Changeset 972 for cpp/frams/genetics

Timestamp:

07/03/20 00:32:23 (4 years ago)

Author:

Maciej Komosinski

Message:

• separate "0" and "0s" formats (for SHAPE_BALL_AND_STICK and SHAPE_SOLIDS, respectively)
• converting to format list (Geno::F0_FORMAT_LIST = "0,0s")
• (optional) declaring Model as SHAPE_BALL_AND_STICK or SHAPE_SOLIDS (or SHAPE_UNKNOWN)

Location:

cpp/frams/genetics

Files:

• geno.cpp (modified) (13 diffs)
• geno.h (modified) (1 diff)
• genoconv.cpp (modified) (7 diffs)
• genoconv.h (modified) (1 diff)

cpp/frams/genetics/geno.cpp

@@ -24 +24 @@
 }
 
+bool Geno::formatIsOneOf(const SString& format, const SString& format_list)
+{
+        if (strchr(format_list.c_str(), ',') == NULL)
+                return format == format_list;
+        else
+        {
+                SString item; int pos = 0;
+                while (format_list.getNextToken(pos, item, ','))
+                        if (item == format)
+                                return true;
+        }
+        return false;
+}
+
 const SString Geno::INVALID_FORMAT = "invalid";
 const SString Geno::UNKNOWN_FORMAT = "";
+const SString Geno::F0_FORMAT_LIST = "0,0s";
+
+bool Geno::isF0Format(const SString& format_list)
+{
+        if (strchr(format_list.c_str(), ',') == NULL)
+                return formatIsOneOf(format_list, F0_FORMAT_LIST);
+        SString item; int pos = 0;
+        while (format_list.getNextToken(pos, item, ','))
+                if (!formatIsOneOf(item, F0_FORMAT_LIST))
+                        return false;
+        return true;
+}
 
 void Geno::init(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment)
@@ -41 +67 @@
 {
         SString format = trim(input);
-        if (format.len() == 0 || strContainsOneOf(format.c_str(), " \r\n\t"))
+        if (format.length() == 0 || strContainsOneOf(format.c_str(), " \r\n\t"))
                 return Geno::INVALID_FORMAT;
         return format;
@@ -73 +99 @@
                                         genformat = trimAndValidateFormat(genstring.substr(2));
                                         gencopy = "";
-                                        mapinshift = genstring.len();
+                                        mapinshift = genstring.length();
                                 }
                                 break;
@@ -88 +114 @@
                                         genformat = trimAndValidateFormat(genstring.substr(2));
                                         gencopy = "";
-                                        mapinshift = genstring.len();
+                                        mapinshift = genstring.length();
                                 }
                                 break;
@@ -95 +121 @@
                         {
                                 SString cut;
-                                if (error_end < 0) error_end = genstring.len();
+                                if (error_end < 0) error_end = genstring.length();
                                 static const int MAX_ERROR = 20;
                                 if (error_end > MAX_ERROR)
@@ -104 +130 @@
                                 if (lf >= 0) { if ((lf > 0) && (cut[lf - 1] == '\r')) lf--; cut = cut.substr(0, lf); }
                                 sstringQuote(cut);
-                                logPrintf("Geno", "init", LOG_ERROR, "Invalid genotype format declaration: '%s'%s", cut.c_str(), name.len() ? SString::sprintf(" in '%s'", name.c_str()).c_str() : "");
+                                logPrintf("Geno", "init", LOG_ERROR, "Invalid genotype format declaration: '%s'%s", cut.c_str(), name.length() ? SString::sprintf(" in '%s'", name.c_str()).c_str() : "");
                         }
 
@@ -212 +238 @@
 int Geno::mapGenToString(int genpos) const
 {
-        if (genpos > gen.len()) return -2;
+        if (genpos > gen.length()) return -2;
         if (genpos < 0) return -1;
         return mapinshift + genpos;
@@ -220 +246 @@
 {
         stringpos -= mapinshift;
-        if (stringpos > gen.len()) return -2;
+        if (stringpos > gen.length()) return -2;
         if (stringpos < 0) return -1;
         return stringpos;
@@ -232 +258 @@
 int ModelGenoValidator::testGenoValidity(Geno& g)
 {
-        if (g.getFormat() == "0")
-        {
-                Model mod(g);
+        if (Geno::formatIsOneOf(g.getFormat(), Geno::F0_FORMAT_LIST))
+        {
+                Model mod(g, Model::SHAPE_UNKNOWN);
                 return mod.isValid();
         }
@@ -240 +266 @@
         {
                 bool converter_missing;
-                Geno f0geno = g.getConverted("0", NULL, false, &converter_missing);
+                Geno f0geno = g.getConverted(Geno::F0_FORMAT_LIST, NULL, false, &converter_missing);
                 if (converter_missing)
                         return -1;//no result
@@ -250 +276 @@
 {
         if (isvalid >= 0) return;
-        if (gen.len() == 0) { isvalid = 0; return; }
+        if (gen.length() == 0) { isvalid = 0; return; }
         if (format == INVALID_FORMAT) { isvalid = 0; return; }
         Validators* vals = getValidators();
@@ -309 +335 @@
 }
 
