Changeset 150 for cpp/frams/genetics/genoconv.cpp

Timestamp:

03/01/14 22:05:02 (10 years ago)

Author:

sz

Message:

Warn against missing converter, convert() caller can differentiate between conversion failure and missing converter.

File:

• cpp/frams/genetics/genoconv.cpp (modified) (3 diffs)

cpp/frams/genetics/genoconv.cpp

@@ -18 +18 @@
 ///////////////////////////////////////////////////////////////////////////
 
-GenoConvParam::GenoConvParam(GenoConvManager *g):Param(0),gcm(g)
-{
-updatetab();
+GenoConvParam::GenoConvParam(GenoConvManager *g) :Param(0), gcm(g)
+{
+        updatetab();
 }
 
 void GenoConvParam::freetab()
 {
-if (tab) free(tab);
-tab=0;
+        if (tab) free(tab);
+        tab = 0;
 }
 
 const char *GenoConvParam::id(int i)
 {
-if (i>=gcm->converters.size()) return 0;
-sprintf(tmp_id,"genkonw%d",i);
-return tmp_id;
+        if (i >= gcm->converters.size()) return 0;
+        sprintf(tmp_id, "genkonw%d", i);
+        return tmp_id;
 }
 
 void GenoConvParam::updatetab()
 {
-int i;
-GenoConverter *gk;
-ParamEntry *pe;
-int ile=gcm->converters.size();
-freetab();
-tab=(ParamEntry*)calloc(2+ile,sizeof(ParamEntry));
-tab[0].id="Genetics: Conversions";
-tab[0].group=1;
-tab[0].flags=(short)ile;
-tab[0].name="gkparam:";
-gcnames.clear();
-for (i=0,pe=tab+1;gk=(GenoConverter *)gcm->converters(i);pe++,i++)
-        {
-        pe->id="?";
-        pe->group=0;
-        pe->flags=0;
-        std::string descr="f";
-        descr+=gk->in_format;
-        descr+=" -> f";
-        descr+=gk->out_format;
-        descr+=" : ";
-        descr+=gk->name;
-        gcnames.push_back(descr);
-        pe->name=descr.c_str();
-        pe->type="d 0 1";
-        pe->help=gk->info;
-        }
-pe->id=0;
+        int i;
+        GenoConverter *gk;
+        ParamEntry *pe;
+        int ile = gcm->converters.size();
+        freetab();
+        tab = (ParamEntry*)calloc(2 + ile, sizeof(ParamEntry));
+        tab[0].id = "Genetics: Conversions";
+        tab[0].group = 1;
+        tab[0].flags = (short)ile;
+        tab[0].name = "gkparam:";
+        gcnames.clear();
+        for (i = 0, pe = tab + 1; gk = (GenoConverter *)gcm->converters(i); pe++, i++)
+        {
+                pe->id = "?";
+                pe->group = 0;
+                pe->flags = 0;
+                std::string descr = "f";
+                descr += gk->in_format;
+                descr += " -> f";
+                descr += gk->out_format;
+                descr += " : ";
+                descr += gk->name;
+                gcnames.push_back(descr);
+                pe->name = descr.c_str();
+                pe->type = "d 0 1";
+                pe->help = gk->info;
+        }
+        pe->id = 0;
 }
 
 GenoConvParam::~GenoConvParam()
 {
-freetab();
+        freetab();
 }
 
 void *GenoConvParam::getTarget(int i)
 {
-GenoConverter *gk=(GenoConverter *)gcm->converters(i);
-return &gk->enabled;
+        GenoConverter *gk = (GenoConverter *)gcm->converters(i);
+        return &gk->enabled;
 }
 
