[Avida-SVN] r1249 - in development: Avida.xcodeproj documentation documentation/glossary source/analyze
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Thu Feb 8 13:47:34 PST 2007
Author: blwalker
Date: 2007-02-08 16:47:33 -0500 (Thu, 08 Feb 2007)
New Revision: 1249
Added:
development/documentation/glossary/help.Complement-Label.html
development/documentation/glossary/help.Label.html
Removed:
development/documentation/glossary/help.Complement-Template.html
development/documentation/glossary/help.Template.html
Modified:
development/Avida.xcodeproj/project.pbxproj
development/documentation/inst_set.html
development/source/analyze/cAnalyze.cc
Log:
fixed mispelling of "lineage" in analyze warnings (was "linege")
some typo cleanup in inst_set.html
changed inst_set.html and relevant glossary htmls to refer to labels instead of templates, as that's the term we use most often now; also changed the names of the relevant glossary htmls
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/Avida.xcodeproj/project.pbxproj 2007-02-08 21:47:33 UTC (rev 1249)
@@ -381,6 +381,23 @@
};
/* End PBXBuildRule section */
+/* Begin PBXBuildStyle section */
+ 156428B60AD599A7000248FB /* Development */ = {
+ isa = PBXBuildStyle;
+ buildSettings = {
+ COPY_PHASE_STRIP = NO;
+ };
+ name = Development;
+ };
+ 156428B70AD599A7000248FB /* Deployment */ = {
+ isa = PBXBuildStyle;
+ buildSettings = {
+ COPY_PHASE_STRIP = YES;
+ };
+ name = Deployment;
+ };
+/* End PBXBuildStyle section */
+
/* Begin PBXContainerItemProxy section */
70DCF67509D4E10500924128 /* PBXContainerItemProxy */ = {
isa = PBXContainerItemProxy;
@@ -1833,6 +1850,12 @@
DCC30C4D0762532C008F7A48 /* Project object */ = {
isa = PBXProject;
buildConfigurationList = 702442D70859E0B00059BD9B /* Build configuration list for PBXProject "Avida" */;
+ buildSettings = {
+ };
+ buildStyles = (
+ 156428B60AD599A7000248FB /* Development */,
+ 156428B70AD599A7000248FB /* Deployment */,
+ );
hasScannedForEncodings = 0;
mainGroup = DCC30C490762532C008F7A48;
productRefGroup = DCC3164E07626CF3008F7A48 /* Products */;
Copied: development/documentation/glossary/help.Complement-Label.html (from rev 1248, development/documentation/glossary/help.Complement-Template.html)
===================================================================
--- development/documentation/glossary/help.Complement-Template.html 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/documentation/glossary/help.Complement-Label.html 2007-02-08 21:47:33 UTC (rev 1249)
@@ -0,0 +1,10 @@
+<html>
+<title>Other Notation : Complement-Label</title>
+
+<h1>Complement-Label</h1>
+
+The complement of a <a href="help.Label.html">label</a> is found by taking each
+<a href="help.nop-instructions.html">no-operation</a> instruction that makes up that label,
+and shifting it to the next in alphabetical order, looping around at the end.
+Thus, in the default instruction set, nop-A -> nop-B -> nop-C -> nop-A. The label
+"nop-B nop-A nop-C nop-C" has the complement "nop-C nop-B nop-A nop-A".
Deleted: development/documentation/glossary/help.Complement-Template.html
===================================================================
--- development/documentation/glossary/help.Complement-Template.html 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/documentation/glossary/help.Complement-Template.html 2007-02-08 21:47:33 UTC (rev 1249)
@@ -1,6 +0,0 @@
-<html>
-<title>Other Notation : Complement-Template</title>
-
-<h1>Complement-Template</h1>
-
-The complement of a <a href="help.Template.html">template</a> is found by taking each <a href="help.nop-instructions.html">no-operation</a> instruction that makes up that template, and shifting it to the next in alphabetical order, looping around at the end. Thus, in the default instruction set, nop-A -> nop-B -> nop-C -> nop-A. The template "nop-B nop-A nop-C nop-C" has the complement "nop-C nop-B nop-A nop-A".
