Changeset 420 for cpp/frams


Ignore:
Timestamp:
08/03/15 01:43:55 (9 years ago)
Author:
Maciej Komosinski
Message:

Improved docs and code formatting

Location:
cpp/frams/vm/classes
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • cpp/frams/vm/classes/genoobj.cpp

    r415 r420  
    99
    1010#define FIELDSTRUCT GenoObj
    11 ParamEntry geno_paramtab[]=
     11ParamEntry geno_paramtab[] =
    1212{
    13 {"Geno",1,15,"Geno","All information about a single genotype.\nThis is a genetics-only object which does not contain any performance data. See also: Genotype class"},
    14 {"name",0,PARAM_NOSTATIC,"Name","s 0 40",GETSET(name),},
    15 {"rawgenotype",0,PARAM_NOSTATIC | PARAM_READONLY,"Raw genotype","s 1",GETONLY(genotype),"Genotype, excluding the format specifier"},
    16 {"info",0,PARAM_NOSTATIC,"Info","s 1",GETSET(info),"Additional information or comments",},
    17 {"format",0,PARAM_NOSTATIC | PARAM_READONLY,"Format","d",GETONLY(format),"Genotype format",},
    18 {"genotype",0,PARAM_NOSTATIC | PARAM_READONLY,"Genotype","s 1",GETONLY(string),"Genes as a string of characters",},
    19 {"isValid",0,PARAM_NOSTATIC | PARAM_READONLY | PARAM_DEPRECATED,"Valid","d 0 1",GETONLY(isvalid),},
    20 {"is_valid",0,PARAM_NOSTATIC,"Valid","d -1 1 -1",GETSET(isvalid),},
    21 {"getConverted",0,PARAM_NOSTATIC,"get converted genotype","p oGeno(d format)",PROCEDURE(p_getconvert),},
    22 {"f0genotype",0,PARAM_NOSTATIC | PARAM_READONLY,"f0 genotype","s 1",GETONLY(f0genotype),"converted to f0 genotype",},
    23 {"new",0,0,"create new empty object","p oGeno()",PROCEDURE(p_new),},
    24 {"newFromString",0,0,"create new object from supplied string argument","p oGeno(s genotype)",PROCEDURE(p_newfromstring),},
    25 {"newFrom",0,0,"create new object","p oGeno(s genotype,d format,s name,s description)",PROCEDURE(p_newfrom),},
    26 {"autoname",0,PARAM_NOSTATIC | PARAM_READONLY,"Autogenerated name","s",GETONLY(autoname),},
    27 {"toVector",0,PARAM_READONLY | PARAM_NOSTATIC,"serialization support","oVector",GETONLY(toVector),},
    28 {"newFromVector",0,0,"serialization support","p oGeno(oVector)",PROCEDURE(p_newfromvector),},
    29 {0,0,0,},
     13        { "Geno", 1, 15, "Geno", "All information about a single genotype.\nThis is a genetics-only object which does not contain any performance data. See also: Genotype class" },
     14        { "name", 0, PARAM_NOSTATIC, "Name", "s 0 40", GETSET(name), },
     15        { "rawgenotype", 0, PARAM_NOSTATIC | PARAM_READONLY, "Raw genotype", "s 1", GETONLY(genotype), "Genotype, excluding the format specifier" },
     16        { "info", 0, PARAM_NOSTATIC, "Info", "s 1", GETSET(info), "Additional information or comments", },
     17        { "format", 0, PARAM_NOSTATIC | PARAM_READONLY, "Format", "d", GETONLY(format), "Genotype format", },
     18        { "genotype", 0, PARAM_NOSTATIC | PARAM_READONLY, "Genotype", "s 1", GETONLY(string), "Genes as a string of characters", },
     19        { "isValid", 0, PARAM_NOSTATIC | PARAM_READONLY | PARAM_DEPRECATED, "Valid", "d 0 1", GETONLY(isvalid), "Use 'is_valid' instead of 'isValid'." },
     20        { "is_valid", 0, PARAM_NOSTATIC, "Validity", "d -1 1 -1", GETSET(isvalid),
     21        "0 = invalid genotype\n"
     22        "1 = valid genotype\n"
     23        "-1 = validity is not known. This is a transient state. The value of \"is_valid\" will never be -1 when read. It is safe to treat is_valid as boolean in statements like \"if (g.is_valid) ...\". Setting \"is_valid=-1\" will make it 0 or 1 again. This third state (-1) is only needed for loading Genotype objects from files where the \"is_valid\" field might not be present."
