| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP e4.hlp |
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| 3 | |
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| 4 | #Please insert subtopic references (line starts with keyword SUB) |
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| 5 | #SUB xxx.hlp |
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| 6 | |
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| 7 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 8 | |
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| 9 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 10 | |
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| 11 | TITLE ARB_EDIT4 Options |
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| 12 | |
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| 13 | OCCURRENCE ARB_EDIT4/Properties/Options... |
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| 14 | |
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| 15 | DESCRIPTION This window allows you to adjust some display parameters |
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| 16 | |
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| 17 | SECTION Online Sequence Compression |
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| 18 | |
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| 19 | Online Sequence Compression (OSC) is a way to hide column positions |
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| 20 | (normally: column positions containing only or many gaps) in order |
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| 21 | to simplify editing of alignments with wide gaps. |
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| 22 | |
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| 23 | OSC affects only the manner how sequences are DISPLAYED in the |
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| 24 | editor and does not affect the sequences themselves. |
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| 25 | |
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| 26 | Available modes: |
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| 27 | |
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| 28 | Show all gaps: Nothing is hidden. |
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| 29 | |
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| 30 | Show some gaps: For each column range (consisting of gaps only) a different |
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| 31 | amount of gaps is shown, depending on the width of that column range. |
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| 32 | In detail: |
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| 33 | |
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| 34 | sequence has less than gaps => display that many gaps |
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| 35 | 100 G/10+1 |
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| 36 | 1000 G/100+1 |
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| 37 | else G/1000+1 |
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| 38 | |
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| 39 | Hide all gaps: |
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| 40 | |
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| 41 | Hide no nucleotides: All column ranges consisting of gaps only are hidden. |
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| 42 | |
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| 43 | Hide columns with less than X% nucleotides: This mode really makes nucleotides |
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| 44 | disappear from display. Use with care! |
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| 45 | |
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| 46 | |
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| 47 | Those above mentioned column values are calculated on the basis of |
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| 48 | all sequences currently loaded in the editor. |
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| 49 | |
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| 50 | Only sequence data is taken into respect while calculating gap positions. |
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| 51 | It is possible, that parts of a SAI get hidden by using OSC. |
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| 52 | |
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| 53 | You may use <CTRL-K> to toggle between 'Show all gaps' and 'Hide all gaps' |
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| 54 | while the focus is inside the sequence view. |
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| 55 | |
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| 56 | SECTION Layout |
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| 57 | |
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| 58 | Sequence-helix spacing: Extra distance between sequence data and helix display (Default=0). |
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| 59 | |
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| 60 | Sequence-sequence spacing: Extra distance between two sequences (Default=0). |
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| 61 | |
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| 62 | Note: You may use negative values for the above settings to get a very compact |
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| 63 | display. Note that this will cause some minor drawbacks like cut-off |
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| 64 | underlengths (e.g. with small 'g') and character overlapping. Additional compaction |
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| 65 | is possible by switching off the helix display (see LINK{helixsym.hlp}). |
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| 66 | |
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| 67 | SECTION Scroll-Speed |
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| 68 | |
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| 69 | Define the horizontal and vertical scroll speed for mouse scrolling (with middle mouse button). |
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| 70 | The default scroll-speed is 10/10, which scrolls with same speed as the mouse is moved. |
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| 71 | |
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| 72 | The display may also be scrolled using the mouse-wheel (optionally together with ALT/META). |
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| 73 | |
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| 74 | SECTION Editing |
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| 75 | |
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| 76 | Gap characters: set of characters which are handled as "gaps" |
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| 77 | |
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| 78 | |
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| 79 | |
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| 80 | EXAMPLES None |
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| 81 | |
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| 82 | WARNINGS None |
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| 83 | |
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| 84 | BUGS None |
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