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History

SeqApp was started Sept. 1990 as MacApp sequence editor/analysis platform on which analysis programs from other authors, typically command line w/ weak user interfaces, could be easily incorporated into a useable Mac interface.

June/July 96: version 0.6d release

+ "bopper" Internet protocol for client/server use of command line programs such as the GCG suite.

+ autoseq base calling app for reading ABI and SCF sequencer trace file data, plus base/trace editing functions.

+ Started expanding maximum sequence limit to 2 megabases (from about 30Kb), however most functions beyond viewing will still fail for >30Kb sequences.

+ Several bug fixes are included for mac, mswin, unix. Added background color in align view, minimum ORF size pref, improved tracking of changed data, improved align editing, save pretty print to PICT or text; fixed child app bugs; fixed mswin edit truncation to 255 bases; editable data tables in selection dialogs

Jan. 96: version 0.5 of SeqPup.

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 mask sequence column (only when sequence mask mode 1..4 is selected in main window popup)

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

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 child app to new version 1.1.1

added configurable child-app launch parameters

-- dialogs in HTML.form format; needs more work, additions

added dna distance/similarity matrix function

added child apps: DeSoete's LSADT, Felsenstein's DrawTree & DrawGram

July 95: Version 0.4 of SeqPup.

This includes most of the features of its ancestor SeqApp. Alignment window: shift & slide sequences, copy/cut/paste/undo sequence entries among windows; Restriction maps and pretty print output; useable child apps for mac, mswin, and unix.

v0.4 corrections:

- File/Open for non-sequence data (text, rtf, etc.) has alternate open menu, to distinguish from sequence data. Added sequence append-open.

- Cut/copy/paste/undo for align-seq view now available

- Sequence menu items that are now ready: Consensus, Pretty print, Restriction Map, nucleic & amino codes. Some of these need further work (pretty, remap options).

- Child apps usage improved, may need more work though.

- The Mac/68K, Mac/PPC, MSWin, Unix now do Child applications.

- Include ClustalW, CAP, FastDNAml, child apps

- Restriction map function is extensively revised and improved.

- FindORF and Find string functions added

- Printing for pretty print, r.e.map now functional on Mac (and maybe MSWin)

v0.4 Known bugs and missing features (see above Bugs section for fuller list):

- Character editing (unlocked text) in the alignment (main) window is not working on Xwindow systems, and may be bugging in MSWindow and Mac systems.

- Single sequence editor (Sequence/Edit) is very slow for long sequences (6,000bases)

- Sequence menu items not yet ready : Dot plot.

- Child Apps fail in various ways on MSWindows and Unix systems.

-- CAP seems most likely to succeed completely.

-- ClustalW and FastDNAml may be launched and run properly, but SeqPup will fail to automatically open their results files.

- MSWindows and XWindows versions are less stable than Mac versions.

- XWindows versions reliable crash/core dump when Quit is chosen. This is an annoyance but doesn't seem to impair use.

- Internet menu needs testing & reworking - I haven't tested any of the e-mail services listed since last year.

- Nucleic codes picture shows PICT processing bug -- misplaced text, and an error in biology -- complement of W is W, not S, and complement of S is S, not W.

- Repeated copy/cut/paste of the alignment window entries might cause problems. Please let me know if you see this.

- There is no printing for X Window systems.

21 Mar 95: Second release of SeqPup, version 0.1.

This release has more parts of the SeqApp program put into it. This includes some alignment view manipulations, limited use of child applications, some undo-able commands, choosing data tables for colors, codon and r.enzymes. This release also includes much of the basics of GopherPup, including display of RTF, HTML, PICT, GIF document formats. However there is still some work to be done to let you open these w/o interpreting them as sequence data.

This release has just a Mac PowerPPC (SeqPup/PPC) and Mac 68000 processor (SeqPup/68K) versions. When more of the basic bugs are worked out, I'll try Sun and MSWindows versions.

v0.1 Known bugs/missing features:

- Use of character editing (unlocked text) in the alignment (main) window will lead to a crash after a few windows have been opened/closed or other manipulations performed.

- File/Open for non-sequence data (text, rtf, etc.) may well mistakenly identify them as sequence data. File/New is probably not doing anything useful, or bombing.

- Single sequence editor (Sequence/Edit) is very slow for long sequences (6,000bases)

- Single seq. editor may be failing in various ways (I've not looked at it carefully yet).

- No cut/copy/paste/undo for align-seq view yet (coming soon I hope).

- Internet menu needs reworking - I haven't tested any of the e-mail services listed there since last year.

- Sequence menu items not yet ready : Consensus, Pretty print, Restriction Map, Dot plot, nucleic & amino codes.

- Child apps usage needs more development to work smoothly.

- The Mac/68K version fails when using Child applications.

- Only the ClustalW child app is ready for distribution (may have FastDNAml, CAP, and DNAml soon -- let me know of programs you would like to see here).

