Changeset 972

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

Files:

• _demos/f0_variants_test.cpp (modified) (3 diffs)
• _demos/full_props.cpp (modified) (2 diffs)
• _demos/genoconv_test.cpp (modified) (9 diffs)
• _demos/genomanipulation.cpp (modified) (4 diffs)
• _demos/geometry/geometrytestutils.cpp (modified) (3 diffs)
• _demos/multiline_f0_test.cpp (modified) (3 diffs)
• _demos/neuro_layout_test.cpp (modified) (2 diffs)
• _demos/neuro_test.cpp (modified) (3 diffs)
• _demos/shapeconvert.cpp (modified) (4 diffs)
• genetics/geno.cpp (modified) (13 diffs)
• genetics/geno.h (modified) (1 diff)
• genetics/genoconv.cpp (modified) (7 diffs)
• genetics/genoconv.h (modified) (1 diff)
• model/model.cpp (modified) (17 diffs)
• model/model.h (modified) (4 diffs)
• model/modelobj.cpp (modified) (3 diffs)
• model/modelparts.h (modified) (1 diff)
• model/similarity/simil_model.cpp (modified) (7 diffs)
• userinput/modelcheckpoints.cpp (modified) (3 diffs)
• vm/classes/genoobj.cpp (modified) (5 diffs)

cpp/frams/_demos/f0_variants_test.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -12 +12 @@
 #include <common/loggers/loggertostdout.h>
 
-void save_as_f0(SString &gen,Model &m,bool omit_default_values)
+void save_as_f0(SString &gen, Model &m, bool omit_default_values)
 {
-// copied from Model::makeGeno() (with small changes)
+        // copied from Model::makeGeno() (with small changes)
 
-static Param modelparam(f0_model_paramtab);
-static Param partparam(f0_part_paramtab);
-static Param jointparam(f0_joint_paramtab);
-static Param neuroparam(f0_neuro_paramtab);
-static Param connparam(f0_neuroconn_paramtab);
+        static Param modelparam(f0_model_paramtab);
+        static Param partparam(f0_part_paramtab);
+        static Param jointparam(f0_joint_paramtab);
+        static Param neuroparam(f0_neuro_paramtab);
+        static Param connparam(f0_neuroconn_paramtab);
 
-static Part defaultpart;
-static Joint defaultjoint;
-static Neuro defaultneuro;
-static Model defaultmodel;
-static NeuroConn defaultconn;
+        static Part defaultpart;
+        static Joint defaultjoint;
+        static Neuro defaultneuro;
+        static Model defaultmodel;
+        static NeuroConn defaultconn;
 
-modelparam.select(&m);
-gen+="m:";
-modelparam.saveSingleLine(gen,omit_default_values ? &defaultmodel : NULL);
+        modelparam.select(&m);
+        gen += "m:";
+        modelparam.saveSingleLine(gen, omit_default_values ? &defaultmodel : NULL);
 
-Part *p;
-Joint *j;
-Neuro *n;
+        Part *p;
+        Joint *j;
+        Neuro *n;
 
-for (int i=0;p=(Part*)m.getPart(i);i++)
+        for (int i = 0; p = (Part*)m.getPart(i); i++)
         {
-        partparam.select(p);
-        gen+="p:";
-        partparam.saveSingleLine(gen,omit_default_values ? &defaultpart : NULL);
+                partparam.select(p);
+                gen += "p:";
+                partparam.saveSingleLine(gen, omit_default_values ? &defaultpart : NULL);
         }
-for (int i=0;j=(Joint*)m.getJoint(i);i++)
+        for (int i = 0; j = (Joint*)m.getJoint(i); i++)
         {
-        jointparam.select(j);
-        jointparam.setParamTab(j->usedelta?f0_joint_paramtab:f0_nodeltajoint_paramtab);
-        gen+="j:";
-        jointparam.saveSingleLine(gen,omit_default_values ? &defaultjoint : NULL);
+                jointparam.select(j);
+                jointparam.setParamTab(j->usedelta ? f0_joint_paramtab : f0_nodeltajoint_paramtab);
+                gen += "j:";
+                jointparam.saveSingleLine(gen, omit_default_values ? &defaultjoint : NULL);
         }
-for (int i=0;n=(Neuro*)m.getNeuro(i);i++)
+        for (int i = 0; n = (Neuro*)m.getNeuro(i); i++)
         {
-        neuroparam.select(n);
-        gen+="n:";
-        neuroparam.saveSingleLine(gen,omit_default_values ? &defaultneuro : NULL);
+                neuroparam.select(n);
+                gen += "n:";
+                neuroparam.saveSingleLine(gen, omit_default_values ? &defaultneuro : NULL);
         }
-for (int a=0;n=(Neuro*)m.getNeuro(a);a++)
+        for (int a = 0; n = (Neuro*)m.getNeuro(a); a++)
         { // inputs
-        for (int b=0;b<n->getInputCount();b++)
+                for (int b = 0; b < n->getInputCount(); b++)
                 {
-                double w;
-                NeuroConn nc;
-                Neuro* n2=n->getInput(b,w);
-                nc.n1_refno=n->refno; nc.n2_refno=n2->refno;
-                nc.weight=w;
-                nc.info=n->getInputInfo(b);
-                connparam.select(&nc);
-                gen+="c:";
-                connparam.saveSingleLine(gen,omit_default_values ? &defaultconn : NULL);
+                        double w;
+                        NeuroConn nc;
+                        Neuro* n2 = n->getInput(b, w);
+                        nc.n1_refno = n->refno; nc.n2_refno = n2->refno;
+                        nc.weight = w;
+                        nc.info = n->getInputInfo(b);
+                        connparam.select(&nc);
+                        gen += "c:";
+                        connparam.saveSingleLine(gen, omit_default_values ? &defaultconn : NULL);
                 }
         }
 }
 
-int main(int argc,char*argv[])
+int main(int argc, char*argv[])
 {
-LoggerToStdout messages_to_stdout(LoggerBase::Enable);
+        LoggerToStdout messages_to_stdout(LoggerBase::Enable);
 
-//without converters the application would only handle "format 0" genotypes
-DefaultGenoConvManager gcm;
-gcm.addDefaultConverters();
-Geno::useConverters(&gcm);
+        //without converters the application would only handle "format 0" genotypes
+        DefaultGenoConvManager gcm;
+        gcm.addDefaultConverters();
+        Geno::useConverters(&gcm);
 
-Geno::Validators validators;
-Geno::useValidators(&validators);
-ModelGenoValidator model_validator;
-validators+=&model_validator; //This simple validator handles all cases where a converter for a particular format is available but there is no genetic operator. Converters may be less strict in detecting invalid genotypes but it is better than nothing
+        Geno::Validators validators;
+        Geno::useValidators(&validators);
+        ModelGenoValidator model_validator;
+        validators += &model_validator; //This simple validator handles all cases where a converter for a particular format is available but there is no genetic operator. Converters may be less strict in detecting invalid genotypes but it is better than nothing
 
