sped up align.seqs appending of files

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 9bdbc4479f19bd7e1aa8297ed4e1f278e0de912f..01f38e45ff55518238894a79503928759124679c 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -31,21 +31,30 @@ class ClusterFragmentsCommand : public Command {
        
 public:
        ClusterFragmentsCommand(string);
+       ClusterFragmentsCommand();
        ~ClusterFragmentsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
 private:
        bool abort;
        string fastafile, namefile, outputDir;
+       int diffs, percent;
        vector<seqRNode> alignSeqs; 
        map<string, string> names; //represents the names file first column maps to second column
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
        map<string, int>::iterator itSize; 
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();
        void printData(string, string); //fasta filename, names file name
+       bool isFragment(string, string);
        
 };