olle@isagel.sunet.se (Olle Nilsson at ISAGEL.SUNET.SE) (08/13/88)
I am looking for a Mac program that can handle block-character inversions
of text. Why? We are a group of scientists (Oh yes. Molecular Biology!)
working with DNA and peptide sequences, and we would like to invert areas of
text (sequence symbol characters) that are of interest in a larger manu-
script of text.
Example:
1 50
B1.GSP MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGL..HNVSI SQVELRSHIQ
T4B1.GSP .MQLINVIKS SGVSQSFDPQ KIIKVLSWAA EG.....TSV DPYELYENIK
M1.GSP ....MHVIKR DG.RQRVMFD KITSRIQKLC YGLNMDFVDP AQITMKV.IQ
VZVB1.GSP .......... .......... .......MEF KRIFNTVHDI INRLCQHGYK
HSV1B1.GSP ALMLEYFCRC AREETKRVPP RTFGSPPRLT EDDFGLLNYA LVEMQRLCLD
HSV2B1.GSP ALMLEYFCRC AREDSKRVPP RTFGSAPRLT EDDFGLLNYA LAEMRRLCLD
EBVB1.GSP .......... .......... .......... .......... ..........
Consensus ---------- ---------- ---------- ---------- ----------
51 100
B1.GSP FYDGIKTSDI HETIIKAAAD LISRDAPDYQ YLAARLAIFH LRKKAYGQFE
T4B1.GSP SYLRDGMTTD DIQTIVIKAA ANSISVEEPD YQYVAARCLM FALRKHVYGQ
M1.GSP GLYSGVTTVE ldtlaaetaa TLTTKHPDYA ILAARIAVSN LHKETKKVFS
VZVB1.GSP EYIIPPESTT PVElmeyisT IVSKLKAVTR QDERVYRCCG ELIHCRINLR
HSV1B1.GSP VPPVPPNAYM Pyylreyvtr LVNGFKPLVS RSARLYRILG VLVHLRIRTR
HSV2B1.GSP LPPVPPNAYT pyhlreyaTR LVNGLKPLVR RSARLYRILG ILVHLRIRTR
EBVB1.GSP MATTSHVEHE LLSKLIDELK VKANSDPEAD VLAGRLLHRL KAESVTHTVA
Consensus ---------- ---------- ---------- ---------- ----------
I might want to "box in" or rather invert the area here marked with non-versals
(small characters) since I cannot post an item with inverted text. You'll find
the area in the region with sequence number 60-70.
I have used MacDraft, FreeHand etc to do this, but MacDraft is not precice
in printing on a LaserWriter Plus, and FreeHand is a bit uncomfortable to work
with to do this simple task (though it can produce perfect printouts!)
-----
Requirements for this unknown program:
1. The program MUST treet all characters with equal length, so that lines
of characters can be aligned. If possible even with proportional fonts,
bold, outline e.t.c.
2. The inverted area of text must be precise. No overlaps between characters.
And it must print out well enough for submission to a journal.
3. It MUST be easy to invert the text. Preferable this could be done by
a normal mouse click-and-select of one string of characters and then a
selection of an invert option somewhere. (Why not Cmd-I?)
4. The program must handle pages of text (alignments) easily. Alignments can
be longer then one A4. And the page format can be landscape or portrait.
5. It would help if the text could be imported to this unexisting (?)
program in many different formats. Text, WriteNow, Word and MacWrite.
It would be even better is the output of this program could be pasted in
to a word-processor document without loss of quality.
6. Of course. The program must be able to print out the processed
(now "slightly" inverted) text on a LaserWritePlus in any font size.
We noramlly use 5-12 points for alignment printouts.
-----
Could it be possible to write a patch to WriteNow or Word to produce in-
verted text? We use WN, and the task could be done easily if one could
handle inversions, and printouts of inversions on a laser, with a normal
word processor. The Currier font would take care of the character-by-character
alignment of sequences.
If there is someone knowing of such a program, could you please e-mail me.
If any one would be interested to develop such a program, I could probably
find a market for it. Contact me.
________________________________________________________________________________
____ . Olle Nilsson
/ / . Dept. of Molecular Biology, University of Stockholm, Sweden
/___/ o . OLLE@ISAGEL.SUNET.SE (@SEKTH.BITNET)
________________________________________________________________________________stejk@caen.engin.umich.edu (Steven J Kassarjian) (08/15/88)
In article <159@isagel.sunet.se>, olle@isagel.sunet.se (Olle Nilsson at ISAGEL.SUNET.SE) writes: > I am looking for a Mac program that can handle block-character inversions > of text. Why? We are a group of scientists (Oh yes. Molecular Biology!) > working with DNA and peptide sequences, and we would like to invert areas of > text (sequence symbol characters) that are of interest in a larger manu- > script of text. There may be such a word processor with that feature, but I haven't heard of it (but then I haven't been looking :-). A solution to your need may be to edit an existing font, making it the inverse of what it was originally was. Then of course you could use any word processor you preferred. Let's see. ResEdit can edit bit-map fonts, but there are better ones available. Fontographer (my memory is not clear here) can edit Postscript fonts. good luck! steve. steve kassarjian +-----------------------------------------------------------------+ | All opinions are Eunichs: the operating | | local and undefined system for | | outside of unit. real men. | +-----------------------------------------------------------------+ stejk@caen.engin.umich.edu