[Avida-SVN] r3111 - in development: documentation source/actions

[blwalker at myxo.css.msu.edu]

Author: blwalker
Date: 2009-01-12 15:01:52 -0500 (Mon, 12 Jan 2009)
New Revision: 3111

Modified:
   development/documentation/actions.html
   development/source/actions/PopulationActions.cc
Log:

Fixed documentation for SetMutProb and ModMutProb.

'Cause, see, I wanted my events.cfg file to be readable, so I typed in the defaults instead of letting them default.  But the default mut_type value in the documentation was actually not a valid option at all, and there went 13 sets of 50 runs each, down the drain.

So I've fixed that, and added what the other options for mut_type are.


Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html	2009-01-12 18:08:54 UTC (rev 3110)
+++ development/documentation/actions.html	2009-01-12 20:01:52 UTC (rev 3111)
@@ -1224,8 +1224,9 @@
 </li>
 <li><p>
   <strong><a name="ModMutProb">ModMutProb</a></strong>
-  <i>[string mut_type="copy"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
+  <i>[string mut_type="COPY_MUT"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
   </p>
+    For a list of values for mut_type, see <a href="#SetMutProb">SetMutProb<a/>.
   <p>
   
   </p>
@@ -1322,8 +1323,15 @@
 </li>
 <li><p>
   <strong><a name="SetMutProb">SetMutProb</a></strong>
-  <i>[string mut_type="copy"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
+  <i>[string mut_type="COPY_MUT"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
   </p>
+    Values for mut_type are POINT, COPY_MUT, COPY_INS, COPY_DEL, COPY_UNIFORM, 
+  COPY_SLIP, DIV_MUT, DIV_INS, DIV_DEL, DIV_UNIFORM, DIV_SLIP, DIVIDE_MUT, 
+  DIVIDE_INS, DIVIDE_DEL, DIVIDE_UNIFORM, DIVIDE_SLIP, PARENT, INJECT_MUT, 
+  INJECT_INS, and INJECT_DEL.  These correspond to their counterparts in avida.cfg.
+  <br>
+  <br>
+  To turn off all mutations, use <a href="#ZeroMuts">ZeroMuts</a>.
   <p>
   
   </p>

Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc	2009-01-12 18:08:54 UTC (rev 3110)
+++ development/source/actions/PopulationActions.cc	2009-01-12 20:01:52 UTC (rev 3111)
@@ -1062,7 +1062,7 @@
     if (m_end > m_world->GetPopulation().GetSize()) m_end = m_world->GetPopulation().GetSize();
   }
   
-  static const cString GetDescription() { return "Arguments: [string mut_type='copy'] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]"; }
+  static const cString GetDescription() { return "Arguments: [string mut_type='COPY_MUT'] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]"; }
   
   void Process(cAvidaContext& ctx)
   {
@@ -1194,7 +1194,7 @@
       if (m_end > m_world->GetPopulation().GetSize()) m_end = m_world->GetPopulation().GetSize();
   }
   
-  static const cString GetDescription() { return "Arguments: [string mut_type='copy'] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]"; }
+  static const cString GetDescription() { return "Arguments: [string mut_type='COPY_MUT'] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]"; }
   
   void Process(cAvidaContext& ctx)
   {