[Avida-SVN] r1822 - in development: documentation source/main source/tools tests/_testrunner tests/analyze_truncate_lineage_fulllandscape
baerb at myxo.css.msu.edu
baerb at myxo.css.msu.edu
Thu Jul 19 06:57:08 PDT 2007
Author: baerb
Date: 2007-07-19 09:57:08 -0400 (Thu, 19 Jul 2007)
New Revision: 1822
Modified:
development/documentation/environment.html
development/source/main/cAvidaContext.h
development/source/main/cEnvReqs.h
development/source/main/cEnvironment.cc
development/source/main/cEnvironment.h
development/source/main/cResource.h
development/source/main/cSpatialCountElem.cc
development/source/main/cSpatialResCount.h
development/source/tools/cRandom.cc
development/source/tools/cRandom.h
development/tests/_testrunner/testrunner.py
development/tests/analyze_truncate_lineage_fulllandscape/test_list
Log:
Minor corrections to comments and documentation
Make test analyze_truncate_lineage_fulllandscape a long test
testrunner now prints out the name of the test it is performing (in addition
to the "x of y" notation).
Modified: development/documentation/environment.html
===================================================================
--- development/documentation/environment.html 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/documentation/environment.html 2007-07-19 13:57:08 UTC (rev 1822)
@@ -343,8 +343,8 @@
requisites on when they can occur.
</p>
-<h3>REACTION Command</h3>
- <pre>REACTION reaction_name task [process:...] [requisite:...]</pre>
+<h3><A NAME = "REACTION">REACTION Command</A></h3>
+ <pre>REACTION reaction_name task[:argument:...] [process:...] [requisite:...]</pre>
<blockquote>
<p>
Where <code>reaction_name</code> is a unique name for a reaction.
@@ -353,18 +353,22 @@
Where <code>task</code> is the name of the task that must be be performed to
trigger the reaction. A list of common tasks is listed in Table 3.
</P>
+ <P>
+ Where <code>argument</code> is a list of specific arguments needed by the
+ particular task.
+ </P>
Where <code>process</code> is a colon delimited list of information about how
resources are consumed/produced. Process settings are described in Table 4.
</P>
<p>
Where <code>requisite</code> is a colon delimited list describing when
reactions can be triggered. Requisite settings are described in Table 5.
- <p>
- Each reaction must have a task that triggers it. Currently, eighty tasks
- have been implemented, as summarized in the following table (in approximate
- order of complexity):
- </p>
</blockquote>
+<p>
+Each reaction must have a task that triggers it. Currently, eighty tasks
+have been implemented, as summarized in the following table (in approximate
+order of complexity):
+</p>
<div align="center">
<p> </p>
@@ -788,7 +792,7 @@
<h3>SET_ACTIVE Command</h3>
<p>
Allows user to activate or deactivate a reaction. If this command is not
-used all reactionsare active.
+used all reactions are active.
</p>
<pre>
<a name="SET_ACTIVE">SET_ACTIVE</a> type name new_status(default=true)
@@ -806,6 +810,7 @@
deactivate).
