|
Last change
on this file was
16469,
checked in by westram, 8 years ago
|
- reintegrates 'textedit' into 'trunk'
- fixes #586
- editor now always started asynchronously
- uses inotify to track file changes
also use inotify to track directory updates (in order to update file selections when needed)
 by [16515] ff.; merged by [16551]
- adds: log:branches/textedit@16448:16468
|
-
Property svn:eol-style set to
native
-
Property svn:keywords set to
Author Date Id Revision
|
|
File size:
2.0 KB
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| 1 | item:Phylip PROML |
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| 2 | seqtype: A |
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| 3 | itemmeta: O |
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| 4 | itemmethod:(GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \ |
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| 5 | RUN_IN_WINDOW((arb_proml $BOOTSTRAP $MODEL $VIEWOUT $ANALYSIS $RANDOM $REARRANGE \ |
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| 6 | $RATE_VARIATION $VARIATION_COEFF $HMM_RATES $INV_FRACTION \ |
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| 7 | $INTERACTIVE && \ |
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| 8 | $DISPLAY_FUNC));\ |
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| 9 | RM_LOCAL_FILES(TmpInputFile) )& |
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| 10 | itemhelp:proml.help |
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| 11 | |
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| 12 | arg:DISPLAY_FUNC |
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| 13 | argtype:choice_menu |
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| 14 | arglabel:What to do with the tree? |
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| 15 | argchoice:ARB ('tree_proml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_proml_$$ outtree "PRG=proml FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRAP MODEL=$MODEL ANALYSIS=$ANALYSIS" |
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| 16 | argchoice:TextEdit:arb_textedit outfile |
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| 17 | argchoice:Treetool:treetool outtree |
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| 18 | |
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| 19 | arg:MODEL |
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| 20 | argtype:choice_menu |
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| 21 | arglabel:Model |
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| 22 | argchoice:Jones-Taylor-Thornton:JTT |
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| 23 | argchoice:Dayhoff PAM:PAM |
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| 24 | |
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| 25 | arg:ANALYSIS |
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| 26 | argtype:choice_menu |
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| 27 | arglabel:Analysis |
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| 28 | argchoice:Rough & fast:rough |
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| 29 | argchoice:Fine & slow:fine |
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| 30 | |
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| 31 | arg:REARRANGE |
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| 32 | argtype:choice_menu |
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| 33 | arglabel:Global rearrangements |
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| 34 | argchoice:No:0 |
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| 35 | argchoice:Yes:1 |
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| 36 | |
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| 37 | arg:RANDOM |
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| 38 | argtype:choice_menu |
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| 39 | arglabel:Randomize sequence order |
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| 40 | argchoice:Yes:1 |
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| 41 | argchoice:No:0 |
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| 42 | |
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| 43 | arg:RATE_VARIATION |
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| 44 | argtype:choice_menu |
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| 45 | arglabel:Rate variation among sites? |
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| 46 | argchoice:Constant rate of change:0 |
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| 47 | argchoice:Gamma distributed rates:1 |
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| 48 | argchoice:Gamma+Invariant sites:2 |
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| 49 | |
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| 50 | arg:VARIATION_COEFF |
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| 51 | argtype:text |
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| 52 | arglabel:Variation coeff. (gamma only) |
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| 53 | argtext:4 |
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| 54 | |
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| 55 | arg:HMM_RATES |
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| 56 | argtype:text |
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| 57 | arglabel:Rates in HMM (gamma only) |
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| 58 | argtext:4 |
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| 59 | |
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| 60 | arg:INV_FRACTION |
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| 61 | argtype:text |
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| 62 | arglabel:Fraction of invariant sites |
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| 63 | argtext:0.1 |
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| 64 | |
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| 65 | arg:BOOTSTRAP |
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| 66 | argtype:choice_menu |
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| 67 | arglabel:How many bootstraps? |
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| 68 | argchoice:Do not bootstrap:0 |
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| 69 | argchoice:10:10 |
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| 70 | argchoice:100:100 |
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| 71 | argchoice:500:500 |
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| 72 | argchoice:1000:1000 |
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| 73 | argchoice:5000:5000 |
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| 74 | argchoice:10000:10000 |
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| 75 | |
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| 76 | arg:VIEWOUT |
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| 77 | argtype:choice_menu |
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| 78 | arglabel:View report |
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| 79 | argchoice:No:0 |
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| 80 | argchoice:Yes:1 |
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| 81 | |
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| 82 | arg:INTERACTIVE |
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| 83 | argtype:choice_menu |
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| 84 | arglabel:Interactive? (no for bootstrap) |
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| 85 | argchoice:No:0 |
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| 86 | argchoice:Yes:1 |
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| 87 | |
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| 88 | in:TmpInputFile |
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| 89 | informat:genbank |
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| 90 | insave: |
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| 91 | |
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