public:
AlignCheckCommand(string);
- ~AlignCheckCommand(){};
- int execute();
- void help();
-
+ AlignCheckCommand();
+ ~AlignCheckCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "align.check"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+ string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
vector<int> structMap;
- string mapfile, fastafile, outputDir;
+ string mapfile, fastafile, outputDir, namefile;
bool abort;
- int seqLength;
+ int seqLength, haderror;
+ vector<string> outputNames;
+ map<string, int> nameMap;
void readMap();
statData getStats(string sequence);