-SString gen(argc>1?argv[1]:"X[|G:1.23]");
-if (!strcmp(gen.c_str(),"-"))
+        SString gen(argc > 1 ? argv[1] : "X[|G:1.23]");
+        if (!strcmp(gen.c_str(), "-"))
         {
-        gen=0;
-        StdioFILEDontClose in(stdin);
-        loadSString(&in,gen);
+                gen = 0;
+                StdioFILEDontClose in(stdin);
+                loadSString(&in, gen);
         }
-Geno g(gen);
-printf("\nSource genotype: '%s'\n",g.getGenes().c_str());
-printf("                  ( format %s %s)\n",
-       g.getFormat().c_str(), g.getComment().c_str());
+        Geno g(gen);
+        printf("\nSource genotype: '%s'\n", g.getGenes().c_str());
+        printf("                  ( format %s %s)\n",
+                g.getFormat().c_str(), g.getComment().c_str());
 
-Model m(g);//.getConverted('0'));
+        Model m(g, Model::SHAPE_UNKNOWN);//.getConverted('0'));
 
-if (!m.isValid())
+        if (!m.isValid())
         {
-        printf("Cannot build Model from this genotype!\n");
-        return 2;       
+                printf("Cannot build Model from this genotype!\n");
+                return 2;
         }
 
-printf("\nthis example shows how to save a f0 genotype using low-level ParamInterface::saveSingleLine() calls\n");
+        printf("\nthis example shows how to save a f0 genotype using low-level ParamInterface::saveSingleLine() calls\n");
 
-SString f0_skipping_defaults;
-SString f0_no_skipping_defaults;
+        SString f0_skipping_defaults;
+        SString f0_no_skipping_defaults;
 
-save_as_f0(f0_skipping_defaults,m,true);
-save_as_f0(f0_no_skipping_defaults,m,false);
+        save_as_f0(f0_skipping_defaults, m, true);
+        save_as_f0(f0_no_skipping_defaults, m, false);
 
-printf("\n==== with defdata (skips default values) ======\n%s\n",f0_skipping_defaults.c_str());
-printf("\n==== without defdata (saves all fields) ======\n%s\n",f0_no_skipping_defaults.c_str());
+        printf("\n==== with defdata (skips default values) ======\n%s\n", f0_skipping_defaults.c_str());
+        printf("\n==== without defdata (saves all fields) ======\n%s\n", f0_no_skipping_defaults.c_str());
 
-return 0;
+        return 0;
 }
 
@@ -123 +123 @@
 
 Source genotype: 'X[|G:1.23]'
-                  ( format 1 )
+                                  ( format 1 )
 
 this example shows how to save a f0 genotype using low-level ParamInterface::saveSingleLine() calls

cpp/frams/_demos/full_props.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -47 +47 @@
 */
 
-int main(int argc,char*argv[])
+int main(int argc, char*argv[])
 {
-StdioFILE::setStdio();//setup VirtFILE::Vstdin/out/err
-LoggerToStdout messages_to_stderr(LoggerBase::Enable | LoggerBase::DontBlock,VirtFILE::Vstderr); //errors -> stderr, don't interfere with stdout
+        StdioFILE::setStdio();//setup VirtFILE::Vstdin/out/err
+        LoggerToStdout messages_to_stderr(LoggerBase::Enable | LoggerBase::DontBlock, VirtFILE::Vstderr); //errors -> stderr, don't interfere with stdout
 
-PreconfiguredGenetics genetics;
+        PreconfiguredGenetics genetics;
 
-bool reverse=false;
-char* gen_arg=0;
-for(int i=1;i<argc;i++)
+        bool reverse = false;
+        char* gen_arg = 0;
+        for (int i = 1; i < argc; i++)
         {
-        char* ar=argv[i];
-        if (ar[0]=='-')
-                switch(ar[1])
+                char* ar = argv[i];
+                if (ar[0] == '-')
+                        switch (ar[1])
                         {
-                        case 'r': reverse=true; break;
+                        case 'r': reverse = true; break;
                         case 'h': puts("usage: full_props [-r[everse]] [genotype_or_stdin]\n"); break;
                         }
+                else
+                        if (!gen_arg)
+                                gen_arg = ar;
+        }
+        SString gen;
+        if (gen_arg)
+                gen = gen_arg;
         else
-                if (!gen_arg)
-                        gen_arg=ar;
-        }
-SString gen;
-if (gen_arg)
-        gen=gen_arg;
-else
-        loadSString(VirtFILE::Vstdin,gen);
-Geno g(gen);
-Model m(g);
+                loadSString(VirtFILE::Vstdin, gen);
+        Geno g(gen);
+        Model m(g, Model::SHAPE_UNKNOWN);
 
-if (!m.isValid())
+        if (!m.isValid())
         {
-        logPrintf("","full_props",LOG_ERROR,"Cannot build Model from the supplied genotype\n");
-        return 2;       
+                logPrintf("", "full_props", LOG_ERROR, "Cannot build Model from the supplied genotype\n");
+                return 2;
         }
 
-m.open();
-for(int i=0;i<m.getNeuroCount();i++)
+        m.open();
+        for (int i = 0; i < m.getNeuroCount(); i++)
         {
-        Neuro *n=m.getNeuro(i);
-        SyntParam p=n->classProperties(reverse);
-        p.update();// ...so everyone reading the source can recognize that p was created to update the neuro d field
-        // but actually, calling update() here is not necessary, because ~SyntParam() would do it anyway
+                Neuro *n = m.getNeuro(i);
+                SyntParam p = n->classProperties(reverse);
+                p.update();// ...so everyone reading the source can recognize that p was created to update the neuro d field
+                // but actually, calling update() here is not necessary, because ~SyntParam() would do it anyway
         }
-m.close();
+        m.close();
 
-// normal f0 (omitting default values) would be retrieved using m.getF0Geno()
-// the following form allows for more control:
-Geno f0_g;
-m.makeGeno(f0_g,NULL,reverse);//third arg is "handle_defaults" == whether f0 should omit default property values
-puts(f0_g.getGenesAndFormat().c_str());
+        // normal f0 (omitting default values) would be retrieved using m.getF0Geno()
+        // the following form allows for more control:
+        Geno f0_g;
+        m.makeGeno(f0_g, NULL, reverse);//third arg is "handle_defaults" == whether f0 should omit default property values
+        puts(f0_g.getGenesAndFormat().c_str());
 
-return 0;
+        return 0;
 }
 

cpp/frams/_demos/genoconv_test.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.
 
@@ -16 +16 @@
  */
 
-/// Sample Geno converter not using Model class.
-/// (This converter generates the same output for each input).
-/// Such a converter is responsible for doing valid f0 (or other format) output and storing temporary data.
+ /// Sample Geno converter not using Model class.
+ /// (This converter generates the same output for each input).
+ /// Such a converter is responsible for doing valid f0 (or other format) output and storing temporary data.
 class GenoConv_Test : public GenoConverter
 {
@@ -84 +84 @@
         for (t = src; *t; t++)
         {
-                if (insideneuron&&*t == ']') insideneuron = 0;
+                if (insideneuron && *t == ']') insideneuron = 0;
                 if (*t == '[') insideneuron = 1;
                 if ((!insideneuron) && isdigit(*t) && t[1])
@@ -93 +93 @@
                                 dst += *t;
                         if (map) // fill in the map only if requested
-                                map->add(t - src, t - src, dst.len() - n, dst.len() - 1);
+                                map->add(t - src, t - src, dst.length() - n, dst.length() - 1);
                         // meaning: source character (t-src) becomes (dst.len()-n ... dst.len()-1)
                 }
@@ -100 +100 @@
                         dst += *t;
                         if (map)
-                                map->add(t - src, t - src, dst.len() - 1, dst.len() - 1);
+                                map->add(t - src, t - src, dst.length() - 1, dst.length() - 1);
                         // meaning: map single to single character: (t-src) into (dst.len()-1)
                 }
@@ -113 +113 @@
 {
         printf("Genotype:\n%s\nFormat: %s\nValid: %s\nComment: %s\n",
-               g.getGenes().c_str(), g.getFormat().c_str(), g.isValid() ? "yes" : "no", g.getComment().c_str());
+                g.getGenes().c_str(), g.getFormat().c_str(), g.isValid() ? "yes" : "no", g.getComment().c_str());
 }
 