     24        },
     25        { "getConverted", 0, PARAM_NOSTATIC, "get converted genotype", "p oGeno(d format)", PROCEDURE(p_getconvert), },
     26        { "f0genotype", 0, PARAM_NOSTATIC | PARAM_READONLY, "f0 genotype", "s 1", GETONLY(f0genotype), "converted to f0 genotype", },
     27        { "new", 0, 0, "create new empty object", "p oGeno()", PROCEDURE(p_new), },
     28        { "newFromString", 0, 0, "create new object from supplied string argument", "p oGeno(s genotype)", PROCEDURE(p_newfromstring), },
     29        { "newFrom", 0, 0, "create new object", "p oGeno(s genotype,d format,s name,s description)", PROCEDURE(p_newfrom), },
     30        { "autoname", 0, PARAM_NOSTATIC | PARAM_READONLY, "Autogenerated name", "s", GETONLY(autoname), },
     31        { "toVector", 0, PARAM_READONLY | PARAM_NOSTATIC, "serialization support", "oVector", GETONLY(toVector), },
     32        { "newFromVector", 0, 0, "serialization support", "p oGeno(oVector)", PROCEDURE(p_newfromvector), },
     33        { 0, 0, 0, },
    3034};
    3135#undef FIELDSTRUCT
    3236
    3337void GenoObj::get_isvalid(ExtValue *ret)
    34 {ret->setInt(isValid());}
     38{
     39        ret->setInt(isValid());
     40}
    3541
    3642int GenoObj::set_isvalid(const ExtValue *v)
    3743{
    38 paInt n=v->getInt();
    39 if (getValid()!=n)
     44        paInt n = v->getInt();
     45        if (getValid() != n)
    4046        {
    41         setValid(n);
    42         return PSET_CHANGED;
     47                setValid(n);
     48                return PSET_CHANGED;
    4349        }
    44 return 0;
     50        return 0;
    4551}
    4652
    4753void GenoObj::get_genotype(ExtValue *ret)
    48 {ret->setString(getGene());}
     54{
     55        ret->setString(getGene());
     56}
    4957
    5058void GenoObj::get_name(ExtValue *ret)
    51 {ret->setString(getName());}
     59{
     60        ret->setString(getName());
     61}
    5262
    5363void GenoObj::get_autoname(ExtValue *ret)
    5464{
    55 Model m(*this);
    56 ret->setString(AutoName::makeName(m));
     65        Model m(*this);
     66        ret->setString(AutoName::makeName(m));
    5767}
    5868
    5969int GenoObj::set_name(const ExtValue *v)
    60 {setName(v->getString());
    61 return PSET_CHANGED;}
     70{
     71        setName(v->getString());
     72        return PSET_CHANGED;
     73}
    6274
    6375void GenoObj::get_info(ExtValue *ret)
    64 {ret->setString(getComment());}
     76{
     77        ret->setString(getComment());
     78}
    6579
    6680void GenoObj::get_string(ExtValue *ret)
    67 {ret->setString(shortString());}
     81{
     82        ret->setString(shortString());
     83}
    6884
    6985void GenoObj::get_format(ExtValue *ret)
    70 {ret->setInt(getFormat());}
     86{
     87        ret->setInt(getFormat());
     88}
    7189
    7290int GenoObj::set_info(const ExtValue *v)
    73 {setComment(v->getString());
    74 return PSET_CHANGED;}
     91{
     92        setComment(v->getString());
     93        return PSET_CHANGED;
     94}
    7595
    7696void GenoObj::get_f0genotype(ExtValue *ret)
    77 {ret->setString(getConverted('0').getGene());}
     97{
     98        ret->setString(getConverted('0').getGene());
     99}
    78100
    79 void GenoObj::p_getconvert(ExtValue *args,ExtValue *ret)
    80 {*ret=makeDynamicObjectAndDecRef(new Geno(getConverted((char)args[0].getInt())));}
     101void GenoObj::p_getconvert(ExtValue *args, ExtValue *ret)
     102{
     103        *ret = makeDynamicObjectAndDecRef(new Geno(getConverted((char)args[0].getInt())));
     104}
