Changeset 988 for cpp/frams/genetics

Timestamp:

07/09/20 00:13:20 (4 years ago)

Author:

Maciej Komosinski

Message:

Building a Model from Geno now fails when Model.shape is incompatible with Geno.format; renamed enum constants for genetic formats: xxx_FORMAT => FORMAT_xxx

Location:

cpp/frams/genetics

Files:

• genman.cpp (modified) (8 diffs)
• geno.cpp (modified) (7 diffs)
• geno.h (modified) (2 diffs)
• genoconv.cpp (modified) (4 diffs)
• genoconv.h (modified) (2 diffs)

cpp/frams/genetics/genman.cpp

@@ -289 +289 @@
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str()));
+                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str()));
         char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
         int res = gf->validate(g2, geny.getName().c_str());
@@ -297 +297 @@
                 return Geno(sg2, format, geny.getName(), geny.getComment());
         else
-                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str()));
+                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str()));
 }
 
@@ -307 +307 @@
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str()));
+                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str()));
         Geno gv = g;
         bool canvalidate = true;
         if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
-                return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
+                return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
         bool ok = false;
         int pcount = count;
@@ -354 +354 @@
 {
         SString format = g1.getFormat();
-        if (format != g2.getFormat()) return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str()));
+        if (format != g2.getFormat()) return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str()));
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str()));
+                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str()));
         Geno g1v = g1, g2v = g2;
 
@@ -364 +364 @@
                 bool canvalidate = true;
                 if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
-                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
+                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
                 canvalidate = true;
                 if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
-                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
+                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
         }
 
@@ -405 +405 @@
                 {
                         logPrintf("GenMan", "CrossOver", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
-                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
+                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
                 }
         }
@@ -428 +428 @@
 {
         SString format = G->getFormat();
-        if (format == Geno::INVALID_FORMAT)
+        if (format == Geno::FORMAT_INVALID)
                 return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
         if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
@@ -445 +445 @@
 {
         SString format = G->getFormat();
-        if (format == Geno::INVALID_FORMAT)
+        if (format == Geno::FORMAT_INVALID)
         {
                 for (unsigned int pos = 0; pos < strlen(g); pos++)

cpp/frams/genetics/geno.cpp

@@ -38 +38 @@
 }
 
-const SString Geno::INVALID_FORMAT = "invalid";
-const SString Geno::UNKNOWN_FORMAT = "";
+const SString Geno::FORMAT_INVALID = "invalid";
+const SString Geno::FORMAT_UNKNOWN = "";
 const SString Geno::F0_FORMAT_LIST = "0,0s";
 
@@ -68 +68 @@
         SString format = trim(input);
         if (format.length() == 0 || strContainsOneOf(format.c_str(), " \r\n\t"))
-                return Geno::INVALID_FORMAT;
+                return Geno::FORMAT_INVALID;
         return format;
 }
@@ -78 +78 @@
         SString gencopy(genstring);
         SString genformat = in_genformat;
-        if (genformat == UNKNOWN_FORMAT)
+        if (genformat == FORMAT_UNKNOWN)
         { // unknown format
                 genformat = "1";
@@ -118 +118 @@
                                 break;
                         }
-                        if (genformat == INVALID_FORMAT)
+                        if (genformat == FORMAT_INVALID)
                         {
                                 SString cut;
@@ -191 +191 @@
 Geno::Geno(const SString& src)
 {
-        init(src, UNKNOWN_FORMAT, SString::empty(), SString::empty());
+        init(src, FORMAT_UNKNOWN, SString::empty(), SString::empty());
 }
 
@@ -204 +204 @@
 {
         freeF0();
-        init(g, UNKNOWN_FORMAT, SString::empty(), SString::empty());
+        init(g, FORMAT_UNKNOWN, SString::empty(), SString::empty());
 }
 