@@ -167 +167 @@
         if (using_checkpoints)
         { // using Model with checkpoints
-                Model m1(g2, false, true);//true=using_checkpoints
+                Model m1(g2, Model::SHAPE_UNKNOWN, false, true);//true=using_checkpoints
                 printf("\nModel built from the converted f%s genotype has %d checkpoints\n", g2.getFormat().c_str(), m1.getCheckpointCount());
-                Model m2(g1, false, true);//true=using_checkpoints
+                Model m2(g1, Model::SHAPE_UNKNOWN, false, true);//true=using_checkpoints
                 printf("Model built from the source f%s genotype has %d checkpoints\n", g1.getFormat().c_str(), m2.getCheckpointCount());
                 // accessing individual checkpoint models (if available)
@@ -195 +195 @@
                 }
 
-                Model mod1(g1, 1);
+                Model mod1(g1, Model::SHAPE_UNKNOWN, 1);
                 printf("\nModel map for f%s genotype:\n", g1.getFormat().c_str());
                 ModelDisplayMap dm1(mod1);
@@ -202 +202 @@
                 mod1combined.addCombined(mod1.getMap(), dm1.getMap());
                 mod1combined.print();
-                Model mod2(g2, 1);
+                Model mod2(g2, Model::SHAPE_UNKNOWN, 1);
                 printf("\nModel map for f%s genotype:\n", g2.getFormat().c_str());
                 ModelDisplayMap dm2(mod2);

cpp/frams/_demos/genomanipulation.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2019  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -210 +210 @@
                         else
                                 printf("(This class does not have its own properties\n"
-                                " - Neuro::classProperties().getPropCount()==0)\n");
+                                        " - Neuro::classProperties().getPropCount()==0)\n");
                 }
         }
@@ -230 +230 @@
         {
                 SyntParam p = n->classProperties();
-                if (p.getPropCount()>0)
+                if (p.getPropCount() > 0)
                 {
                         printProperties(p);
@@ -284 +284 @@
                 g.getFormat().c_str(), g.getComment().c_str());
 
-        Model m(g);//.getConverted('0'));
+        Model m(g, Model::SHAPE_UNKNOWN);//.getConverted('0'));
 
         if (!m.isValid())

cpp/frams/_demos/geometry/geometrytestutils.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2017  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -24 +24 @@
         {
                 count++;
-                totalSize += genotype->genotype.len();
-
-                fprintf(stderr, "%d. (%6d chars) %s\n", count, genotype->genotype.len(),
+                totalSize += genotype->genotype.length();
+
+                fprintf(stderr, "%d. (%6d chars) %s\n", count, genotype->genotype.length(),
                         genotype->name.c_str());
         }
@@ -63 +63 @@
                 if ((genoIndex == count) || (strcmp(genotype->name.c_str(), genoName) == 0))
                 {
-                        Model model(genotype->genotype);
+                        Model model(genotype->genotype, Model::SHAPE_UNKNOWN);
 
                         if (!model.isValid())

cpp/frams/_demos/multiline_f0_test.cpp

@@ -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) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -13 +13 @@
 #include <common/virtfile/stringfile.h>
 
-int main(int argc,char*argv[])
+int main(int argc, char*argv[])
 {
-LoggerToStdout messages_to_stdout(LoggerBase::Enable);
-PreconfiguredGenetics genetics;
+        LoggerToStdout messages_to_stdout(LoggerBase::Enable);
+        PreconfiguredGenetics genetics;
 
-SString gen(argc>1?argv[1]:"X[|G:1.23]");
-if (!strcmp(gen.c_str(),"-"))
+        SString gen(argc > 1 ? argv[1] : "X[|G:1.23]");
+        if (!strcmp(gen.c_str(), "-"))
         {
-        gen=0;
-        StdioFILEDontClose in(stdin);
-        loadSString(&in,gen);
+                gen = 0;
+                StdioFILEDontClose in(stdin);
+                loadSString(&in, gen);
         }
-Geno g(gen);
-printf("\nSource genotype: '%s'\n",g.getGenes().c_str());
-printf("                  ( format %s %s)\n",
-       g.getFormat().c_str(), g.getComment().c_str());
+        Geno g(gen);
+        printf("\nSource genotype: '%s'\n", g.getGenes().c_str());
+        printf("                  ( format %s %s)\n",
+                g.getFormat().c_str(), g.getComment().c_str());
 
-Model m(g);//.getConverted('0'));
+        Model m(g, Model::SHAPE_UNKNOWN);//.getConverted('0'));
 
-if (!m.isValid())
+        if (!m.isValid())
         {
-        printf("Cannot build Model from this genotype!\n");
-        return 2;       
+                printf("Cannot build Model from this genotype!\n");
+                return 2;
         }
-printf("Converted to f0:\n%s\n",m.getF0Geno().getGenes().c_str());
+        printf("Converted to f0:\n%s\n", m.getF0Geno().getGenes().c_str());
 
-printf("\nusing Param::saveMultiLine() to create the \"expanded\" form of the f0 genotype...\n(MultiParamLoader should be able to load this)");
+        printf("\nusing Param::saveMultiLine() to create the \"expanded\" form of the f0 genotype...\n(MultiParamLoader should be able to load this)");
 
-StringFILE2 f;
+        StringFILE2 f;
 
-static Param modelparam(f0_model_paramtab);
-static Param partparam(f0_part_paramtab);
-static Param jointparam(f0_joint_paramtab);
-static Param neuroparam(f0_neuro_paramtab);
-static Param connparam(f0_neuroconn_paramtab);
+        static Param modelparam(f0_model_paramtab);
+        static Param partparam(f0_part_paramtab);
+        static Param jointparam(f0_joint_paramtab);
+        static Param neuroparam(f0_neuro_paramtab);
+        static Param connparam(f0_neuroconn_paramtab);
 
-modelparam.select(&m);
-modelparam.saveMultiLine(&f,"m");
+        modelparam.select(&m);
+        modelparam.saveMultiLine(&f, "m");
 
-Part *p;
-Joint *j;
-Neuro *n;
+        Part *p;
+        Joint *j;
+        Neuro *n;
 