 GenoConvManager::GenoConvManager()
-        :param(this)
+:param(this)
 {
 }
@@ -86 +86 @@
 GenoConvManager::~GenoConvManager()
 {
-GenoConverter *gc;
-for (converters.start();gc=(GenoConverter*)converters();) delete gc;
+        FOREACH(GenoConverter*, gc, converters) delete gc;
 }
 
 void GenoConvManager::addConverter(GenoConverter *gc)
 {
-converters+=gc;
-param.updatetab();
+        converters += gc;
+        param.updatetab();
 }
 void GenoConvManager::removeConverter(GenoConverter *gc)
 {
-converters-=gc;
-param.updatetab();
-}
-
-GenoConverter *GenoConvManager::findConverters(SListTempl<GenoConverter*>* result,char in,char out,int enabled,char* name)
-{
-GenoConverter *gk,*retval=0;
-int i=0;
-for (;gk=(GenoConverter*)converters(i);i++)
-        {
-        if ((in!=-1)&&(in!=gk->in_format)) continue;
-        if ((out!=-1)&&(out!=gk->out_format)) continue;
-        if ((enabled!=-1)&&(enabled!=gk->enabled)) continue;
-        if ((name)&&(strcmp(name,gk->name))) continue;
-        if (!retval) {retval=gk; if (!result) break;}
-        if (result) result->append(gk);
-        }
-return retval;
-}
-
-/// write path into 'path'
+        converters -= gc;
+        param.updatetab();
+}
+
+GenoConverter *GenoConvManager::findConverters(SListTempl<GenoConverter*>* result, char in, char out, int enabled, char* name)
+{
+        GenoConverter *gk, *retval = 0;
+        int i = 0;
+        for (; gk = (GenoConverter*)converters(i); i++)
+        {
+                if ((in != -1) && (in != gk->in_format)) continue;
+                if ((out != -1) && (out != gk->out_format)) continue;
+                if ((enabled != -1) && (enabled != gk->enabled)) continue;
+                if ((name) && (strcmp(name, gk->name))) continue;
+                if (!retval) { retval = gk; if (!result) break; }
+                if (result) result->append(gk);
+        }
+        return retval;
+}
+
+/// Writes path into 'path'.
 /// return the last path element (return >= path)
 /// null -> path not found
@@ -123 +122 @@
 /// (can be NULL if you don't need this information)
 
