Draw pretty views of biosequences, Java command-line version,
     to output in various graphic formats.
  
  drawseq example 

  Usage: jre -cp drawseq.jar run [options] input-file(s)

  Options
    styles=seqstyle.properties  use file with style properties instead of defaults
    colors=seqcolor.properties  use file with base color properties instead of defaults

    format=name         Format name for output
          see Formats   list below for names

    out[put]=out.pict   output file name
    in[put]=input.seq   input file name ('in=' not required)

    nativeawt           use native AWT toolkit (not good for Unix commandline use)
    pipe                Pipe (command line, stdout)
    verb[ose]           Verbose progress
    inform[at]=#        input sequence format number,  or
    inform[at]=Name     input sequence format name.  Assume input data is this format

    range=10..100       select sequences subrange
    range=join(10..100,200..300,500..600)
          
    feat[ures]=exon,CDS...   extract sequence of selected features
    nofeat[ures]=repeat_region,intron... remove sequence of selected features 
          Can't mix feature and nofeature. 
          Applies only with input feature tables.
          

   Styles values include (see example styles file for more)
    Sequence.width=50          sequence line width
    Sequence.nameleft=false    name on left/right side
    Sequence.nameright=true
    Sequence.numleft=true      seq index on left/right side
    Sequence.numright=true
    Sequence.numtop=true       index on top/bottom
    Sequence.numbot=false

This program requires a Java runtime (jre) program, version 1.1.x 
All non-options (no '=') are used as input file names.



Drawseq version 1.0 (7++ September 1999)

Home of this package is http://iubio.bio.indiana.edu/soft/molbio/java/apps/drawseq/

An instance of the Web form for this is http://iubio.bio.indiana.edu/cgi-bin/drawseq.cgi


Available graphic output formats:
application/pdf
image/pict
image/gif
application/postscript
application/printer
Available biosequence input formats:
 ID  Name             Read  Document  
  1  IG|Stanford      yes        --   
  2  GenBank|GB       yes       yes   
  3  NBRF             yes        --   
  4  EMBL             yes       yes   
  5  GCG              yes        --   
  6  DNAStrider       yes        --   
  8  Pearson|Fasta    yes        --   
 11  Phylip3.2        yes        --   
 12  Phylip|Phylip4   yes        --   
 13  Plain|Raw        yes        --   
 14  PIR|CODATA       yes        --   
 15  MSF              yes        --   
 17  PAUP|NEXUS       yes        --   
 19  BLAST            yes        --   
 20  XML              yes       yes   

Also available in this package:

For the current help document, use
jre -cp drawseq.jar help


  Graphic interface to Drawseq (Java swing)
  Usage:
    java -cp drawseq.jar iubio.drawseq.app (java version 1.2)
    jre -cp drawseq.jar:/path/to/swingall.jar iubio.drawseq.app (java version 1.1.x)
  Drawseq version 1.0 (7++ September 1999)

  Java Foundation Classes (Swing) are required for this interface
  This is available for Java versions 1.1.7 and newer at
     http://java.sun.com/products/jfc/download.html
  Put the swingall.jar of this package in your classpath, as with
    jre -cp drawseq.jar:swingall.jar iubio.drawseq.app (java version 1.1.x)

  Macintosh users: See also Drawseq.macapp, a small Mac Java application
  to launch drawseq.jar without a jre commandline.


HTTP server common gateway interface to Drawseq Usage (example as cgi on unix system): Install shell script like this as '/cgi-bin/drawseq.cgi' for your web server #!/bin/sh envtemp=/tmp/rseq$$.env env > ${envtemp} /usr/java/bin/jre -cp drawseq.jar iubio.drawseq.cgi env=${envtemp} /bin/rm ${envtemp} Drawseq version 1.0 (7++ September 1999) See also iubio.drawseq.run.usage()