Changeset 955 for cpp/frams/genetics/geno.cpp

Timestamp:

06/25/20 00:34:29 (5 years ago)

Author:

Maciej Komosinski

Message:

Genetic format ID becomes a string (no longer limited to a single character)

File:

• cpp/frams/genetics/geno.cpp (modified) (17 diffs)

cpp/frams/genetics/geno.cpp ¶

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -24 +24 @@
 }
 
-void Geno::init(const SString& genstring, char genformat, const SString& genname, const SString& comment)
+const SString Geno::INVALID_FORMAT = "invalid";
+const SString Geno::UNKNOWN_FORMAT = "";
+
+void Geno::init(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment)
 {
         refcount = 1;
@@ -35 +38 @@
 }
 
-void Geno::setGenesAndFormat(const SString& genstring, char genformat)
+static SString trimAndValidateFormat(const SString& input) //the new requirement for genotype format name: no whitespace
+{
+        SString format = trim(input);
+        if (format.len() == 0 || strContainsOneOf(format.c_str(), " \r\n\t"))
+                return Geno::INVALID_FORMAT;
+        return format;
+}
+
+void Geno::setGenesAndFormat(const SString& genstring, const SString& in_genformat)
 {
         mapinshift = 0;
         mapoutshift = 0;
         SString gencopy(genstring);
-        if (genformat == -1)
+        SString genformat = in_genformat;
+        if (genformat == UNKNOWN_FORMAT)
         { // unknown format
-                genformat = '1';
+                genformat = "1";
                 if (genstring.charAt(0) == '/')
                 {
@@ -49 +61 @@
                         {
                         case '/':
-                                genformat = genstring.charAt(2);
                                 if ((end = genstring.indexOf('\n')) >= 0)
                                 {
+                                        genformat = trimAndValidateFormat(genstring.substr(2, end - 2));
                                         mapinshift = end + 1;
                                         gencopy = genstring.substr(end + 1);
                                         if ((end > 0) && (genstring[end - 1] == '\r')) end--;
                                         error_end = end;
-                                        if (end != 3) genformat = INVALID_FORMAT;
                                 }
                                 else
                                 {
-                                        if (genstring.len() != 3) genformat = INVALID_FORMAT;
-                                        gencopy = 0;
+                                        genformat = trimAndValidateFormat(genstring.substr(2));
+                                        gencopy = "";
                                         mapinshift = genstring.len();
                                 }
                                 break;
                         case '*':
-                                genformat = genstring.charAt(2);
                                 if ((end = genstring.indexOf("*/")) >= 0)
                                 {
+                                        genformat = trimAndValidateFormat(genstring.substr(2, end - 2));
                                         error_end = end + 2;
-                                        if (end != 3) genformat = INVALID_FORMAT;
                                         gencopy = genstring.substr(end + 2);
                                         mapinshift = end + 2;
@@ -76 +86 @@
                                 else
                                 {
-                                        if (genstring.len() != 5) genformat = INVALID_FORMAT;
-                                        gencopy = 0;
+                                        genformat = trimAndValidateFormat(genstring.substr(2));
+                                        gencopy = "";
                                         mapinshift = genstring.len();
                                 }
                                 break;
                         }
-                        if (!isalnum(genformat)) genformat = INVALID_FORMAT;
                         if (genformat == INVALID_FORMAT)
                         {
                                 SString cut;
-                                if (error_end<0) error_end = genstring.len();
+                                if (error_end < 0) error_end = genstring.len();
                                 static const int MAX_ERROR = 20;
-                                if (error_end>MAX_ERROR)
+                                if (error_end > MAX_ERROR)
                                         cut = genstring.substr(0, MAX_ERROR) + "...";
                                 else
@@ -113 +122 @@
 }
 
+Geno::Geno(const char *genstring, const char* genformat, const char *genname, const char *comment)
+{
+        init(SString(genstring), SString(genformat), SString(genname), SString(comment));
+}
+
 Geno::Geno(const char *genstring, char genformat, const char *genname, const char *comment)
 {
-        init(SString(genstring), genformat, SString(genname), SString(comment));
-}
-
-Geno::Geno(const SString& genstring, char genformat, const SString& genname, const SString& comment)
+        SString genformat_string;
+        if (genformat > 0)
+                genformat_string = SString(&genformat, 1);
+        init(genstring, genformat_string, genname, comment);
+}
+
+Geno::Geno(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment)
 {
         init(genstring, genformat, genname, comment);
@@ -148 +165 @@
 Geno::Geno(const SString& src)
 {
-        init(src, -1, SString::empty(), SString::empty());
+        init(src, UNKNOWN_FORMAT, SString::empty(), SString::empty());
 }
 