-char *GenoConvManager::getPath(char in,char out,char *path,int maxlen,int *mapavailable)
-{
-if (!maxlen) return 0;
-GenoConverter *gk;
-int i=0;
-for (;gk=(GenoConverter*)converters(i);i++)
-        {
-        if ((gk->enabled)&&(gk->in_format == in))
+char *GenoConvManager::getPath(char in, char out, char *path, int maxlen, int *mapavailable)
+{
+        if (!maxlen) return 0;
+        GenoConverter *gk;
+        int i = 0;
+        for (; gk = (GenoConverter*)converters(i); i++)
+        {
+                if ((gk->enabled) && (gk->in_format == in))
                 {
-                *path=(char)i;
-                if (gk->out_format == out)
-                        {
-                        if (mapavailable)
-                                *mapavailable=gk->mapsupport;
-                        return path;
-                        }
-                else
-                        {
-                        int mapavail;
-                        char *ret=getPath(gk->out_format,out,path+1,maxlen-1,&mapavail);
-                        if (ret)
+                        *path = (char)i;
+                        if (gk->out_format == out)
+                        {
+                                if (mapavailable)
+                                        *mapavailable = gk->mapsupport;
+                                return path;
+                        }
+                        else
+                        {
+                                int mapavail;
+                                char *ret = getPath(gk->out_format, out, path + 1, maxlen - 1, &mapavail);
+                                if (ret)
                                 {
-                                if (mapavailable)
-                                        *mapavailable=gk->mapsupport && mapavail;
-                                return ret;
+                                        if (mapavailable)
+                                                *mapavailable = gk->mapsupport && mapavail;
+                                        return ret;
                                 }
                         }
                 }
         }
-return 0;
-}
-
-char *GenoConvManager::getFormatPath(char in,char out,char *path,int maxlen,int *mapavailable)
-{
-char *ret=getPath(in,out,path,maxlen,mapavailable);
-if (ret)
-        {
-        for (char*t=path;t<=ret;t++)
-                *t=((GenoConverter*)converters(*t))->out_format;
-        }
-return ret;
-}
-
-Geno GenoConvManager::convert(Geno &in,char format,MultiMap *map)
-{
-if (in.getFormat()==format) return in;
-char path[10];
-int dep;
-char *ret;
-if (in.isInvalid()) { return Geno("",0,"","invalid genotype cannot be converted"); }
-int mapavail;
-for (dep=1;dep<(int)sizeof(path);dep++) // sogenannte iteracyjne poglebianie...
-        if (ret=getPath(in.getFormat(),format,path,dep,&mapavail)) break;
-if (!ret) { return Geno("",0,"","converter not found"); }
-if (!map) mapavail=0;
-char *t=path;
-SString tmp;
-tmp=in.getGene();
-MultiMap lastmap,tmpmap;
-int firstmap=1;
-for (;t<=ret;t++)
-        {
-        GenoConverter *gk=(GenoConverter*)converters(*t);
-        tmp=gk->convert(tmp,mapavail?&tmpmap:0);
-        if (!tmp.len())
+        return 0;
+}
+
+char *GenoConvManager::getFormatPath(char in, char out, char *path, int maxlen, int *mapavailable)
+{
+        char *ret = getPath(in, out, path, maxlen, mapavailable);
+        if (ret)
+        {
+                for (char*t = path; t <= ret; t++)
+                        *t = ((GenoConverter*)converters(*t))->out_format;
+        }
+        return ret;
+}
+
+Geno GenoConvManager::convert(Geno &in, char format, MultiMap *map, bool *converter_missing)
+{
+        if (in.getFormat() == format) { if (converter_missing) *converter_missing = false; return in; }
+        char path[10];
+        int dep;
+        char *ret;
+        if (in.isInvalid()) { if (converter_missing) *converter_missing = false; return Geno("", 0, "", "invalid genotype cannot be converted"); }
+        int mapavail;
+        for (dep = 1; dep < (int)sizeof(path); dep++) //iterative deepening
+                if (ret = getPath(in.getFormat(), format, path, dep, &mapavail)) break;
+        if (!ret) { if (converter_missing) *converter_missing = true; return Geno("", 0, "", "converter not found"); }
+        if (converter_missing) *converter_missing = false;
+        if (!map) mapavail = 0;
+        char *t = path;
+        SString tmp;
+        tmp = in.getGene();
+        MultiMap lastmap, tmpmap;
+        int firstmap = 1;
+        for (; t <= ret; t++)
+        {
+                GenoConverter *gk = (GenoConverter*)converters(*t);
+                tmp = gk->convert(tmp, mapavail ? &tmpmap : 0);
+                if (!tmp.len())
                 {
-                char t[100];
-                sprintf(t,"f%c->f%c conversion failed (%s)",gk->in_format,gk->out_format,gk->name);
-                return Geno(0,0,0,t);
+                        char t[100];
+                        sprintf(t, "f%c->f%c conversion failed (%s)", gk->in_format, gk->out_format, gk->name);
+                        return Geno(0, 0, 0, t);
                 }
-        if (mapavail)
+                if (mapavail)
                 {
-                if (firstmap)
-                        {
-                        lastmap=tmpmap;
-                        firstmap=0;
-                        }
-                else
-                        {
-                        MultiMap m;
-                        m.addCombined(lastmap,tmpmap);
-                        lastmap=m;
-                        }
-                tmpmap.clear();
+                        if (firstmap)
+                        {
+                                lastmap = tmpmap;
+                                firstmap = 0;
+                        }
+                        else
+                        {
+                                MultiMap m;
+                                m.addCombined(lastmap, tmpmap);
+                                lastmap = m;
+                        }
+                        tmpmap.clear();
                 }
         }
-if (map)
-        *map=lastmap;
-return Geno(tmp, format, in.getName(), in.getComment());
-}
+        if (map)
+                *map = lastmap;
+        return Geno(tmp, format, in.getName(), in.getComment());
+}