new alignment |
---|
23 | |
---|
24 | Database Searching: |
---|
25 | |
---|
26 | To perform database searching within the individual databases |
---|
27 | use the left or right part of the 'TRANSFER SPECIES' window for |
---|
28 | source and target database (DB), respectively. |
---|
29 | |
---|
30 | The database is scanned for 'species' (see LINK{glossary.hlp}) |
---|
31 | which contain (or do not contain) the search string within the |
---|
32 | specified 'field' (see LINK{glossary.hlp}). The corresponding |
---|
33 | 'species' and the respective 'field' entries are listed in the |
---|
34 | 'HIT LIST' subwindow. The number of hits is displayed after the |
---|
35 | 'Hits:' prompt. |
---|
36 | |
---|
37 | Define whether matching or non matching species should be |
---|
38 | listed by pressing the appropriate combination of left |
---|
39 | and right buttons in the 'QUERY TYPE' area. Performing |
---|
40 | multiple searches, define whether the list of 'species' |
---|
41 | should be replaced by the new results, whether newly |
---|
42 | found 'species' should be removed from or appended |
---|
43 | to the existing list. |
---|
44 | |
---|
45 | Select a 'field' from the 'Fields' subwindow. |
---|
46 | |
---|
47 | Type the search string to the 'Search string' subwindow. |
---|
48 | |
---|
49 | Press the 'RUN QUERY' button of the results area. |
---|
50 | |
---|
51 | See also LINK{searching.hlp} and LINK{search_equal_fields.hlp}. |
---|
52 | |
---|
53 | Data Transfer: |
---|
54 | |
---|
55 | To transfer a single 'species' and all its 'field' entries, |
---|
56 | select the species from the list displayed in the 'HIT |
---|
57 | LIST' subwindow and press The 'TRANSFER SELECTED |
---|
58 | SPECIES' button in the middle column of the 'TRANSFER |
---|
59 | SPECIES' window. |
---|
60 | |
---|
61 | To transfer all listed 'species' and all corresponding 'field' |
---|
62 | entries, press the 'TRANSFER ALL LISTED SPECIES' button |
---|
63 | in the middle column of the 'TRANSFER SPECIES' window. |
---|
64 | |
---|
65 | To transfer the entries of a 'field' selected from the 'Search |
---|
66 | field' subwindow for all listed 'species, press the |
---|
67 | 'TRANSFER A FIELD FOR ALL LISTED SPECIES' button in the |
---|
68 | middle column of the 'TRANSFER SPECIES' window. |
---|
69 | |
---|
70 | To save modifications press the 'Save result' button of the |
---|
71 | 'ARB_MERGE' window. |
---|
72 | |
---|
73 | Adapt Alignment: |
---|
74 | |
---|
75 | ARB Merge tries to keep the alignment correct. Normally people |
---|
76 | have inserted new gaps in either the left or right database. |
---|
77 | By entering the ID(s) of some reference species in the input |
---|
78 | box in the upper center of the TRANSFER SPECIES window, the |
---|
79 | program will try to find those species in both databases, |
---|
80 | create a column reference list, and realign all transferred |
---|
81 | sequences. |
---|
82 | To enable this feature, enable the 'Adapt alignment' toggle. |
---|
83 | |
---|
84 | |
---|
85 | NOTES None |
---|
86 | |
---|
87 | |
---|
88 | EXAMPLES For examples for database searching see LINK{sp_search.hlp}. |
---|
89 | |
---|
90 | |
---|
91 | WARNINGS The data will always be transferred from the source DB to |
---|
92 | the target DB. |
---|
93 | If you want to align sequences during transfer, it is recommended |
---|
94 | that the left database has fewer gaps than the right one. |
---|
95 | |
---|
96 | If there are entries (for selected data) in both databases, |
---|
97 | those in the target DB will be overwritten! |
---|
98 | |
---|
99 | |
---|
100 | BUGS No bugs known |
---|