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spup-updates.txt
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1996-07-05
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// spup-updates.txt
// seqpup v 0.5a
fixed Save file in place -- now saves in proper folder, not in
seqpup folder
improved seqpup folder path finding
- MacOS: now should always find :tables:, :apps: if they exist
w/in SeqPup folder, and prefs paths are relative
(e.g., apps=apps, tables=tables in .prefs)
- UnixOS: now can 'setenv SEQPUPHOME /path/to/seqpup/folder'
- MSDOS : ditto with 'setenv SEQPUPHOME c:\path\to\seqpup'
NOTE: must use "APPNAME"HOME, so if you change name of SeqPup
to PeekUp, you need to change env var to PEEKUPHOME.
added click-top-index-line to select sequence columns
added mask-to-selection, selection-to-mask commands -- mask-to-
selection is not yet useful because base DTableView selection
methods need to be rewritten to allow disjoint selections.
added seq-index display -- lists base number that mouse pointer is at
added mac file bundle rez & finder-open, finder-print
-- needs double check
added save of pretty print in PICT format (mac),
metafile (mswin - still buggy?!)
added variable position grey coloring in align display
added mswin/xwin sticky menubar window
fixed mswin mouse-shift commands
added mswin menu command keys
fixed mac/mswin text edit command keys: cut/copy/paste
many updates to mswin version for micsoft win32/winnt/win95
updated fastdnaml app to version 1.1.1
added configurable child-app launch parameters
-- dialogs in HTML.form format
-- needs more work
added dna distance/similarity matrix function
added child apps: DeSoete's LSADT, Felsenstein's DrawTree & DrawGram
fixed bomb during cut/copy of pretty print view
fixed - cut/clear last seq in list, can't select new last seq (can see it)
fixed - scroll multi-align view w/ arrow when in Edit bases mode
leads to overlapped draw of bases.
fixed - crash & failure when use Find w/ Edit bases mode
in progress
------------
add network "child-apps" - e.g., call apps on remote (Unix)
computer w/ sequence inputs and get results returned, esp. w/ GCG and like
useful apps
>> can do some of this; need persistence on client; bopper delete & other;
problems w/ tcp failures; need to handle gcg graphics;
add disjoint selections to DTableView -- need for copy/paste among
masks (using table selection as clipboard for masks)
>> see seq selections when disjoint mask is front view -- not yet right
add/improve max. sequence length to be handled, from kilobases to megabases
(target is 10MB sequences) -- ? use disk caching of seq. segments
>> can now open about 300KB up from about 30KB...
todo
-----------
fix child app results - repeated runs sometimes will reopen old output files!
- unix: fastdnaml fails to return results after 1st run?
add undo for edit text in aln window
fix mswin edit align text
fix mswin edits - mswin toolbox limiting to 255 chars !@
fix mswin rich text display (bombs on scroll of HELP doc !!)
fix seqprint - writeto text or pict (only pict now??)
add consensus for aminos (only for nucs now)
add sequence documentation options (user additions + save current
genbank/embl/etc docs)
improve seq mask operations and usage
- annotate masks, choose which are used for pretty print, which for
align view
debug mswin save tableview picture as win metafile format (?)
add other child apps - primer analysis, others ??
add user-configurable menus - read all menus from config file?
add dialogs for configuring child-apps? (current html.form is now
a widespread syntax).
add variable color display in alignment window, as aids to aligning:
done/1. color change as alignment improves/worsens
2. mask colors (e.g., stem & loop areas for RNA)
add color picker dialog for color tables
add editable data table interface
add name window pane resizer
fix DAlnEditCommand to handle cut/copy/paste of selected block within
alignview (now only does full rows, selected alnindex)
add/create new main app for base calling from API/other traces, and
sequence assembly? - use autoseq.C (Reece Hart (reece@ibc.wustl.edu))
as ? extern-app or build into program? -- want to display traces +
called bases and allow user to edit bases...
add ORF maps, R.E. Maps, other items for sequence assembly validation?
add seq Annotation/Feature handling (part of seq documentaion handling), and
highlighting of bases by features.
add basic HTTP/HTML forms processing for simple cli/server dialogs
-- will want to hand off most result html docs to alt. viewer
add user-configurable menus - read all menus from config file?
add user-configurable dialogs - convert most to html forms?