@@ -161 +178 @@
 {
         freeF0();
-        init(g, -1, SString::empty(), SString::empty());
+        init(g, UNKNOWN_FORMAT, SString::empty(), SString::empty());
 }
 
@@ -177 +194 @@
 {
         SString out;
-        if (format != '1')
+        if (format != "1")
         {
                 if (multiline)
@@ -183 +200 @@
                 else
                         out += "/*";
-                if (format == 0)
-                        out += "invalid";
-                else
-                        out += format;
+                out += format;
                 if (multiline)
                         out += "\n";
@@ -213 +227 @@
 SString Geno::getGenes(void) const { return gen; }
 SString Geno::getName(void) const { return name; }
-char Geno::getFormat(void) const { return format; }
+SString Geno::getFormat(void) const { return format; }
 SString Geno::getComment(void) const { return txt; }
 
 int ModelGenoValidator::testGenoValidity(Geno& g)
 {
-        if (g.getFormat() == '0')
+        if (g.getFormat() == "0")
         {
                 Model mod(g);
@@ -226 +240 @@
         {
                 bool converter_missing;
-                Geno f0geno = g.getConverted('0', NULL, false, &converter_missing);
+                Geno f0geno = g.getConverted("0", NULL, false, &converter_missing);
                 if (converter_missing)
                         return -1;//no result
@@ -243 +257 @@
 #ifdef WARN_VALIDATION_INCONSISTENCY
                 vector<int> results;
-                int first_result=-1;
+                int first_result = -1;
                 FOREACH(GenoValidator*, v, (*vals))
                 {
-                        int r=v->testGenoValidity(*this);
-                        if (first_result<0) first_result=r;
+                        int r = v->testGenoValidity(*this);
+                        if (first_result < 0) first_result = r;
                         results.push_back(r);
                 }
-                int N=vals->size();
-                for(int i=1;i<N;i++)
-                        if (results[i]!=results[0])
+                int N = vals->size();
+                for (int i = 1; i < N; i++)
+                        if (results[i] != results[0])
                         {
-                        SString txt="Inconsistent validation results";
-                        for(int i=0;i<N;i++)
-                                txt+=SString::sprintf(" %d",results[i]);
-                        txt+=" for genotype '";
-                        txt+=getGene();
-                        txt+="'";
-                        logPrintf("Geno","validate",LOG_WARN,txt.c_str());
-                        break;
+                                SString txt = "Inconsistent validation results";
+                                for (int i = 0; i < N; i++)
+                                        txt += SString::sprintf(" %d", results[i]);
+                                txt += " for genotype '";
+                                txt += getGene();
+                                txt += "'";
+                                logPrintf("Geno", "validate", LOG_WARN, txt.c_str());
+                                break;
                         }
-                isvalid=first_result;
-                if (isvalid>=0)
+                isvalid = first_result;
+                if (isvalid >= 0)
                         return;
 #else
@@ -273 +287 @@
         }
         isvalid = 0;
-        logPrintf("Geno", "validate", LOG_WARN, "Wrong configuration? No genotype validators defined for genetic format 'f%c'.", format);
+        logPrintf("Geno", "validate", LOG_WARN, "Wrong configuration? No genotype validators defined for genetic format 'f%s'.", format.c_str());
 }
 
@@ -295 +309 @@
 }
 
-Geno Geno::getConverted(char otherformat, MultiMap *m, bool using_checkpoints, bool *converter_missing)
+Geno Geno::getConverted(SString otherformat, MultiMap *m, bool using_checkpoints, bool *converter_missing)
 {
         if (otherformat == getFormat()) { if (converter_missing) *converter_missing = false; return *this; }
@@ -302 +316 @@
         if (converters)
         {
-                if ((otherformat == '0') && (!m) && (!using_checkpoints))
+                if ((otherformat == "0") && (!m) && (!using_checkpoints))
                 {
                         if (!f0gen)
@@ -317 +331 @@
 #endif
         if (converter_missing) *converter_missing = true;
-        return (otherformat == getFormat()) ? *this : Geno(0, 0, 0, "GenConvManager not available");
+        return (otherformat == getFormat()) ? *this : Geno("", "", "", "GenConvManager not available");
 }