public:
SensSpecCommand(string);
+ SensSpecCommand();
~SensSpecCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
void processPhylip();
-/// void processColumn(map<string, int>);
+ void processColumn();
+ void setUpOutput();
+ void outputStatistics(string, string);
- string listFile, distFile, nameFile, outputDir;
+ string listFile, distFile, nameFile, sensSpecFileName;
+ string outputDir;
string format;
-// int numSeqs, numDists;
- int truePositives, falsePositives, trueNegatives, falseNegatives;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
+ long int truePositives, falsePositives, trueNegatives, falseNegatives;
bool abort;
bool hard;
string lineLabel;
double cutoff;
+ int precision;
};
-#endif
\ No newline at end of file
+#endif
+
+
+