1 Mar 94: First public release of SeqPup, version -1.

It has plenty of bugs and missing features, including:

no Undo (this is a real bite to those used to it)

mostly no cut/copy/paste/clear

limited printing of documents or views

mostly no align-view manipulations (move,cut/copy,edit in place, shift, ...)

no pretty print views

no restriction maps

no dot plots

no ...

problems w/ window display & keeping track of active window (x,mswin)

I'll be adding back many of these features from the Macintosh SeqApp as time permits.

SeqApp 12+ June 93, version 1.9a157+

a semi-major update, and time extension release with various enhancements and corrections. These include

-- lock/unlock indels (alignment gaps). Useful when sliding bases around

during hand alignment, to keep alignment fixed in some sections.

-- color amino (and nucleic) acids of your choice.

-- added support for more sequence file formats: MSF, PAUP, PIR. SeqApp now relies on the current Readseq code for sequence reading & writing.

-- save selection option to save subset of bases to file.

-- addition the useful contig assembly program CAP, written by Xiaoqiu Huang.

-- major revision of preference saving method (less buggy, I hope)

-- major revision of the underlying application framework, due to moving from MacApp 2 to MacApp 3.

-- fixed a bug that caused loss of data when alignment with a selection was saved to disk.

5 Oct 92, version 1.8a152+ -- a semi-major update with various enhancements and corrections. These include

- corrections to the main alignment display,

- improvements to the help system,

- major changes to the sequence print-out options,

-- including addition of a dotplot display (curtesy of DottyPlot),

-- a phylogeny tree display (curtesy of TreeDraw Deck & J. Felsenstein's DrawTree),

-- improved Pretty Print, which now has a single sequence form and a better aligned sequence form,

-- improved Restriction map display,

- addition and updating of several e-mail service links,

-- including Blast Search and Genbank Fetch via NCBI,

-- BLOCKS, Genmark, and Pythia services,

- updated Internet gopher client (equal to GopherApp),

- editable Child Tasks dialogs

- addition of links to Phylip applications as Child Tasks

- addition of Phylip interleaved format as sequence output option

11 June 92, version 1.6a35 is primarily a bug fix release. Several of the disasterous bugs have been squashed. This version now works on the Mac SE model, except for sendmail. No new features have been added.

7Jun92, v. 1.5a?? -- fixed several of the causes of mysterious bombs (mostly uninitialized handles), link b/n multiseq and 1-seq views is better now, folded in GopherApp updates, death date moved to Jan 93,

25Mar92, v1.5a32 (or later). First release to general public. Includes Internet Gopher client. Also released subset as GopherApp for non-biologists.

4Mar92, v 1.4a38 -- added base sliding in align view. Bases now slide something like beads on an abucus. Select a section with mouse, then grab section and shift left or right. Gaps are inserted/removed as needed. For use as contig aligner, still needs equivalent of GCG GelOverlap to automatically find contig/fragment overlaps.

Also added "Degap" menu item, to remove "." and "-". Fixed several small bugs including Align pretty print which again should display.

2Mar92, v 1.4a19 -- fixed several annoying bugs, see SeqApp.Help, section on bugs for their resolution. These include Complement/Reverse/Dna2Rna/ Translation which should work now in align view; Consensus menu item; entering sequence in align window now doesn't freeze after 30+ bases; pearson/fasta format reading; ...

10Feb92, v 1.4a6 -- fix for Mac System 6; add Internet service dialogs for Univ. Houston gene-server, Geneid @ BU, Grail @ ORNL; correct About Clustalv attribution.

5Feb92, v 1.4a4 -- limited release to network resource managers, clustalv authors, testers.

Vers 1.4, Dec91 - Feb92. Dropped multi-sequence picker window, made multi-align window the primary view (no need for both; extra confusion for users). added pretty print, restriction map, sequence conversions. Generalized "call clustal" to Hypercard-like, System 7 aware menu for calling external tasks. Fleshed out internet e-mail objects, added help objects, window menu, nucleic/amino help windows. Many major/minor revisions to all aspects to clean out bugs. Preliminary release to a limited set of testers (1.4a?)

Vers. 1.3, Sept - Dec91. Modified clustalv for use as external app (commandline file, background task, ...). Added basic Internet e-mail routines call clustal routine (preliminary child task) Many major/minor revisions to all aspects to clean out bugs.

Jun91-Aug91: overwork at other tasks kept SeqApp on back burner.

Mar91-Jun91: not much work on SeqApp, fleshed out TCP methods (UTCP, USMTP, UPOP).

Feb 1991, vers 1.2? made available to Indiana University biologists and NCBI biocomputists.

Vers. 1.1, Oct 1990, multiple sequence picker and multiple sequence alignement window, including colored bases, added to deal with alignment and common multi-sequence file formats.

Version 1, Sep 1990. Single sequence edit window + TextEdit window, from MacApp skeleton/example source + readseq.


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