conf/settings/AAConPresets.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <presets>\r
   3 <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
   4         <preset>\r
   5                 <name>Quick conservation</name>\r
   6                 <description>Collection of fast conservation methods</description>\r
   7                 <optlist>\r
   8                         <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option>\r
   9                 </optlist>\r
  10         </preset>\r
  11         <preset>\r
  12                 <name>Slow conservation</name>\r
  13                 <description>Collection of most expensive (slow) conservation methods</description>\r
  14                 <optlist>\r
  15                         <option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
  16                 </optlist>\r
  17         </preset>\r
  18         <preset>\r
  19                 <name>Complete conservation</name>\r
  20                 <description>Calculate conservation with all supported methods</description>\r
  21                 <optlist>\r
  22                         <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option><option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
  23                 </optlist>\r
  24         </preset>\r
  25 </presets>\r