Changeset 530 for cpp/frams/genetics/geno.cpp

Timestamp:

07/18/16 04:16:11 (9 years ago)

Author:

Maciej Komosinski

Message:

Strict parsing of genotype format prefix

File:

• cpp/frams/genetics/geno.cpp (modified) (7 diffs)

cpp/frams/genetics/geno.cpp ¶

@@ -29 +29 @@
         owner = 0;
         f0gen = 0;
+        isvalid = -1;
+        name = genname;
+        txt = comment;
+        setGeneAndFormat(genstring,genformat);
+}
+
+void Geno::setGeneAndFormat(const SString& genstring, char genformat)
+{
         mapinshift = 0;
         mapoutshift = 0;
-        isvalid = -1;
         SString gencopy(genstring);
         if (genformat == -1)
@@ -43 +50 @@
                         case '/':
                                 genformat = genstring.charAt(2);
-                                if ((genformat == '\0') || isspace(genformat))
-                                        genformat = INVALID_FORMAT;
                                 if ((end = genstring.indexOf('\n')) >= 0)
                                 {
+                                        mapinshift = end + 1;
+                                        gencopy = genstring.substr(end + 1);
+                                        if ((end>0) && (genstring[end-1]=='\r')) end--;
                                         error_end = end;
                                         if (end != 3) genformat = INVALID_FORMAT;
-                                        gencopy = genstring.substr(end + 1);
-                                        mapinshift = end + 1;
                                 }
                                 else
@@ -61 +67 @@
                         case '*':
                                 genformat = genstring.charAt(2);
-                                if ((genformat == '\0') || isspace(genformat))
-                                        genformat = INVALID_FORMAT;
                                 if ((end = genstring.indexOf("*/")) >= 0)
                                 {
@@ -78 +82 @@
                                 break;
                         }
+                        if (!isalnum(genformat)) genformat=INVALID_FORMAT;
                         if (genformat == INVALID_FORMAT)
                         {
@@ -88 +93 @@
                                         cut = genstring.substr(0, error_end);
                                 int lf = cut.indexOf('\n');
-                                if (lf >= 0) cut = cut.substr(0, lf);
-                                logPrintf("Geno", "init", LOG_ERROR, "Invalid genotype format declaration: '%s'%s", cut.c_str(), genname.len() ? SString::sprintf(" in '%s'", genname.c_str()).c_str() : "");
+                                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() : "");
                         }
 
                 }
         }
-
         gen = gencopy;
+        multiline = (strchr(gen.c_str(), '\n') != 0);
         format = genformat;
-        name = genname;
-        txt = comment;
-        multiline = (strchr(gen.c_str(), '\n') != 0);
+        freeF0();
+        isvalid = -1;
         // mapoutshift...?
 }
@@ -146 +151 @@
 }
 
-void Geno::setGene(const SString& g, char newformat)
+void Geno::setGeneOnly(const SString& g)
 {
         gen = g;
         isvalid = -1;
         freeF0();
-        if (newformat >= 0) format = newformat;
 }
 
@@ -170 +174 @@
 }
 
-SString Geno::toString(void) const
-{
-        SString out;
-        int comment = 0;
-        if ((format != '1') || (comment = (txt.len() || name.len())))
-        {
-                if (multiline)
-                        out += "//";
-                else
-                        out += "/*";
-                out += format;
-                if (comment)
-                {
-                        if (txt.len()) { out += ";"; out += txt; }
-                        if (name.len()){ out += ";"; out += name; }
-                }
-                if (multiline)
-                        out += "\n";
-                else
-                        out += "*/";
-        }
-        out += gen;
-        return out;
-}
-
-SString Geno::shortString(void) const
+SString Geno::getGeneAndFormat(void) const
 {
         SString out;