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>\r
   7             Collection of fast conservation methods\r
   8         </description>\r
   9         <optlist>\r
  10             <option>-m=KABAT</option>\r
  11             <option>-m=JORES</option>\r
  12             <option>-m=SCHNEIDER</option>\r
  13             <option>-m=SHENKIN</option>\r
  14             <option>-m=GERSTEIN</option>\r
  15             <option>-m=TAYLOR_GAPS</option>\r
  16             <option>-m=TAYLOR_NO_GAPS</option>\r
  17             <option>-m=ZVELIBIL</option>\r
  18             <option>-m=ARMON</option>\r
  19             <option>-m=THOMPSON</option>\r
  20             <option>-m=NOT_LANCET</option>\r
  21             <option>-m=MIRNY</option>\r
  22             <option>-m=WILLIAMSON</option>\r
  23         </optlist>\r
  24     </preset>\r
  25 \r
  26     <preset>\r
  27         <name>Slow conservation</name>\r
  28         <description>\r
  29             Collection of most expensive (slow) conservation methods\r
  30         </description>\r
  31         <optlist>\r
  32             <option>-m=LANDGRAF</option>\r
  33             <option>-m=KARLIN</option>\r
  34             <option>-m=SANDER</option>\r
  35             <option>-m=VALDAR</option>\r
  36             <option>-m=SMERFS</option>\r
  37         </optlist>\r
  38     </preset>\r
  39 \r
  40     <preset>\r
  41         <name>Complete conservation</name>\r
  42         <description>\r
  43             Calculate conservation with all supported methods\r
  44         </description>\r
  45         <optlist>\r
  46             <option>-m=KABAT</option>\r
  47             <option>-m=JORES</option>\r
  48             <option>-m=SCHNEIDER</option>\r
  49             <option>-m=SHENKIN</option>\r
  50             <option>-m=GERSTEIN</option>\r
  51             <option>-m=TAYLOR_GAPS</option>\r
  52             <option>-m=TAYLOR_NO_GAPS</option>\r
  53             <option>-m=ZVELIBIL</option>\r
  54             <option>-m=ARMON</option>\r
  55             <option>-m=THOMPSON</option>\r
  56             <option>-m=NOT_LANCET</option>\r
  57             <option>-m=MIRNY</option>\r
  58             <option>-m=WILLIAMSON</option>\r
  59             <option>-m=LANDGRAF</option>\r
  60             <option>-m=KARLIN</option>\r
  61             <option>-m=SANDER</option>\r
  62             <option>-m=VALDAR</option>\r
  63             <option>-m=SMERFS</option>\r
  64         </optlist>\r
  65     </preset>\r
  66 </presets>\r