-Geno Geno::getConverted(SString otherformat, MultiMap *m, bool using_checkpoints, bool *converter_missing)
-{
-        if (otherformat == getFormat()) { if (converter_missing) *converter_missing = false; return *this; }
+Geno Geno::getConverted(SString otherformat_list, MultiMap *m, bool using_checkpoints, bool *converter_missing)
+{
+        if (formatIsOneOf(getFormat(), otherformat_list)) { if (converter_missing) *converter_missing = false; return *this; }
 #ifndef NO_GENOCONVMANAGER
         GenoConvManager *converters = getConverters();
         if (converters)
         {
-                if ((otherformat == "0") && (!m) && (!using_checkpoints))
+                if ((isF0Format(otherformat_list)) && (!m) && (!using_checkpoints))
                 {
                         if (!f0gen)
-                                f0gen = new Geno(converters->convert(*this, otherformat, NULL, using_checkpoints, converter_missing));
+                                f0gen = new Geno(converters->convert(*this, otherformat_list, NULL, using_checkpoints, converter_missing));
                         else
                         {
@@ -327 +353 @@
                 }
                 else
-                        return converters->convert(*this, otherformat, m, using_checkpoints, converter_missing);
+                        return converters->convert(*this, otherformat_list, m, using_checkpoints, converter_missing);
         }
 #endif
         if (converter_missing) *converter_missing = true;
-        return (otherformat == getFormat()) ? *this : Geno("", "", "", "GenConvManager not available");
+        return (formatIsOneOf(getFormat(), otherformat_list)) ? *this : Geno("", "", "", "GenConvManager not available");
 }
 

cpp/frams/genetics/geno.h

@@ -129 +129 @@
         static GenoConvManager* useConverters(GenoConvManager* gcm);
         static GenoConvManager* getConverters();
+
+        static bool formatIsOneOf(const SString& format, const SString& format_list);
+        static bool isF0Format(const SString& format_list);
+        static const SString F0_FORMAT_LIST;
 };
 

cpp/frams/genetics/genoconv.cpp

@@ -123 +123 @@
 /// (can be NULL if you don't need this information)
 
-GenoConverter **GenoConvManager::getPath(const SString& in, const SString& out, GenoConverter **path, int maxlen, int *mapavailable)
+GenoConverter **GenoConvManager::getPath(const SString& in_format, const SString& out_format_list, GenoConverter **path, int maxlen, int *mapavailable)
 {
         if (!maxlen) return 0;
@@ -130 +130 @@
         for (; gk = (GenoConverter*)converters(i); i++)
         {
-                if ((gk->enabled) && (gk->in_format == in))
+                if ((gk->enabled) && (gk->in_format == in_format))
                 {
                         *path = gk;
-                        if (gk->out_format == out)
+                        if (Geno::formatIsOneOf(gk->out_format, out_format_list))
                         {
                                 if (mapavailable)
@@ -142 +142 @@
                         {
                                 int mapavail;
-                                GenoConverter **ret = getPath(gk->out_format, out, path + 1, maxlen - 1, &mapavail);
+                                GenoConverter **ret = getPath(gk->out_format, out_format_list, path + 1, maxlen - 1, &mapavail);
                                 if (ret)
                                 {
@@ -155 +155 @@
 }
 
-Geno GenoConvManager::convert(Geno &in, SString format, MultiMap *map, bool using_checkpoints, bool *converter_missing)
-{
-        if (in.getFormat() == format) { if (converter_missing) *converter_missing = false; return in; }
+Geno GenoConvManager::convert(Geno &in, SString format_list, MultiMap *map, bool using_checkpoints, bool *converter_missing)
+{
+        if (Geno::formatIsOneOf(in.getFormat(), format_list))
+        {
+                if (converter_missing) *converter_missing = false; return in;
+        }
         GenoConverter *path[10];
         int dep;
@@ -164 +167 @@
         int mapavail;
         for (dep = 1; dep < (int)sizeof(path); dep++) //iterative deepening
-                if (ret = getPath(in.getFormat(), format, path, dep, &mapavail)) break;
+                if (ret = getPath(in.getFormat(), format_list, path, dep, &mapavail)) break;
         if (!ret) { if (converter_missing) *converter_missing = true; return Geno("", Geno::INVALID_FORMAT, "", "converter not found"); }
         if (converter_missing) *converter_missing = false;
         if (!map) mapavail = 0;
         GenoConverter **t = path;
-        SString tmp;
+        SString tmp, out_format;
         tmp = in.getGenes();
         MultiMap lastmap, tmpmap;
@@ -177 +180 @@
                 GenoConverter *gk = *t;
                 tmp = gk->convert(tmp, mapavail ? &tmpmap : 0, using_checkpoints);
-                if (!tmp.len())
+                out_format = gk->out_format;
+                if (!tmp.length())
                 {
                         string t = ssprintf("f%s->f%s conversion failed (%s)", gk->in_format.c_str(), gk->out_format.c_str(), gk->name);
@@ -200 +204 @@
         if (map)
                 *map = lastmap;
-        return Geno(tmp, format, in.getName(), in.getComment());
-}
+        return Geno(tmp, out_format, in.getName(), in.getComment());
+}

cpp/frams/genetics/genoconv.h

@@ -77 +77 @@
         /// make a genotype in other format. genotype will be invalid
         /// if GenoConvManager cannot convert it.
-        Geno convert(Geno &in, SString format, MultiMap *map = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
+        Geno convert(Geno &in, SString format_list, MultiMap *map = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
         /// register GenoConverter, the added object will be automatically deleted when GenoConvManager is destructed (call removeConverter() if this is not desirable)
         void addConverter(GenoConverter *conv);