worked on hcluster. made .single command run using a sharedfile. and various other...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index ed2819bcc6c7a3adf335b8e7cd79ceb29e3ae01a..0255bd2409c043abfa1a7d261aa2910c78f9440e 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -41,17 +41,22 @@ private:
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
+       vector<string> fastaFileNames;
+       vector<string> namefileNames;
+       map<string, int> nameMap;
+       map<string, int>::iterator itNames;
        
        Classify* classify;
        
-       string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
-       int processors, kmerSize, numWanted, cutoff;
+       string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName;
+       int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
-       bool abort;
+       bool abort, probs;
        
-       int driver(linePair*, string, string);
+       int driver(linePair*, string, string, string);
        void appendTaxFiles(string, string);
-       void createProcesses(string, string); 
+       void createProcesses(string, string, string); 
+       string addUnclassifieds(string, int);
 };
 
 #endif