    81105
    82 void GenoObj::p_new(ExtValue *args,ExtValue *ret)
    83 {*ret=makeDynamicObjectAndDecRef(new Geno());}
     106void GenoObj::p_new(ExtValue *args, ExtValue *ret)
     107{
     108        *ret = makeDynamicObjectAndDecRef(new Geno());
     109}
    84110
    85 void GenoObj::p_newfromstring(ExtValue *args,ExtValue *ret)
    86 {*ret=makeDynamicObjectAndDecRef(new Geno(args[0].getString()));}
     111void GenoObj::p_newfromstring(ExtValue *args, ExtValue *ret)
     112{
     113        *ret = makeDynamicObjectAndDecRef(new Geno(args[0].getString()));
     114}
    87115
    88 void GenoObj::p_newfrom(ExtValue *args,ExtValue *ret)
    89 {*ret=makeDynamicObjectAndDecRef(new Geno(args[3].getString(),(char)args[2].getInt(),
    90                                  args[1].getString(),args[0].getString()));}
     116void GenoObj::p_newfrom(ExtValue *args, ExtValue *ret)
     117{
     118        *ret = makeDynamicObjectAndDecRef(new Geno(args[3].getString(), (char)args[2].getInt(),
     119                args[1].getString(), args[0].getString()));
     120}
    91121
    92122Param& GenoObj::getStaticParam()
    93123{
    94124#ifdef __CODEGUARD__
    95 static GenoObj static_genoobj;
    96 static Param static_genoparam(geno_paramtab,&static_genoobj);
     125        static GenoObj static_genoobj;
     126        static Param static_genoparam(geno_paramtab,&static_genoobj);
    97127#else
    98 static Param static_genoparam(geno_paramtab);
     128        static Param static_genoparam(geno_paramtab);
    99129#endif
    100 return static_genoparam;
     130        return static_genoparam;
    101131}
    102132
    103133Param& GenoObj::getDynamicParam()
    104134{
    105 static Param dynamic_genoparam(geno_paramtab);
    106 return dynamic_genoparam;
     135        static Param dynamic_genoparam(geno_paramtab);
     136        return dynamic_genoparam;
    107137}
    108138
    109 ParamInterface* GenoObj::getInterface() {return &getStaticParam();}
     139ParamInterface* GenoObj::getInterface() { return &getStaticParam(); }
    110140
    111141ExtObject GenoObj::makeStaticObject(Geno* g)
    112 {return ExtObject(&getStaticParam(),(void*)g);}
     142{
     143        return ExtObject(&getStaticParam(), (void*)g);
     144}
    113145
    114146ExtObject GenoObj::makeDynamicObject(Geno* g)
    115 {return ExtObject(&getDynamicParam(),(DestrBase*)g);}
     147{
     148        return ExtObject(&getDynamicParam(), (DestrBase*)g);
     149}
    116150
    117151ExtObject GenoObj::makeDynamicObjectAndDecRef(Geno* g)
    118152{
    119 const ExtObject& o=makeDynamicObject(g);
    120 g->decref();
    121 return o;
     153        const ExtObject& o = makeDynamicObject(g);
     154        g->decref();
     155        return o;
    122156}
    123157
    124158Geno* GenoObj::fromObject(const ExtValue& v, bool warn)
    125159{
    126 return (Geno*)v.getObjectTarget(getStaticParam().getName(), warn);
     160        return (Geno*)v.getObjectTarget(getStaticParam().getName(), warn);
    127161}
    128162
    129163void GenoObj::get_toVector(ExtValue *ret)
    130164{
    131 VectorObject *vec=new VectorObject;
    132 vec->data+=new ExtValue(shortString());
    133 vec->data+=new ExtValue(getName());
    134 vec->data+=new ExtValue(getComment());
    135 ret->setObject(ExtObject(&VectorObject::par,vec));
     165        VectorObject *vec = new VectorObject;
     166        vec->data += new ExtValue(shortString());
     167        vec->data += new ExtValue(getName());
     168        vec->data += new ExtValue(getComment());
     169        ret->setObject(ExtObject(&VectorObject::par, vec));