-for (int i=0;p=(Part*)m.getPart(i);i++)
+        for (int i = 0; p = (Part*)m.getPart(i); i++)
         {
-        partparam.select(p);
-        partparam.saveMultiLine(&f,"p");
+                partparam.select(p);
+                partparam.saveMultiLine(&f, "p");
         }
-for (int i=0;j=(Joint*)m.getJoint(i);i++)
+        for (int i = 0; j = (Joint*)m.getJoint(i); i++)
         {
-        jointparam.select(j);
-        jointparam.setParamTab(j->usedelta?f0_joint_paramtab:f0_nodeltajoint_paramtab);
-        jointparam.saveMultiLine(&f,"j");
+                jointparam.select(j);
+                jointparam.setParamTab(j->usedelta ? f0_joint_paramtab : f0_nodeltajoint_paramtab);
+                jointparam.saveMultiLine(&f, "j");
         }
-for (int i=0;n=(Neuro*)m.getNeuro(i);i++)
+        for (int i = 0; n = (Neuro*)m.getNeuro(i); i++)
         {
-        neuroparam.select(n);
-        neuroparam.saveMultiLine(&f,"n");
+                neuroparam.select(n);
+                neuroparam.saveMultiLine(&f, "n");
         }
-for (int a=0;n=(Neuro*)m.getNeuro(a);a++)
+        for (int a = 0; n = (Neuro*)m.getNeuro(a); a++)
         { // inputs
-        for (int b=0;b<n->getInputCount();b++)
+                for (int b = 0; b < n->getInputCount(); b++)
                 {
-                double w;
-                NeuroConn nc;
-                Neuro* n2=n->getInput(b,w);
-                nc.n1_refno=n->refno; nc.n2_refno=n2->refno;
-                nc.weight=w;
-                nc.info=n->getInputInfo(b);
-                connparam.select(&nc);
-                connparam.saveMultiLine(&f,"c");
+                        double w;
+                        NeuroConn nc;
+                        Neuro* n2 = n->getInput(b, w);
+                        nc.n1_refno = n->refno; nc.n2_refno = n2->refno;
+                        nc.weight = w;
+                        nc.info = n->getInputInfo(b);
+                        connparam.select(&nc);
+                        connparam.saveMultiLine(&f, "c");
                 }
         }
 
-printf("\n============================\n%s\n",f.getString().c_str());
+        printf("\n============================\n%s\n", f.getString().c_str());
 
-return 0;
+        return 0;
 }
 
@@ -95 +95 @@
 
 Source genotype: 'X[|G:1.23]'
-                  ( format 1 )
+                                  ( format 1 )
 Converted to f0:
 p:

cpp/frams/_demos/neuro_layout_test.cpp

@@ -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) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -21 +21 @@
 
 // stl is fun? ;-) ForwardIterator implementation for element coordinates (required by min_element/max_element)
-template <int MEMBER> struct NNIter: public std::iterator<std::forward_iterator_tag,int> //MEMBER: 0..3=x/y/w/h
+template <int MEMBER> struct NNIter : public std::iterator<std::forward_iterator_tag, int> //MEMBER: 0..3=x/y/w/h
 {
-NNLayoutState *nn; int index;
-NNIter() {}
-NNIter(NNLayoutState *_nn, int _index):nn(_nn),index(_index) {}
-int operator*() {return nn->GetXYWH(index)[MEMBER];}
-NNIter& operator++() {index++; return *this;}
-bool operator!=(const NNIter& it) {return index!=it.index;}
-bool operator==(const NNIter& it) {return index==it.index;}
+        NNLayoutState *nn; int index;
+        NNIter() {}
+        NNIter(NNLayoutState *_nn, int _index) :nn(_nn), index(_index) {}
+        int operator*() { return nn->GetXYWH(index)[MEMBER]; }
+        NNIter& operator++() { index++; return *this; }
+        bool operator!=(const NNIter& it) { return index != it.index; }
+        bool operator==(const NNIter& it) { return index == it.index; }
 
-static NNIter begin(NNLayoutState *_nn) {return NNIter(_nn,0);}
-static NNIter end(NNLayoutState *_nn) {return NNIter(_nn,_nn->GetElements());}
+        static NNIter begin(NNLayoutState *_nn) { return NNIter(_nn, 0); }
+        static NNIter end(NNLayoutState *_nn) { return NNIter(_nn, _nn->GetElements()); }
 };
 
 class Screen
 {
-int min_x,max_x,min_y,max_y,scale_x,scale_y;
-int rows,columns;
-char* screen;
+        int min_x, max_x, min_y, max_y, scale_x, scale_y;
+        int rows, columns;
+        char* screen;
 
 public:
 
-Screen(int _min_x,int _max_x,int _min_y,int _max_y,int _scale_x,int _scale_y)
-        :min_x(_min_x),max_x(_max_x),min_y(_min_y),max_y(_max_y),scale_x(_scale_x),scale_y(_scale_y)
+        Screen(int _min_x, int _max_x, int _min_y, int _max_y, int _scale_x, int _scale_y)
+                :min_x(_min_x), max_x(_max_x), min_y(_min_y), max_y(_max_y), scale_x(_scale_x), scale_y(_scale_y)
+        {
+                columns = (max_x - min_x + scale_x - 1) / scale_x;
+                rows = (max_y - min_y + scale_y - 1) / scale_y;
+                screen = new char[rows * columns];
+                memset(screen, ' ', rows * columns);
+        }
+
+        ~Screen()
+        {
+                delete[] screen;
+        }
+
+        void put(int x, int y, const char *str)
+        {
+                x = (x - min_x) / scale_x;
+                y = (y - min_y) / scale_y;
+                if (x < 0) return;
+                if (y < 0) return;
+                if (y >= rows) return;
+                for (; *str; str++, x++)
                 {
-                columns=(max_x-min_x+scale_x-1)/scale_x;
-                rows=(max_y-min_y+scale_y-1)/scale_y;
-                screen=new char[rows*columns];
-                memset(screen,' ',rows*columns);
-                }
-
-~Screen()
-                {
-                delete[] screen;
-                }
-
-void put(int x,int y,const char *str)
-        {
-        x=(x-min_x)/scale_x;
-        y=(y-min_y)/scale_y;
-        if (x<0) return;
-        if (y<0) return;
-        if (y>=rows) return;
-        for(;*str;str++,x++)
-                {
-                if (x>=columns) return;
-                screen[columns*y+x]=*str;
+                        if (x >= columns) return;
+                        screen[columns * y + x] = *str;
                 }
         }
 
-void print()
+        void print()
         {
-        for(int y=0;y<rows;y++)
+                for (int y = 0; y < rows; y++)
                 {
-                fwrite(&screen[columns*y],1,columns,stdout);
-                printf("\n");
+                        fwrite(&screen[columns * y], 1, columns, stdout);
+                        printf("\n");
                 }
         }
 };
 
-int main(int argc,char*argv[])
+int main(int argc, char*argv[])
 {
-LoggerToStdout messages_to_stdout(LoggerBase::Enable);
-PreconfiguredGenetics genetics;
+        LoggerToStdout messages_to_stdout(LoggerBase::Enable);
+        PreconfiguredGenetics genetics;
 
-if (argc<=1)
+        if (argc <= 1)
         {
                 puts("Parameters:\n"
-                     " 1. Genotype (or - character indicating the genotype will be read from stdin)\n"
-                     " 2. (Optional) layout type (the only useful layout is 2, which is the default, see nn_simple_layout.cpp");
-          return 10;
+                        " 1. Genotype (or - character indicating the genotype will be read from stdin)\n"
+                        " 2. (Optional) layout type (the only useful layout is 2, which is the default, see nn_simple_layout.cpp");
+                return 10;
         }
-SString gen(argv[1]);
-if (!strcmp(gen.c_str(),"-"))
+        SString gen(argv[1]);
+        if (!strcmp(gen.c_str(), "-"))
         {
-        gen=0;
-        StdioFILEDontClose in(stdin);
-        loadSString(&in,gen);
+                gen = 0;
+                StdioFILEDontClose in(stdin);
+                loadSString(&in, gen);
         }
-int layout_type=2;
-if (argc>2) layout_type=atol(argv[2]);
-Geno g(gen);
-if (!g.isValid()) {puts("invalid genotype");return 5;}
-Model m(g);
-if (!m.getNeuroCount()) {puts("no neural network");return 1;}
-printf("%d neurons,",m.getNeuroCount());
+        int layout_type = 2;
+        if (argc > 2) layout_type = atol(argv[2]);
+        Geno g(gen);
+        if (!g.isValid()) { puts("invalid genotype"); return 5; }
+        Model m(g, Model::SHAPE_UNKNOWN);
+        if (!m.getNeuroCount()) { puts("no neural network"); return 1; }
+        printf("%d neurons,", m.getNeuroCount());
 
