Changeset 534 for cpp/frams/genetics

Timestamp:

07/20/16 01:17:14 (8 years ago)

Author:

Maciej Komosinski

Message:

Renamed: get/setGene -> get/setGenes, setGeneOnly -> setGenesAssumingSameFormat

Location:

cpp/frams/genetics

Files:

• f1/conv_f1.cpp (modified) (1 diff)
• f4/conv_f4.cpp (modified) (1 diff)
• f9/conv_f9.cpp (modified) (1 diff)
• genman.cpp (modified) (11 diffs)
• geno.cpp (modified) (4 diffs)
• geno.h (modified) (2 diffs)
• genoconv.cpp (modified) (1 diff)

cpp/frams/genetics/f1/conv_f1.cpp

@@ -111 +111 @@
 builder.model.close(); // model is ready to use now
 if (map) builder.model.getCurrentToF0Map(*map); // generate f1-to-f0 conversion map
-return builder.model.getF0Geno().getGene();
+return builder.model.getF0Geno().getGenes();
 }
 

cpp/frams/genetics/f4/conv_f4.cpp

@@ -32 +32 @@
                 // generate to-f0 conversion map
                 model->getCurrentToF0Map(*map);
-        SString out = model->getF0Geno().getGene();
+        SString out = model->getF0Geno().getGenes();
         delete model;
         return out;

cpp/frams/genetics/f9/conv_f9.cpp

@@ -56 +56 @@
         if (map != NULL)
                 m.getCurrentToF0Map(*map);
-        return m.getF0Geno().getGene();
+        return m.getF0Geno().getGenes();
 }
 

cpp/frams/genetics/genman.cpp

@@ -198 +198 @@
 int GenMan::testValidity(Geno &g, bool &canvalidate)
 {
-        SString ggs=g.getGene();
+        SString ggs=g.getGenes();
         const char *gg = ggs.c_str();
         GenoOperators *gf = getOper_f(g.getFormat());
@@ -210 +210 @@
         if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
         {
-                g.setGeneOnly(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
+                g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
         }
         int check2 = gf->checkValidity(g2, "validated");
-        if (check2 == GENOPER_OK) g.setGeneOnly(g2);
+        if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
         free(g2);
         if (check2 == GENOPER_OK) return check1;
@@ -237 +237 @@
         if (gf == NULL)
                 return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
-        char *g2 = strdup(geny.getGene().c_str()); //copy for validation
+        char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
         int res = gf->validate(g2, geny.getName().c_str());
         SString sg2 = g2;
@@ -263 +263 @@
         while (!ok)
         {
-                char *gn = strdup(gv.getGene().c_str()); //copy for mutation
+                char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
                 chg = 0;
                 if (gf->mutate(gn, chg, method) == GENOPER_OK)
@@ -284 +284 @@
                 if (!ok && (count - pcount > 100))
                 {
-                        logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGene().c_str());
+                        logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGenes().c_str());
                         return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
                 }
         }
         mutchg += chg;
-        if (history) saveLink(g.getGene().c_str(), "", gv.getGene().c_str(), chg);
+        if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
         SString mutinfo;
         if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
@@ -324 +324 @@
         {
                 float chg1, chg2;
-                char *g1n = strdup(g1.getGene().c_str()); //copy for crossover
-                char *g2n = strdup(g2.getGene().c_str()); //copy for crossover
+                char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
+                char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
                 chg1 = chg2 = 0;
                 if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
@@ -351 +351 @@
                 if (!ok && (count - pcount > 100))
                 {
-                        logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGene().c_str(), g2.getGene().c_str());
+                        logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
                         return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
                 }
@@ -357 +357 @@
         // result in g1v
         xochg += chg;
-        if (history) saveLink(g1.getGene().c_str(), g2.getGene().c_str(), g1v.getGene().c_str(), chg);
+        if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
         SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
                 g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
@@ -369 +369 @@
         if (format != g2.getFormat()) return GENOPER_NOOPER;
         GenoOperators *gf = getOper_f(format);
-        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene().c_str(), g2.getGene().c_str());
+        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
 }
 
@@ -380 +380 @@
         GenoOperators *gf = getOper_f(format);
         if (!gf) return GENSTYLE_CS(0, 0); //black & valid
-        else return gf->style(G->getGene().c_str(), pos);
+        else return gf->style(G->getGenes().c_str(), pos);
 }
 
@@ -399 +399 @@
         }
         GenoOperators *gf = getOper_f(format);
-        SString geny=G->getGene();
+        SString geny=G->getGenes();
         for (unsigned int pos = 0; pos < strlen(g); pos++)
         {

cpp/frams/genetics/geno.cpp

@@ -32 +32 @@
         name = genname;
         txt = comment;
-        setGeneAndFormat(genstring,genformat);
-}
-
-void Geno::setGeneAndFormat(const SString& genstring, char genformat)
+        setGenesAndFormat(genstring,genformat);
+}
+
+void Geno::setGenesAndFormat(const SString& genstring, char genformat)
 {
         mapinshift = 0;
@@ -151 +151 @@
 }
 
-void Geno::setGeneOnly(const SString& g)
+void Geno::setGenesAssumingSameFormat(const SString& g)
 {
         gen = g;
@@ -174 +174 @@
 }
 
-SString Geno::getGeneAndFormat(void) const
+SString Geno::getGenesAndFormat(void) const
 {
         SString out;
@@ -211 +211 @@
 }
 
-SString Geno::getGene(void) const { return gen; }
+SString Geno::getGenes(void) const { return gen; }
 SString Geno::getName(void) const { return name; }
 char Geno::getFormat(void) const { return format; }

cpp/frams/genetics/geno.h

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -85 +85 @@
 
         /// return string representation, with format comment at the beginning
-        SString getGeneAndFormat(void) const;
+        SString getGenesAndFormat(void) const;
 
         void setString(const SString& genewithcomments);
 
-        /** @param genformat=-1 -> take from genstring comment (like the constructor) else specify the valid format in genformat and pure gene in genstring */
-        void setGeneAndFormat(const SString& genstring, char genformat=-1);
-        /** g must be pure gene, without format. for the standard behavior use setGeneAndFormat() */
-        void setGeneOnly(const SString& g);
-        SString getGene(void) const;
+        /** @param genformat=-1 -> detect genotype format from genstring comment (like the constructor does), else specify the valid format in genformat and pure genes in genstring. */
+        void setGenesAndFormat(const SString& genstring, char genformat=-1);
+        /** g must be pure genes, without format. For the standard behavior use setGenesAndFormat() */
+        void setGenesAssumingSameFormat(const SString& g);
+        SString getGenes(void) const;
 
         SString getName(void) const;

cpp/frams/genetics/genoconv.cpp

@@ -181 +181 @@
         char *t = path;
         SString tmp;
-        tmp = in.getGene();
+        tmp = in.getGenes();
         MultiMap lastmap, tmpmap;
         int firstmap = 1;