| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | #Please insert subtopic references (line starts with keyword SUB) |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 9 | |
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| 10 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 11 | TITLE View differences to selected |
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| 12 | |
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| 13 | OCCURRENCE ARB_EDIT4/View/View differences ... |
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| 14 | |
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| 15 | DESCRIPTION Select a species, SAI or group consensus by clicking into its sequence data. |
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| 16 | |
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| 17 | Then check 'Selected' or press 'SET' to restrict the sequence display |
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| 18 | of all other sequences (i.e. all but the selected sequence) to |
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| 19 | show only the differences to the selected sequence (aka reference sequence). |
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| 20 | |
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| 21 | Checking 'Follow cursor' will instantly set a new reference sequence, |
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| 22 | as soon as you set the cursor into a new sequence. |
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| 23 | |
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| 24 | To revert display to standard mode, select 'None'. |
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| 25 | |
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| 26 | Key bindings: |
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| 27 | |
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| 28 | * CTRL-D: toggles "View differences" mode |
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| 29 | * CTRL-R: sets reference sequence to the cursor terminal (this only |
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| 30 | works if "View differences" mode is active, otherwise CTRL-R sets |
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| 31 | the aligner reference species; see LINK{faligner.hlp}) |
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| 32 | |
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| 33 | You may define the character used for positions where the displayed |
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| 34 | sequence does NOT differ from the reference sequence. |
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| 35 | Default is to display a space, other recommended values |
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| 36 | are '|' (esp. w/o helix display and smaller seq-spacing), |
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| 37 | '_', '~', ':' or single quotes. |
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| 38 | |
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| 39 | If 'Mind case?' is checked, characters only differing in case are displayed as |
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| 40 | differences. |
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| 41 | |
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| 42 | If 'Mind gap type?' is checked, different gaps are displayed as "differences". |
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| 43 | What is regarded as "gap" may be defined in the text field behind the toggle. |
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| 44 | |
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| 45 | NOTES Useful to manually correct alignments. |
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| 46 | |
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| 47 | The IUPAC field in the top area can be used to guess the sequence |
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| 48 | data at cursor position. |
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| 49 | |
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| 50 | EXAMPLES None |
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| 51 | |
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| 52 | WARNINGS Editing works as usual, even if you do not see what you edit. |
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| 53 | |
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| 54 | BUGS No bugs known |
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