// spup-updates.txt // seqpup v 0.5b, Jan 1996 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 --- todo fix mswin edit align text fix mswin rich text display (bombs on scroll of HELP doc !!) fix unix seqpup crash after installing new SeqPup.Prefs (rerun after install is okay) fix child app results - repeated runs sometimes will reopen old output files! - unix: fastdnaml fails to return results after 1st run? - various childapp usage failures unique to specific systems... 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 disjoint selections to DTableView -- need for copy/paste among masks (using table selection as clipboard for masks) add sequence documentation options (user additions + save current genbank/embl/etc docs) 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) improve seq mask operations and usage - annotate masks, choose which are used for pretty print, which for align view add color picker dialog for color tables add editable data table interface add name window pane resizer debug mswin save tableview picture as win metafile format (?) fix DAlnEditCommand to handle cut/copy/paste of selected block within alignview (now only does full rows, selected alnindex) fix bomb during cut/copy of pretty print view