Copied: development/documentation/glossary/help.Label.html (from rev 1248, development/documentation/glossary/help.Template.html)
===================================================================
--- development/documentation/glossary/help.Template.html 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/documentation/glossary/help.Label.html 2007-02-08 21:47:33 UTC (rev 1249)
@@ -0,0 +1,12 @@
+<html>
+<title>Other Notation : Label</title>
+
+<h1>Label</h1>
+
+A label (sometimes called a template -- for example, in biology) is a sequence of
+<a href="help.nop-instructions.html">no-operation</a> instructions used to mark
+regions of code within a <a href="help.Genome.html">genome</a>. Some instructions
+(such a <a href="help.h-search.html">h-search</a>) are followed by a label; the
+<a href="help.Complement-Label.html">complement</a> of that label is then used
+to match against other labels. See the descriptions of the individual
+<a href="help.Instruction.html">instructions</a> for how they use labels.
Deleted: development/documentation/glossary/help.Template.html
===================================================================
--- development/documentation/glossary/help.Template.html 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/documentation/glossary/help.Template.html 2007-02-08 21:47:33 UTC (rev 1249)
@@ -1,6 +0,0 @@
-<html>
-<title>Other Notation : Template</title>
-
-<h1>Template</h1>
-
-A template (sometimes called a label) is a sequence of <a href="help.nop-instructions.html">no-operation</a> instructions used to mark regions of code within a <a href="help.Genome.html">genome</a>. Some instructions (such a <a href="help.h-search.html">h-search</a>) are followed by a template; the <a href="help.Complement-Template.html">complement</a> of that template is then used to match against other templates. See the descriptions of the individual <a href="help.Instruction.html">instructions</a> for how they use templates.
Modified: development/documentation/inst_set.html
===================================================================
--- development/documentation/inst_set.html 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/documentation/inst_set.html 2007-02-08 21:47:33 UTC (rev 1249)
@@ -91,7 +91,7 @@
component that it affects; see also
<a href="glossary/help.Nop-Register-Notation.html">nop-register</a> notation and
<a href="glossary/help.Nop-Head-Notation.html">nop-head</a> notation) or act as part
-of a <a href="glossary/help.Template.html">template</a> to denote positions in the
+of a <a href="glossary/help.Label.html">label</a> to denote positions in the
<a href="glossary/help.Genome.html">genome</a>.
@@ -99,7 +99,7 @@
This instruction compares the
<a href="glossary/help.Nop-Register-Notation.html">?BX?</a> register to its
-<a href="glossary/help.Complement-Template.html">complement</a>. If they are not
+<a href="glossary/help.Complement-Label.html">complement</a>. If they are not
equal, the next instruction (after a modifying
<a href="glossary/help.nop-instructions.html">no-operation</a> instruction, if one is
present) is executed. If they are equal, that next instruction is skipped.
@@ -108,7 +108,7 @@
<h3>(e) <code>if-less</code></h3>
This instruction compares the <a href="glossary/help.Nop-Register-Notation.html">?BX?</a>
-register to its <a href="glossary/help.Complement-Template.html">complement</a>. If ?BX?
+register to its <a href="glossary/help.Complement-Label.html">complement</a>. If ?BX?
is the lesser of the pair, the next instruction (after a modifying
<a href="glossary/help.nop-instructions.html">no-operation</a> instruction, if one is
present) is executed. If it is greater or equal, then that next instruction is skipped.
@@ -140,7 +140,7 @@
This instruction swaps the contents of the
<a href="glossary/help.Nop-Register-Notation.html">?BX?</a> register with its
-<a href="glossary/help.Complement-Template.html">complement</a>.
+<a href="glossary/help.Complement-Label.html">complement</a>.