</Blockquote>
<p>
+<H3>MUTATION Command</H3>
O.K. I don't know what the following commands does, but it is in the code:
</P>
<pre>
Modified: development/source/main/cAvidaContext.h
===================================================================
--- development/source/main/cAvidaContext.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cAvidaContext.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -17,11 +17,15 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! Class to to hold a random number generator. Used to keep random
+ number creation in a given context seperate from rest of the program
+ helps with reapeatablity???? */
+
#ifndef cAvidaContext_h
#define cAvidaContext_h
Modified: development/source/main/cEnvReqs.h
===================================================================
--- development/source/main/cEnvReqs.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cEnvReqs.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -17,11 +17,12 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! Support for extensible input from the environment. */
#ifndef cEnvReqs_h
#define cEnvReqs_h
Modified: development/source/main/cEnvironment.cc
===================================================================
--- development/source/main/cEnvironment.cc 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cEnvironment.cc 2007-07-19 13:57:08 UTC (rev 1822)
@@ -18,11 +18,15 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! * Routines to read the environment files that contains information
+about resources and reactions (which allow rewards or punishments
+to organisms doing certain tasks). */
+
#include "cEnvironment.h"
#include "cAvidaContext.h"
@@ -408,11 +412,17 @@
bool cEnvironment::LoadCell(cString desc)
-/* Routine to read in spatial resources loaded in one cell at a time */
+/*****************************************************************************
+ Routine to read in spatial resources loaded in one cell at a time. Syntax:
+ CELL resource_name:cell_list[:options]
+
+ where options are initial, inflow and outflow
+*****************************************************************************/
+
{
if (desc.GetSize() == 0) {
- cerr << "Warning: Resource line with no resources listed." << endl;
+ cerr << "Warning: CELL line with no resources listed." << endl;
return false;
}
Modified: development/source/main/cEnvironment.h
===================================================================
--- development/source/main/cEnvironment.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cEnvironment.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -18,11 +18,15 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! Classes to hold information about the environmentthat contains information
+ about resources and reactions (which allow rewards or punishments
+ to organisms doing certain tasks). */
+
#ifndef cEnvironment_h
#define cEnvironment_h
Modified: development/source/main/cResource.h
===================================================================
--- development/source/main/cResource.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cResource.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -18,11 +18,13 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! Classes to held global and local information about a given resource */
+
#ifndef cResource_h
#define cResource_h
@@ -34,7 +36,7 @@
#endif
-/* class to hold resource informations for individual cells (mini-chemostats) */
+/*! class to hold resource information for individual cells (mini-chemostats) */
class cCellResource
{
Modified: development/source/main/cSpatialCountElem.cc
===================================================================
--- development/source/main/cSpatialCountElem.cc 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cSpatialCountElem.cc 2007-07-19 13:57:08 UTC (rev 1822)
@@ -18,11 +18,14 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/* Class to store information about amount of local/spatial resource in a
+ given cell. */
+
#include "cSpatialCountElem.h"
const int MAXFLOWPTS = 8;
Modified: development/source/main/cSpatialResCount.h
===================================================================
--- development/source/main/cSpatialResCount.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/main/cSpatialResCount.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -18,11 +18,13 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
+/*! Class to keep track of amounts of localized resources. */
+
#ifndef cSpatialResCount_h
#define cSpatialResCount_h
Modified: development/source/tools/cRandom.cc
===================================================================
--- development/source/tools/cRandom.cc 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/tools/cRandom.cc 2007-07-19 13:57:08 UTC (rev 1822)
@@ -236,7 +236,7 @@
int choice_num = 0;
// @CAO this could be done a lot faster when choose size is close to
- // full size. However we need to rememebr to watch out for larger num_in
+ // full size. However we need to remember to watch out for larger num_in
while (choice_num < out_array.GetSize()) {
int next = static_cast<int>(GetUInt(num_in));
Modified: development/source/tools/cRandom.h
===================================================================
--- development/source/tools/cRandom.h 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/source/tools/cRandom.h 2007-07-19 13:57:08 UTC (rev 1822)
@@ -37,7 +37,7 @@
tMemTrack<cRandom> mt;
#endif
protected:
- // Internal memebers
+ // Internal members
int seed;
int original_seed;
int inext;
Modified: development/tests/_testrunner/testrunner.py
===================================================================
--- development/tests/_testrunner/testrunner.py 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/tests/_testrunner/testrunner.py 2007-07-19 13:57:08 UTC (rev 1822)
@@ -788,7 +788,7 @@
sem.acquire()
ti += 1
- sys.stdout.write("\rPerforming Test: % 4d of %d" % (ti, len(tests)))
+ sys.stdout.write("\rPerforming Test: %4d of %d -- %-45s " % (ti, len(tests), test.name[:45]))
sys.stdout.flush()
tthread = threading.Thread(target=runTestWrapper, args=(test, sem))
tthread.start()
Modified: development/tests/analyze_truncate_lineage_fulllandscape/test_list
===================================================================
--- development/tests/analyze_truncate_lineage_fulllandscape/test_list 2007-07-19 03:20:43 UTC (rev 1821)
+++ development/tests/analyze_truncate_lineage_fulllandscape/test_list 2007-07-19 13:57:08 UTC (rev 1822)
@@ -13,7 +13,7 @@
[consistency]
enabled = yes ; Is this test a consistency test?
-long = no ; Is this test a long test?
+long = yes ; Is this test a long test?
[performance]
enabled = yes ; Is this test a performance test?
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