// spup-updates.txt
// seqpup v 0.6 + 0.5a updates

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

-- ?? vers. 0.6 --

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 of 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 

fixed - mswin edits were truncated to 255 chars (vibtext)

fixed various crash bugs - close, quit failures

fixed child apps where repeated runs would reopen old output files

added seqprint/pretty print save to file in text or pict format - 
    see seqprint prefs dialog

added background coloring and background alignment greyscale to align
     view color options
     
added minimum ORF size preference (seq prefs dialog) to all orf finding

improved tracking of changed data and automatic "Save document?" prompt
  if dirty; added underlining names to show dirty seqs
  
added  "revert to saved file" menu choice

added dialog to locate data files if not automatically found

added editable data table interface, for data choosing dialogs (codons, colors, 
  styles, etc).

added preliminary sequence assembly doc and autoseq base calling child app

improved BOP usage and autoseq data editing (v.0.6d)

fixed another pathname space problem when calling child apps (Mac only, v0.6e)


in progress
------------

added (0.6b) network "child-apps" - called now BOP - 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 fixups?;
     problems w/ tcp failures; need to handle gcg graphics!;
  >> wrote "bopper" program for Unix servers to handle BOP client/server
     Internet interactions with SeqPup.   Taken from popper, allows
     server to offer biocomputing services to individual users w/ passworded
     accounts on server.   See bopper distribution source at
     //iubio.bio.indiana.edu/util/dclap/source/ 
  
added (0.6c) sequence assembly and handling of base calling child app (autoseq
		from Reece Hart).  Very preliminary, but autoseq will read ABI and SCF
		sequencer trace files, and convert to bases.  Seqpup will read the 
		output of autoseq and display bases + traces, and bases can be copied/edited
		into regular alignment set.  Yet to do (much...) -
		better integration, output format (? same as autoseq's 5 files?) for
		called bases + traces, ORF and other views for easy assembly of autoseq
		sections; CAP/other autoasmbly?.
		
		
added/improve (0.6a) max. sequence length to be handled, from kilobases to megabases
  (target is 10MB sequences) -- ? use disk caching of seq. segments
	 >> can now open a 2MB sequence (e.g., the H.flu genome), but still  
	 >> can't do much  with it.

added  (0.6a) 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
  

todo
-----------

add undo for edit text in aln window

fix mswin/unix edit align text - when scrolled, esp. to far right, edit
  text is offset right from real position.

fix mswin rich text display (bombs on scroll of HELP doc!)
	-- 32bit version only; 16bit version seems okay
 -- ? unix also bombs on rtf display (HELP doc)
 
fix child app - unix: fastdnaml fails to return results after 1st run?
 
fix - linux only -- can't edit in multi-align view yet (can but edit
   seq doesn't display...).  Other unices are okay here I think.
   
fix - unices won't take longs for draw point/rect values -- end up w/
   displays offset or worse.  Mac/MSWin have been converted to long
   x,y values
   
fix - unices don't display background color in multalign view

add reduced magnification for align windows and pretty prints
  (e.g., one base per pixel or less)
  
add consensus for aminos (only for nucs now)
 --> fixed to skip amino seqs for now
 
add direct button/link from pretty print doc to pretty option controls !
  (easy to miss options like colored bases that are available!)

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 dotplot

add ORF maps, R.E. Maps, other items for sequence assembly validation?

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...

>> integrate basecalling trace display, ORF & RE maps with align window
>> for single seq, base-by-base graphic views ?

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 table

add rest. enzyme picker dialog for renzyme table

add name window pane resizer

add/enable background color options for align displays

fix DAlnEditCommand to handle cut/copy/paste of selected block within
    alignview (now only does full rows, selected alnindex)

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?