-NNLayoutState_Model nn_layout(&m);
-struct NNLayoutFunction &nnfun=nn_layout_functions[layout_type];
-printf(" using layout type=%d (%s)\n",layout_type,nnfun.name);
-nnfun.doLayout(&nn_layout);
+        NNLayoutState_Model nn_layout(&m);
+        struct NNLayoutFunction &nnfun = nn_layout_functions[layout_type];
+        printf(" using layout type=%d (%s)\n", layout_type, nnfun.name);
+        nnfun.doLayout(&nn_layout);
 
-for(int i=0;i<nn_layout.GetElements();i++)
+        for (int i = 0; i < nn_layout.GetElements(); i++)
         {
-        int *xywh=nn_layout.GetXYWH(i);
-        printf("#%-3d %s\t%d,%d\t%dx%d\n",i,m.getNeuro(i)->getClassName().c_str(),
-               xywh[0],xywh[1],xywh[2],xywh[3]);
+                int *xywh = nn_layout.GetXYWH(i);
+                printf("#%-3d %s\t%d,%d\t%dx%d\n", i, m.getNeuro(i)->getClassName().c_str(),
+                        xywh[0], xywh[1], xywh[2], xywh[3]);
         }
 
-Screen screen(*std::min_element(NNIter<0>::begin(&nn_layout),NNIter<0>::end(&nn_layout))-30,
-              *std::max_element(NNIter<0>::begin(&nn_layout),NNIter<0>::end(&nn_layout))+70,
-              *std::min_element(NNIter<1>::begin(&nn_layout),NNIter<1>::end(&nn_layout)),
-              *std::max_element(NNIter<1>::begin(&nn_layout),NNIter<1>::end(&nn_layout))+30,
-              10,35);
+        Screen screen(*std::min_element(NNIter<0>::begin(&nn_layout), NNIter<0>::end(&nn_layout)) - 30,
+                *std::max_element(NNIter<0>::begin(&nn_layout), NNIter<0>::end(&nn_layout)) + 70,
+                *std::min_element(NNIter<1>::begin(&nn_layout), NNIter<1>::end(&nn_layout)),
+                *std::max_element(NNIter<1>::begin(&nn_layout), NNIter<1>::end(&nn_layout)) + 30,
+                10, 35);
 
-printf("===========================================\n");
-for(int i=0;i<nn_layout.GetElements();i++)
+        printf("===========================================\n");
+        for (int i = 0; i < nn_layout.GetElements(); i++)
         {
-        int *xywh=nn_layout.GetXYWH(i);
-        SString label=SString::sprintf("%d:%s",i,m.getNeuro(i)->getClassName().c_str());
-        screen.put(xywh[0],xywh[1],label.c_str());
+                int *xywh = nn_layout.GetXYWH(i);
+                SString label = SString::sprintf("%d:%s", i, m.getNeuro(i)->getClassName().c_str());
+                screen.put(xywh[0], xywh[1], label.c_str());
         }
-screen.print();
-printf("===========================================\n");
+        screen.print();
+        printf("===========================================\n");
 
 }

cpp/frams/_demos/neuro_test.cpp

@@ -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) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -18 +18 @@
 #ifndef SDK_WITHOUT_FRAMS
 #include <frams/mech/creatmechobj.h>
-int CreatMechObject::modeltags_id=0;
-int CreatMechObject::mechtags_id=0;
+int CreatMechObject::modeltags_id = 0;
+int CreatMechObject::mechtags_id = 0;
 #endif
 
-ParamEntry creature_paramtab[]={0};
+ParamEntry creature_paramtab[] = { 0 };
 
 #ifdef VEYETEST
@@ -33 +33 @@
 #define LEARNINGSTEPS 50
 
-void veyeStep(Model &m,int step)
+void veyeStep(Model &m, int step)
 {
-  static float angle=0;
+        static float angle = 0;
 
-  NeuroNetImpl::getImpl(m.getNeuro(N_Mode))->setState(step>=LEARNINGSTEPS); //0 (learning) or 1 (normal)
+        NeuroNetImpl::getImpl(m.getNeuro(N_Mode))->setState(step >= LEARNINGSTEPS); //0 (learning) or 1 (normal)
 
-        NeuroImpl *ni=NeuroNetImpl::getImpl(m.getNeuro(N_VEye));
-  ((NI_VectorEye*)ni)->relpos.y=0;
-  ((NI_VectorEye*)ni)->relpos.z=0;
-  if (NeuroNetImpl::getImpl(m.getNeuro(N_Mode))->getNewState()<0.5)
-  { //learning
-    ((NI_VectorEye*)ni)->relpos.x=5.0*sin(2*M_PI*step/LEARNINGSTEPS);
-  }
-  else
-  { //VMotor controls location of VEye
-    angle+=NeuroNetImpl::getImpl(m.getNeuro(N_VMotor))->getState();
-    angle=fmod((double)angle,M_PI*2.0);
-    ((NI_VectorEye*)ni)->relpos.x=5*sin(angle);
-  }
+        NeuroImpl *ni = NeuroNetImpl::getImpl(m.getNeuro(N_VEye));
+        ((NI_VectorEye*)ni)->relpos.y = 0;
+        ((NI_VectorEye*)ni)->relpos.z = 0;
+        if (NeuroNetImpl::getImpl(m.getNeuro(N_Mode))->getNewState() < 0.5)
+        { //learning
+                ((NI_VectorEye*)ni)->relpos.x = 5.0 * sin(2 * M_PI * step / LEARNINGSTEPS);
+        }
+        else
+        { //VMotor controls location of VEye
+                angle += NeuroNetImpl::getImpl(m.getNeuro(N_VMotor))->getState();
+                angle = fmod((double)angle, M_PI * 2.0);
+                ((NI_VectorEye*)ni)->relpos.x = 5 * sin(angle);
+        }
 
-  NeuroNetImpl::getImpl(m.getNeuro(N_Fitness))->setState(angle); //wymaga poprawy
-  //oraz trzeba przemyslec kolejnosc get/set'ow neuronow zeby sygnal sie dobrze propagowal.
+        NeuroNetImpl::getImpl(m.getNeuro(N_Fitness))->setState(angle); //wymaga poprawy
+        //oraz trzeba przemyslec kolejnosc get/set'ow neuronow zeby sygnal sie dobrze propagowal.
 }
 #endif
 
-int main(int argc,char*argv[])
+int main(int argc, char*argv[])
 {
-LoggerToStdout messages_to_stdout(LoggerBase::Enable);
-PreconfiguredGenetics genetics;
+        LoggerToStdout messages_to_stdout(LoggerBase::Enable);
+        PreconfiguredGenetics genetics;
 