    136170}
    137171
    138 void GenoObj::p_newfromvector(ExtValue *args,ExtValue *ret)
     172void GenoObj::p_newfromvector(ExtValue *args, ExtValue *ret)
    139173{
    140 VectorObject *vec=VectorObject::fromObject(args->getObject());
    141 if (vec && (vec->data.size()>=3))
     174        VectorObject *vec = VectorObject::fromObject(args->getObject());
     175        if (vec && (vec->data.size() >= 3))
    142176        {
    143         SString g=vec->get(0)?vec->get(0)->getString():SString::empty();
    144         SString n=vec->get(1)?vec->get(1)->getString():SString::empty();
    145         SString c=vec->get(2)?vec->get(2)->getString():SString::empty();
    146         *ret=makeDynamicObjectAndDecRef(new Geno(g,-1,n,c));
     177                SString g = vec->get(0) ? vec->get(0)->getString() : SString::empty();
     178                SString n = vec->get(1) ? vec->get(1)->getString() : SString::empty();
     179                SString c = vec->get(2) ? vec->get(2)->getString() : SString::empty();
     180                *ret = makeDynamicObjectAndDecRef(new Geno(g, -1, n, c));
    147181        }
    148 else
    149         ret->setEmpty();
     182        else
     183                ret->setEmpty();
    150184}
    151185

  • cpp/frams/vm/classes/genoobj.h

    r415 r420  
    1010extern ParamEntry geno_paramtab[];
    1111
    12 class GenoObj: public Geno
     12class GenoObj : public Geno
    1313{
    14   public:
     14public:
    1515#define STATRICKCLASS GenoObj
    16 PARAMGETDEF(isvalid);
    17 PARAMSETDEF(isvalid);
    18 PARAMGETDEF(genotype);
    19 PARAMGETDEF(name);
    20 PARAMSETDEF(name);
    21 PARAMGETDEF(autoname);
    22 PARAMGETDEF(info);
    23 PARAMSETDEF(info);
    24 PARAMGETDEF(format);
    25 PARAMGETDEF(string);
    26 PARAMPROCDEF(p_getconvert);
    27 PARAMGETDEF(f0genotype);
    28 PARAMPROCDEF(p_new);
    29 PARAMPROCDEF(p_newfrom);
    30 PARAMPROCDEF(p_newfromstring);
    31 PARAMPROCDEF(p_newfromvector);
    32 PARAMGETDEF(toVector);
     16        PARAMGETDEF(isvalid);
     17        PARAMSETDEF(isvalid);
     18        PARAMGETDEF(genotype);
     19        PARAMGETDEF(name);
     20        PARAMSETDEF(name);
     21        PARAMGETDEF(autoname);
     22        PARAMGETDEF(info);
     23        PARAMSETDEF(info);
     24        PARAMGETDEF(format);
     25        PARAMGETDEF(string);
     26        PARAMPROCDEF(p_getconvert);
     27        PARAMGETDEF(f0genotype);
     28        PARAMPROCDEF(p_new);
     29        PARAMPROCDEF(p_newfrom);
     30        PARAMPROCDEF(p_newfromstring);
     31        PARAMPROCDEF(p_newfromvector);
     32        PARAMGETDEF(toVector);
    3333#undef STATRICKCLASS
    3434
    35 static ExtObject makeStaticObject(Geno* g);
    36 static ExtObject makeDynamicObject(Geno* g);
    37 static ExtObject makeDynamicObjectAndDecRef(Geno* g);
    38 static Geno* fromObject(const ExtValue& v, bool warn=true);
    39 static ParamInterface* getInterface();
     35        static ExtObject makeStaticObject(Geno* g);
     36        static ExtObject makeDynamicObject(Geno* g);
     37        static ExtObject makeDynamicObjectAndDecRef(Geno* g);
     38        static Geno* fromObject(const ExtValue& v, bool warn = true);
     39        static ParamInterface* getInterface();
    4040
    41 static Param& getStaticParam();
    42 static Param& getDynamicParam();
     41        static Param& getStaticParam();
     42        static Param& getDynamicParam();
    4343};
    4444
    4545#endif
    46 
    47 
    48 
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