<h3>(j) <code>shift-r</code></h3>
@@ -224,14 +224,14 @@
<h3>(u) <code>h-search</code></h3>
-This instruction will read in the <a href="glossary/help.Template.html">template</a>
+This instruction will read in the <a href="glossary/help.Label.html">label</a>
the follows it, and find the location of a
-<a href="glossary/help.Complement-Template.html">complement</a> template in the code.
+<a href="glossary/help.Complement-Label.html">complement</a> label in the code.
The BX <a href="glossary/help.Registers.html">register</a> will be set to the distance
to the complement from the current position of the
<a href="glossary/help.Heads.html">instruction-pointer</a>, and the CX register will
-be set to the size of the template. The <a href="glossary/help.Heads.html">flow-head</a>
-will also be placed at the beginning of the complement template. If no template follows,
+be set to the size of the label. The <a href="glossary/help.Heads.html">flow-head</a>
+will also be placed at the beginning of the complement label. If no label follows,
both BX and CX will be set to zero, and the flow-head will be placed on the instruction
immediatly following the h-search.
@@ -260,9 +260,9 @@
<h3>(y) <code>if-label</code></h3>
-This instruction reads in the <a href="glossary/help.Template.html">template</a> that
-follows it, and tests if its <a href="glossary/help.Complement-Template.html">complement</a>
-template was the most recent series of instructions copied. If so, it executed the next
+This instruction reads in the <a href="glossary/help.Label.html">label</a> that
+follows it, and tests if its <a href="glossary/help.Complement-Label.html">complement</a>
+label was the most recent series of instructions copied. If so, it executed the next
instruction, otherwise it skips it. This instruction is commonly used for an organism to
determine when it has finished producing its offspring.
@@ -280,26 +280,26 @@
These instructions act siminar to <code>push</code> and <code>pop</code> above,
but instead of working with registers, the place the position of the
-?IP? on the stack, or put the ?IP? at the position taken from the stack
-(respectively).
+<a href="glossary/help.Nop-Head-Notation.html">?IP?</a> on the stack, or put
+the ?IP? at the position taken from the stack (respectively).
<h3><code>inject</code></h3>
This instruction acts similar to <code>divide</code>, but instead of splitting
off an offspring, it will remove the section of code between the read and
write heads, and attempt to inject it into the neighbor that the organism
-is facing. The template following this instruction will be used; if an
+is facing. The label following this instruction will be used; if an
<em>exact</em> match is found (with no extre nops in it) in the target organism,
-the injected code will be placed immediately after that template. Otherwise
+the injected code will be placed immediately after that label. Otherwise
the command fails, and the code intended for injection is instead discarded.
<h3><code>rotate-l</code> and <code>rotate-r</code></h3>
-These instructions rotate the facing of an organism. If no teplate follows,
+These instructions rotate the facing of an organism. If no label follows,
the organism will turn one cell in the appropriate direction (left or right).
-If a template is present, it will keep turning in that direction until either
+If a label is present, it will keep turning in that direction until either
it has made a full 360 degree turn, or else it finds an organism that
-possesses the complement template.
+possesses the complement label.
<h3><code>div-asex</code></h3>
Same as h-divide (added for symetry with the divide-sex).
@@ -319,7 +319,7 @@
another one arrives before they are both placed into the population.
<h3><code>die</code></h3>
-When executed, kills the organism, with the probability set by DIE_PROB in genesis.
+When executed, kills the organism.
<hr />
<p><a href="index.html">Return to the Index</a></p>
Modified: development/source/analyze/cAnalyze.cc
===================================================================
--- development/source/analyze/cAnalyze.cc 2007-02-06 20:50:16 UTC (rev 1248)
+++ development/source/analyze/cAnalyze.cc 2007-02-08 21:47:33 UTC (rev 1249)
@@ -7019,7 +7019,7 @@
} else cout << "Running through test CPUs..." << endl;
if (m_world->GetVerbosity() >= VERBOSE_ON && batch[cur_batch].IsLineage() == false) {
- cerr << " Warning: batch may not be a linege; "
+ cerr << " Warning: batch may not be a lineage; "
<< "parent and ancestor distances may not be correct" << endl;
}
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