Revert to previous commit

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
new file mode 100644 (file)
index 0000000..29c1741
--- /dev/null
+++ b/groupmap.h
@@ -0,0 +1,54 @@
+#ifndef GROUPMAP_H
+#define GROUPMAP_H
+/*
+ *  groupmap.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 12/1/08.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "mothurout.h"
+
+/* This class is a representation of the groupfile.  It is used by all the shared commands to determine what group a 
+       certain sequence belongs to. */
+
+class GroupMap {
+public:
+       GroupMap() {};
+       GroupMap(string);
+       ~GroupMap();
+       int readMap();
+       int readDesignMap();
+       int getNumGroups();
+       bool isValidGroup(string);  //return true if string is a valid group
+       string getGroup(string);
+       void setGroup(string, string);
+       vector<string> getNamesOfGroups() {
+               sort(namesOfGroups.begin(), namesOfGroups.end());
+               groupIndex.clear();
+               for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
+               return namesOfGroups;
+       }
+       void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
+       map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+       int getNumSeqs()  {  return groupmap.size();  }
+       vector<string> getNamesSeqs();
+       vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
+       int getNumSeqs(string); //return the number of seqs in a given group
+                       
+private:
+       vector<string> namesOfGroups;
+       MothurOut* m;
+       ifstream fileHandle;
+       string groupFileName;
+       int index;
+       map<string, string>::iterator it;
+       void setNamesOfGroups(string); 
+       map<string, string> groupmap; //sequence name and groupname
+       map<string, int> seqsPerGroup;  //maps groupname to number of seqs in that group
+};
+
+#endif