@@ -277 +277 @@
         if (isvalid >= 0) return;
         if (gen.length() == 0) { isvalid = 0; return; }
-        if (format == INVALID_FORMAT) { isvalid = 0; return; }
+        if (format == FORMAT_INVALID) { isvalid = 0; return; }
         Validators* vals = getValidators();
         if (vals != NULL)

cpp/frams/genetics/geno.h

@@ -55 +55 @@
 
 public:
-        static const SString INVALID_FORMAT;
-        static const SString UNKNOWN_FORMAT;
+        static const SString FORMAT_INVALID;
+        static const SString FORMAT_UNKNOWN;
         typedef SListTempl<GenoValidator*> Validators;
 
@@ -93 +93 @@
 
         /** @param genformat="" -> 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, const SString& genformat = UNKNOWN_FORMAT);
+        void setGenesAndFormat(const SString& genstring, const SString& genformat = FORMAT_UNKNOWN);
         /** g must be pure genes, without format. For the standard behavior use setGenesAndFormat() */
         void setGenesAssumingSameFormat(const SString& g);

cpp/frams/genetics/genoconv.cpp

@@ -107 +107 @@
         for (; gk = (GenoConverter*)converters(i); i++)
         {
-                if ((in != Geno::UNKNOWN_FORMAT) && (in != gk->in_format)) continue;
-                if ((out != Geno::UNKNOWN_FORMAT) && (out != gk->out_format)) continue;
+                if ((in != Geno::FORMAT_UNKNOWN) && (in != gk->in_format)) continue;
+                if ((out != Geno::FORMAT_UNKNOWN) && (out != gk->out_format)) continue;
                 if ((enabled != -1) && (enabled != gk->enabled)) continue;
                 if ((name) && (strcmp(name, gk->name))) continue;
@@ -168 +168 @@
         {
                 if (converter_missing) *converter_missing = false;
-                return Geno("", Geno::INVALID_FORMAT, "", "Invalid genotype cannot be converted");
+                return Geno("", Geno::FORMAT_INVALID, "", "Invalid genotype cannot be converted");
         }
         int mapavail;
@@ -176 +176 @@
         {
                 if (converter_missing) *converter_missing = true;
-                return Geno("", Geno::INVALID_FORMAT, "", "Converter not found");
+                return Geno("", Geno::FORMAT_INVALID, "", "Converter not found");
         }
         if (converter_missing) *converter_missing = false;
@@ -193 +193 @@
                 {
                         string t = ssprintf("f%s->f%s conversion failed (%s)", gk->in_format.c_str(), gk->out_format.c_str(), gk->name);
-                        return Geno("", Geno::INVALID_FORMAT, "", t.c_str());
+                        return Geno("", Geno::FORMAT_INVALID, "", t.c_str());
                 }
                 if (mapavail)

cpp/frams/genetics/genoconv.h

@@ -56 +56 @@
         virtual ~GenoConverter() {}
         /// Don't forget to set public fields in your constructor
-        GenoConverter() :name(""), in_format(Geno::UNKNOWN_FORMAT), out_format("0"), enabled(1), mapsupport(0) {}
+        GenoConverter() :name(""), in_format(Geno::FORMAT_UNKNOWN), out_format("0"), enabled(1), mapsupport(0) {}
 };
 
@@ -87 +87 @@
         /// pass result=0 if you only need one result (by return value)
         /// default criteria values mean "don't care", pass anything else to narrow your search
-        GenoConverter *findConverters(SListTempl<GenoConverter*>* result = 0, const SString& in = Geno::UNKNOWN_FORMAT, const SString& out = Geno::UNKNOWN_FORMAT, int enabled = -1, char* name = 0);
+        GenoConverter *findConverters(SListTempl<GenoConverter*>* result = 0, const SString& in = Geno::FORMAT_UNKNOWN, const SString& out = Geno::FORMAT_UNKNOWN, int enabled = -1, char* name = 0);
 };