gnomap, a Genome map drawing program
d.g. gilbert (gilbertd@bio.indiana.edu)

This is in development, May 2000
You can find a 'live' use of gnomap in the Eukaryotes gene summary at
http://iubio.bio.indiana.edu/eugenes/
Look for chromosome maps in the Fly, Worm, Weed or Yeast sections.

See the file gnomaptest-X.tsv for example data, which is tab-separated-values in this format
#Feature gene    map     range   id      db_xref notes
source  worm    Chr X   1..36900        -
gene    CTEL7X  -       1..2649 -       -       -
tandem_repeat   -       -       129..203        -       -       Note  "4 copies of 15mer"
inverted_repeat -       -       392..434        -       -       Note  "loop 1779, 1 gap"
gene    cTel7X.1        -       complement(709..1328)   MEOW:CEgn0007267        -       -
CDS     cTel7X.1        -       complement(join(709..822,1182..1328))   MEOW:CEgn0007267                
mRNA    cTel7X.1        -       complement(join(709..822,1182..1328))   MEOW:CEgn0007267                
tandem_repeat   -       -       2382..2645      -       -       Note  "43 copies of 6mer"


 ------ summary of gnomap, genome map drawer usage -------
 example java calling command lines (e.g. for Unix system, like will work on MacOS and MSWin)
  jre -Dawt.toolkit=flybase.graf.NullToolkit -cp .:gnomap.jar:readseq.jar flybase.GnoMap httpcall style=pdf spp=worm chr=X bp=1..36900 dataname=gnomaptest env=MAP_DATA=testd/ 
  jre -Dawt.toolkit=flybase.graf.NullToolkit -cp .:gnomap.jar:readseq.jar flybase.GnoMap httpcall debug=1 style=pdf spp=worm chr=X bp=1..36900

 jre parameter -Dawt.toolkit=flybase.graf.NullToolkit 
   is required to run without an OS graphics environment (e.g. Unix commandline w/o XWindows)

 example command set for MacOS MRJ's commandline equivalent
 com.apple.mrj.application.main = flybase.GnoMap
 com.apple.mrj.application.classpath = $APPLICATION/gnomap.jar:$APPLICATION/readseq.jar:$BOOTCLASSPATH 
 com.apple.mrj.application.parameters = style=pdf spp=worm chr=X bp=1..36900 env=MAP_DATA=testd/ dataname=gnomaptest 

 program parameters:
 dataname=xxx and env=MAP_DATA=testd/  - locate input data of this format (tab-separated-values, fields as below)
 data file must now be named 'gnomaptest-X.tsv' in folder testd/worm/ 
 to match spp=worm chr=X and dataname=gnomaptest
 Note that program chooses file name based on chr,spp,bp options
 and will not make new output if one of same name exists

 httpcall -- caller is http server, need now for unix call (small bug)
 chr=X -- chromosome name
 spp=worm -- species name
 bp=1..36900 -- base range to display (otherwise it draws overview map)
 style=pdf or style=html -- for output formats 
 add debug=1 option to get debug output

 See also gnomap.properties to set defaults of some of above 
   (MAP_DATA, MAP_PIX, dataname, ...)