[Avida-SVN] r3031 - development/source/cpu

[brysonda at myxo.css.msu.edu]

Author: brysonda
Date: 2008-12-13 15:30:00 -0500 (Sat, 13 Dec 2008)
New Revision: 3031

Modified:
   development/source/cpu/cHardwareCPU.cc
   development/source/cpu/cHardwareExperimental.cc
   development/source/cpu/cHardwareExperimental.h
Log:
Implement all on copy mutation types in cHardwareExperimental.
Remove extraneous if block in cHardwareCPU::Inst_HeadCopy.

Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc	2008-12-12 22:25:32 UTC (rev 3030)
+++ development/source/cpu/cHardwareCPU.cc	2008-12-13 20:30:00 UTC (rev 3031)
@@ -523,9 +523,7 @@
 : cHardwareBase(world, in_organism, in_m_inst_set)
 , m_last_cell_data(false, 0)
 {
-  /* FIXME:  reorganize storage of m_functions.  -- kgn */
   m_functions = s_inst_slib->GetFunctions();
-  /**/
   
   m_spec_die = false;
   m_epigenetic_state = false;
@@ -5049,12 +5047,6 @@
   
   read_head.Advance();
   write_head.Advance();
-  
-  //Slip mutations
-   if (m_organism->TestCopySlip(ctx)) {
-    
-  }
-  
   return true;
 }
 

Modified: development/source/cpu/cHardwareExperimental.cc
===================================================================
--- development/source/cpu/cHardwareExperimental.cc	2008-12-12 22:25:32 UTC (rev 3030)
+++ development/source/cpu/cHardwareExperimental.cc	2008-12-13 20:30:00 UTC (rev 3031)
@@ -206,9 +206,7 @@
 cHardwareExperimental::cHardwareExperimental(cAvidaContext& ctx, cWorld* world, cOrganism* in_organism, cInstSet* in_m_inst_set)
 : cHardwareBase(world, in_organism, in_m_inst_set)
 {
-  /* FIXME:  reorganize storage of m_functions.  -- kgn */
   m_functions = s_inst_slib->GetFunctions();
-  /**/
   
   m_spec_die = false;
 
@@ -218,6 +216,8 @@
   m_promoters_enabled = m_world->GetConfig().PROMOTERS_ENABLED.Get();
   m_constituative_regulation = m_world->GetConfig().CONSTITUTIVE_REGULATION.Get();
   
+  m_slip_read_head = !m_world->GetConfig().SLIP_COPY_MODE.Get();
+  
   m_memory = in_organism->GetGenome();  // Initialize memory...
   Reset(ctx);                            // Setup the rest of the hardware...
 }
@@ -1368,6 +1368,9 @@
   setInternalValue(m_threads[m_cur_thread].reg[dst], read_inst);
   ReadInst(read_inst);
   
+  if (m_slip_read_head && m_organism->TestCopySlip(ctx))
+    GetHead(head_id).Set(ctx.GetRandom().GetInt(GetHead(head_id).GetMemory().GetSize()));
+  
   GetHead(head_id).Advance();
   return true;
 }
@@ -1386,6 +1389,12 @@
   active_head.SetInst(cInstruction(value));
   active_head.SetFlagCopied();
   
+  if (m_organism->TestCopyIns(ctx)) active_head.InsertInst(m_inst_set->GetRandomInst(ctx));
+  if (m_organism->TestCopyDel(ctx)) active_head.RemoveInst();
+  if (m_organism->TestCopyUniform(ctx)) doUniformCopyMutation(ctx, active_head);
+  if (!m_slip_read_head && m_organism->TestCopySlip(ctx)) 
+    doSlipMutation(ctx, active_head.GetMemory(), active_head.GetPosition());
+  
   // Advance the head after write...
   active_head++;
   return true;
@@ -1412,6 +1421,16 @@
   write_head.SetInst(read_inst);
   write_head.SetFlagCopied();  // Set the copied flag...
   
+  if (m_organism->TestCopyIns(ctx)) write_head.InsertInst(m_inst_set->GetRandomInst(ctx));
+  if (m_organism->TestCopyDel(ctx)) write_head.RemoveInst();
+  if (m_organism->TestCopyUniform(ctx)) doUniformCopyMutation(ctx, write_head);
+  if (m_organism->TestCopySlip(ctx)) {
+    if (m_slip_read_head) {
+      read_head.Set(ctx.GetRandom().GetInt(read_head.GetMemory().GetSize()));
+    } else 
+      doSlipMutation(ctx, write_head.GetMemory(), write_head.GetPosition());
+  }
+  
   read_head.Advance();
   write_head.Advance();
   return true;

Modified: development/source/cpu/cHardwareExperimental.h
===================================================================
--- development/source/cpu/cHardwareExperimental.h	2008-12-12 22:25:32 UTC (rev 3030)
+++ development/source/cpu/cHardwareExperimental.h	2008-12-13 20:30:00 UTC (rev 3031)
@@ -56,6 +56,9 @@
 #ifndef tArray_h
 #include "tArray.h"
 #endif
+#ifndef tManagedPointerArray_h
+#include "tManagedPointerArray.h"
+#endif
 #ifndef tInstLib_h
 #include "tInstLib.h"
 #endif
@@ -195,6 +198,8 @@
     bool m_promoters_enabled:1;
     bool m_constituative_regulation:1;
     
+    bool m_slip_read_head:1;
+
     bool m_io_expire:1;
   };
   
@@ -215,7 +220,7 @@
     inline int GetRegulatedBitCode() { return m_bit_code ^ m_regulation; }
     inline ~cPromoter() { ; }
   };
-  tArray<cPromoter> m_promoters;
+  tManagedPointerArray<cPromoter> m_promoters;
   // Promoter Model -->