-if (argc<=1)
+        if (argc <= 1)
         {
                 puts("Parameters: <genotype> [number of simulation steps]");
-          return 10;
+                return 10;
         }
-SString gen(argv[1]);
-if (!strcmp(gen.c_str(),"-"))
+        SString gen(argv[1]);
+        if (!strcmp(gen.c_str(), "-"))
         {
-        gen=0;
-        StdioFILEDontClose in(stdin);
-        loadSString(&in,gen);
+                gen = 0;
+                StdioFILEDontClose in(stdin);
+                loadSString(&in, gen);
         }
-Geno g(gen);
-if (!g.isValid()) {puts("invalid genotype");return 5;}
-Model m(g);
-if (!m.getNeuroCount()) {puts("no neural network");return 1;}
-printf("%d neurons,",m.getNeuroCount());
-NeuroFactory neurofac;
-neurofac.setStandardImplementation();
-NeuroNetConfig nn_config(&neurofac);
-NeuroNetImpl *nn=new NeuroNetImpl(m,nn_config);
-int i; Neuro *n;
-if (!nn->getErrorCount()) printf(" no errors\n");
-else
+        Geno g(gen);
+        if (!g.isValid()) { puts("invalid genotype"); return 5; }
+        Model m(g, Model::SHAPE_UNKNOWN);
+        if (!m.getNeuroCount()) { puts("no neural network"); return 1; }
+        printf("%d neurons,", m.getNeuroCount());
+        NeuroFactory neurofac;
+        neurofac.setStandardImplementation();
+        NeuroNetConfig nn_config(&neurofac);
+        NeuroNetImpl *nn = new NeuroNetImpl(m, nn_config);
+        int i; Neuro *n;
+        if (!nn->getErrorCount()) printf(" no errors\n");
+        else
         {
-        printf(" %d errors:",nn->getErrorCount());
-        int no_impl=0; SString no_impl_names;
-        int init_err=0; SString init_err_names;
-        for(i=0;i<m.getNeuroCount();i++)
+                printf(" %d errors:", nn->getErrorCount());
+                int no_impl = 0; SString no_impl_names;
+                int init_err = 0; SString init_err_names;
+                for (i = 0; i < m.getNeuroCount(); i++)
                 {
-                n=m.getNeuro(i);
-                NeuroImpl *ni=NeuroNetImpl::getImpl(n);
-                if (!ni)
+                        n = m.getNeuro(i);
+                        NeuroImpl *ni = NeuroNetImpl::getImpl(n);
+                        if (!ni)
                         {
-                        if (no_impl) no_impl_names+=',';
-                        no_impl_names+=SString::sprintf("#%d.%s",i,n->getClassName().c_str());
-                        no_impl++;
+                                if (no_impl) no_impl_names += ',';
+                                no_impl_names += SString::sprintf("#%d.%s", i, n->getClassName().c_str());
+                                no_impl++;
                         }
-                else if (ni->status==NeuroImpl::InitError)
+                        else if (ni->status == NeuroImpl::InitError)
                         {
-                        if (init_err) init_err_names+=',';
-                        init_err_names+=SString::sprintf("#%d.%s",i,n->getClassName().c_str());
-                        init_err++;
+                                if (init_err) init_err_names += ',';
+                                init_err_names += SString::sprintf("#%d.%s", i, n->getClassName().c_str());
+                                init_err++;
                         }
                 }
+                printf("\n");
+                if (no_impl) printf("%d x missing implementation (%s)\n", no_impl, no_impl_names.c_str());
+                if (init_err) printf("%d x failed initialization (%s)\n", init_err, init_err_names.c_str());
+        }
+        int steps = 1;
+        if (argc > 2) steps = atol(argv[2]);
+        int st;
+        printf("step");
+        for (i = 0; i < m.getNeuroCount(); i++)
+        {
+                n = m.getNeuro(i);
+                printf("\t#%d.%s", i, n->getClassName().c_str());
+        }
         printf("\n");
-        if (no_impl) printf("%d x missing implementation (%s)\n",no_impl,no_impl_names.c_str());
-        if (init_err) printf("%d x failed initialization (%s)\n",init_err,init_err_names.c_str());
-        }
-int steps=1;
-if (argc>2) steps=atol(argv[2]);
-int st;
-printf("step");
-for(i=0;i<m.getNeuroCount();i++)
-        {
-        n=m.getNeuro(i);
-        printf("\t#%d.%s",i,n->getClassName().c_str());
-        }
-printf("\n");
-for(st=0;st<=steps;st++)
+        for (st = 0; st <= steps; st++)
         {
 #ifdef VEYETEST
-  veyeStep(m,st);
+                veyeStep(m, st);
 #endif
-        printf("%d",st);
-        for(i=0;i<m.getNeuroCount();i++)
+                printf("%d", st);
+                for (i = 0; i < m.getNeuroCount(); i++)
                 {
-                n=m.getNeuro(i);
-                printf("\t%g",n->state);
+                        n = m.getNeuro(i);
+                        printf("\t%g", n->state);
                 }
-        printf("\n");
-        nn->simulateNeuroNet();
+                printf("\n");
+                nn->simulateNeuroNet();
         }
-neurofac.freeImplementation();
+        neurofac.freeImplementation();
 }

cpp/frams/_demos/shapeconvert.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -46 +46 @@
                 if (ar[0] == '-')
                         switch (ar[1])
-                {
+                        {
                         case 's': shape = (Part::Shape)atol(ar + 2);
                                 if ((shape != Part::SHAPE_ELLIPSOID) && (shape != Part::SHAPE_CUBOID) && (shape != Part::SHAPE_CYLINDER))
@@ -56 +56 @@
                         case 't': thickness = atof(ar + 2); break;
                         case 'h': puts("Usage: shapeconvert [-sSHAPE] [-tTHICKNESS] [genotype_or_stdin]\n\tSHAPE: 1=ellipsoid, 2=cuboid, 3(default)=cylinder\n\tTHICKNESS: used for Part.sy/sz (default=0.2)"); break;
-                }
+                        }
                 else
                         if (!gen_arg)
@@ -67 +67 @@
                 loadSString(VirtFILE::Vstdin, gen);
         Geno g(gen);
-        Model m(g);
+        Model m(g, Model::SHAPE_UNKNOWN);
 
         if (!m.isValid())

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);

cpp/frams/model/model.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2019  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -11 +11 @@
 #define F0_CHECKPOINT_LINE "checkpoint:"
 
-Model::Model()
+Model::Model(ShapeType sh)
 {
         autobuildmaps = false;
-        init();
-}
-
-void Model::init()
+        init(sh);
+}
+
+void Model::init(ShapeType sh)
 {
         partmappingchanged = 0;
@@ -30 +30 @@
         f0genoknown = 1;
         shape = SHAPE_UNKNOWN;
+        declared_shape = sh;
+}
+
+void Model::declareShapeType(ShapeType sh)
+{
+        declared_shape = sh;
 }
 
@@ -51 +57 @@
         f0genoknown = 0;
         shape = mod.shape;
+        declared_shape = mod.declared_shape;
         startenergy = mod.startenergy;
         modelfromgenotype = mod.modelfromgenotype;
@@ -93 +100 @@
 
 
-Model::Model(const Geno &src, bool buildmaps, bool _using_checkpoints, bool _is_checkpoint)
+Model::Model(const Geno &src, ShapeType st, bool buildmaps, bool _using_checkpoints, bool _is_checkpoint)
         :autobuildmaps(buildmaps)
 {
-        init(src, _using_checkpoints, _is_checkpoint);
+        init(src, st, _using_checkpoints, _is_checkpoint);
 }
 
@@ -110 +117 @@
         :autobuildmaps(buildmaps)
 {
-        init();
+        init(mod.declared_shape);
         open(_using_checkpoints, _is_checkpoint);
         internalCopy(mod);
@@ -123 +130 @@
 }
 
-void Model::init(const Geno &src, bool _using_checkpoints, bool _is_checkpoint)
-{
-        init();
+void Model::init(const Geno &src, ShapeType sh, bool _using_checkpoints, bool _is_checkpoint)
+{
+        init(sh);
         using_checkpoints = _using_checkpoints;
         is_checkpoint = _is_checkpoint;
@@ -162 +169 @@
         delMap();
         delF0Map();
-        init();
+        init(declared_shape);
         geno = Geno();
         f0geno = Geno();
@@ -333 +340 @@
         f0warnposition = -1;
         MultiMap *convmap = autobuildmaps ? new MultiMap() : NULL;
-        f0geno = (geno.getFormat() == "0") ? geno : geno.getConverted("0", convmap, using_checkpoints);
+        if (declared_shape == SHAPE_UNKNOWN)
+                f0geno = geno.getConverted(Geno::F0_FORMAT_LIST, convmap, using_checkpoints);
+        else
+                f0geno = geno.getConverted(genoFormatForShapeType(declared_shape), convmap, using_checkpoints);
         f0genoknown = 1;
         if (f0geno.isInvalid())
@@ -467 +477 @@
         modelparam.select(this);
         modelparam.saveSingleLine(mod_props, handle_defaults ? &defaultmodel : NULL, true, !handle_defaults);
-        if (mod_props.len() > 1) //are there any non-default values? ("\n" is empty)
+        if (mod_props.length() > 1) //are there any non-default values? ("\n" is empty)
         {
                 gen += "m:";
@@ -476 +486 @@
         {
                 partparam.select(p);
-                len = gen.len();
+                len = gen.length();
                 gen += "p:";
                 partparam.saveSingleLine(gen, handle_defaults ? &defaultpart : NULL, true, !handle_defaults);
                 if (map)
-                        map->add(len, gen.len() - 1, partToMap(i));
+                        map->add(len, gen.length() - 1, partToMap(i));
         }
         for (i = 0; j = (Joint *)joints(i); i++)
         {
                 jointparam.select(j);
-                len = gen.len();
+                len = gen.length();
                 jointparam.setParamTab(j->usedelta ? f0_joint_paramtab : f0_nodeltajoint_paramtab);
                 gen += "j:";
                 jointparam.saveSingleLine(gen, handle_defaults ? &defaultjoint : NULL, true, !handle_defaults);
                 if (map)
-                        map->add(len, gen.len() - 1, jointToMap(i));
+                        map->add(len, gen.length() - 1, jointToMap(i));
         }
         for (i = 0; n = (Neuro *)neurons(i); i++)
         {
                 neuroparam.select(n);
-                len = gen.len();
+                len = gen.length();
                 gen += "n:";
                 neuroparam.saveSingleLine(gen, handle_defaults ? &defaultneuro : NULL, true, !handle_defaults);
                 if (map)
-                        map->add(len, gen.len() - 1, neuroToMap(i));
+                        map->add(len, gen.length() - 1, neuroToMap(i));
         }
         for (a = 0; a < neurons.size(); a++)
@@ -526 +536 @@
                                 nc.info = **s;
                         connparam.select(&nc);
-                        len = gen.len();
+                        len = gen.length();
                         gen += "c:";
                         connparam.saveSingleLine(gen, handle_defaults ? &defaultconn : NULL, true, !handle_defaults);
                         if (map)
-                                map->add(len, gen.len() - 1, neuroToMap(n->refno));
+                                map->add(len, gen.length() - 1, neuroToMap(n->refno));
                 }
         }
@@ -541 +551 @@
         }
 
-        g = Geno(gen.c_str(), '0');
+        g = Geno(gen.c_str(), genoFormatForShapeType(getShapeType()), "", "");
+}
+
+SString Model::genoFormatForShapeType(ShapeType st)
+{
+        switch (st)
+        {
+        case SHAPE_BALL_AND_STICK:
+                return "0";
+        case SHAPE_SOLIDS:
+                return "0s";
+        default:
+                return Geno::INVALID_FORMAT;
+        }
+}
+
+Model::ShapeType Model::shapeTypeForGenoFormat(const SString& format)
+{
+        if (format == "0")
+                return SHAPE_BALL_AND_STICK;
+        else if (format == "0s")
+                return SHAPE_SOLIDS;
+        else
+                return SHAPE_UNKNOWN;
+
+}
+
+const char* Model::getShapeTypeName(ShapeType sh)
+{
+        switch (sh)
+        {
+        case SHAPE_BALL_AND_STICK: return "ball-and-stick";
+        case SHAPE_SOLIDS: return "solid shapes";
+        case SHAPE_UNKNOWN: return "unknown";
+
+        case SHAPE_ILLEGAL:
+        default:
+                return "illegal";
+        }
 }
 
@@ -653 +701 @@
         if (result < 0)
         {
-                if (error_message.len() == 0) // generic error when no detailed message is available
+                if (error_message.length() == 0) // generic error when no detailed message is available
                         error_message = "Invalid f0 code";
                 if (line_num > 0)
@@ -731 +779 @@
                 {
                         // default class for unparented units: standard neuron
-                        if (nu->getClassName().len() == 0) nu->setClassName("N");
+                        if (nu->getClassName().length() == 0) nu->setClassName("N");
                 }
                 /*
@@ -832 +880 @@
 SString Model::nameForErrors() const
 {
-        if (geno.getName().len() > 0)
+        if (geno.getName().length() > 0)
                 return SString::sprintf(" in '%s'", geno.getName().c_str());
         return SString::empty();
@@ -1061 +1109 @@
         if (shape == SHAPE_ILLEGAL)
                 ret = 0;
+        else if ((declared_shape != SHAPE_UNKNOWN) && (declared_shape != shape))
+        {
+                logPrintf("Model", "internalCheck", LOG_ERROR, "Model shape type '%s' does not match the declared type '%s'", getShapeTypeName(shape), getShapeTypeName(declared_shape));
+                ret = 0;
+        }
+
         return ret;
 }

cpp/frams/model/model.h

@@ -102 +102 @@
 protected:
         ShapeType shape;
+        ShapeType declared_shape;
 
         SString nameForErrors() const;
         int internalcheck(CheckType check);
 
-        void init(const Geno &srcgen, bool _using_checkpoints, bool _is_checkpoint);
-        void init();
+        void init(const Geno &srcgen, ShapeType sh, bool _using_checkpoints, bool _is_checkpoint);
+        void init(ShapeType sh);
 
         void delMap();
@@ -136 +137 @@
         bool isUsingCheckpoints() const { return using_checkpoints; }
         bool isCheckpoint() const { return is_checkpoint; }
+        static SString genoFormatForShapeType(ShapeType st);
+        static ShapeType shapeTypeForGenoFormat(const SString& format);
+        static const char* getShapeTypeName(ShapeType sh);
 
         void updateRefno(); // set ::refno for all elements
@@ -150 +154 @@
         ModelUserTags userdata;
 
-        /// Create empty model with invalid empty genotype
-        Model();
+        /// Create empty model with invalid empty genotype, declaring the shape type for later operations
+        Model(ShapeType sh = SHAPE_UNKNOWN);
+
+        /// Change the declared shape type of the Model
+        void declareShapeType(ShapeType sh);
 
         /** Create a model based on provided genotype
@@ -158 +165 @@
            @see getMap()
            */
-        Model(const Geno &src, bool buildmaps = false, bool _using_checkpoints = false, bool _is_checkpoint = false);
+        Model(const Geno &src, ShapeType sh, bool buildmaps = false, bool _using_checkpoints = false, bool _is_checkpoint = false);
         Model(const Model &mod, bool buildmaps = false, bool _using_checkpoints = false, bool _is_checkpoint = false);
         /** duplicate the model.

cpp/frams/model/modelobj.cpp

@@ -58 +58 @@
 void ModelObj::p_newfromstring(ExtValue *args, ExtValue *ret)
 {
-        *ret = makeDynamicObject(new Model(Geno(args[0].getString())));
+        *ret = makeDynamicObject(new Model(Geno(args[0].getString()), Model::SHAPE_UNKNOWN));
 }
 
@@ -65 +65 @@
         Geno *g = GenoObj::fromObject(args[0].getObject());
         if (g)
-                *ret = makeDynamicObject(new Model(*g));
+                *ret = makeDynamicObject(new Model(*g, Model::SHAPE_UNKNOWN));
         else
                 ret->setEmpty();
@@ -74 +74 @@
         Model *m = NULL;
         if (args[0].getType() == TString)
-                m = new Model(Geno(args[0].getString()), false, true);
+                m = new Model(Geno(args[0].getString()), Model::SHAPE_UNKNOWN, false, true);
         else
         {
                 Geno *g = GenoObj::fromObject(args[0].getObject(), false);
                 if (g)
-                        m = new Model(*g, false, true);
+                        m = new Model(*g, Model::SHAPE_UNKNOWN, false, true);
                 else
                         logPrintf("Model", "newWithCheckpoints", LOG_ERROR, "Geno or string expected, %s found", args[0].typeDescription().c_str());

cpp/frams/model/modelparts.h

@@ -34 +34 @@
 {
 public:
-        enum ShapeType { SHAPE_BALL_AND_STICK, SHAPE_SOLIDS, SHAPE_UNKNOWN, SHAPE_ILLEGAL };
+        enum ShapeType { SHAPE_BALL_AND_STICK = 0, SHAPE_SOLIDS = 1, SHAPE_UNKNOWN, SHAPE_ILLEGAL }; ///< 0 and 1 have special significance - these values allow for bit operations.
 };
 

cpp/frams/model/similarity/simil_model.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2019  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -122 +122 @@
 
         // assign matching function
-        int (ModelSimil::* pfMatchingFunction) () = NULL;
+        int (ModelSimil:: * pfMatchingFunction) () = NULL;
 
         pfMatchingFunction = &ModelSimil::MatchPartsGeometry;
@@ -534 +534 @@
                 return NULL;
         }
-        Model *m = new Model(*g);
+        Model *m = new Model(*g, Model::SHAPE_UNKNOWN);
         if (!m->isValid())
         {
@@ -2058 +2058 @@
                         {
                                 if (geo)
-                                        dist[i*bigger + j] += m_adFactors[3] * m_aPositions[1 - m_iSmaller][i].length();
+                                        dist[i * bigger + j] += m_adFactors[3] * m_aPositions[1 - m_iSmaller][i].length();
                                 else
-                                        dist[i*bigger + j] = m_adFactors[1] * m_aDegrees[1 - m_iSmaller][i][DEGREE] + m_adFactors[2] * m_aDegrees[1 - m_iSmaller][i][NEURONS];
+                                        dist[i * bigger + j] = m_adFactors[1] * m_aDegrees[1 - m_iSmaller][i][DEGREE] + m_adFactors[2] * m_aDegrees[1 - m_iSmaller][i][NEURONS];
                         }
                         // compute distance between parts
@@ -2066 +2066 @@
                         {
                                 if (geo)
-                                        dist[i*bigger + j] += m_adFactors[3] * m_aPositions[1 - m_iSmaller][i].distanceTo(m_aPositions[m_iSmaller][j]);
+                                        dist[i * bigger + j] += m_adFactors[3] * m_aPositions[1 - m_iSmaller][i].distanceTo(m_aPositions[m_iSmaller][j]);
                                 else
-                                        dist[i*bigger + j] = m_adFactors[1] * abs(m_aDegrees[1 - m_iSmaller][i][DEGREE] - m_aDegrees[m_iSmaller][j][DEGREE])
+                                        dist[i * bigger + j] = m_adFactors[1] * abs(m_aDegrees[1 - m_iSmaller][i][DEGREE] - m_aDegrees[m_iSmaller][j][DEGREE])
                                         + m_adFactors[2] * abs(m_aDegrees[1 - m_iSmaller][i][NEURONS] - m_aDegrees[m_iSmaller][j][NEURONS]);
                         }
@@ -2104 +2104 @@
         int nBigger = m_Mod[1 - m_iSmaller]->getPartCount();
 
-        double* partsDistances = new double[nBigger*nBigger]();
+        double* partsDistances = new double[nBigger * nBigger]();
         FillPartsDistances(partsDistances, nBigger, nSmaller, false);
         int *assignment = new int[nBigger]();
@@ -2138 +2138 @@
                         // - models (m_Mod) exist and are available
                         // - all properties are created and available (m_aDegrees and m_aPositions)
-                        double* tmpPartsDistances = new double[nBigger*nBigger]();
+                        double* tmpPartsDistances = new double[nBigger * nBigger]();
                         std::copy(partsDistances, partsDistances + nBigger * nBigger, tmpPartsDistances);
                         // recompute geometric properties according to the transformation iTransform

cpp/frams/userinput/modelcheckpoints.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.
 
@@ -45 +45 @@
         freeModel();
         if (g != NULL)
-                mod = new Model(*g, true, false);
+                mod = new Model(*g, Model::SHAPE_UNKNOWN, true, false);
         toguiCheckpoints(use_checkpoints ? EnabledUnknown : Disabled, 1, 1);
         int ret = model_view.showModel(mod);
@@ -58 +58 @@
         {
                 if (p == current_value) return;
-                mod_checkpoints = new Model(mod->getGeno(), false, true);
+                mod_checkpoints = new Model(mod->getGeno(), Model::SHAPE_UNKNOWN, false, true);
                 if (mod_checkpoints->getCheckpointCount() > 1)
                 {

cpp/frams/vm/classes/genoobj.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.
 
@@ -64 +64 @@
 void GenoObj::get_autoname(ExtValue *ret)
 {
-        Model m(*this);
+        Model m(*this, Model::SHAPE_UNKNOWN);
         ret->setString(AutoName::makeName(m));
 }
@@ -97 +97 @@
 void GenoObj::get_f0genotype(ExtValue *ret)
 {
-        ret->setString(getConverted('0').getGenes());
+        ret->setString(getConverted(Geno::F0_FORMAT_LIST).getGenes());
 }
 
@@ -105 +105 @@
         {
                 char ch = v.getInt();
-                return SString(&ch,1);
+                return SString(&ch, 1);
         }
         if (v.getType() == TString)
@@ -144 +144 @@
 #ifdef __CODEGUARD__
         static GenoObj static_genoobj;
-        static Param static_genoparam(geno_paramtab,&static_genoobj);
+        static Param static_genoparam(geno_paramtab, &static_genoobj);
 #else
         static Param static_genoparam(geno_paramtab);