added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index d5b7e5f806b54bdd2b9c8283cd6d781d5fe2abe1..0f34d0296020b8a3ebcf457084c10a80e25c27bb 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -132,7 +132,7 @@ class MothurOut {
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
                bool anyLabelsToProcess(string, set<string>&, string);
-               bool inUsersGroups(vector<string>, vector<string>);
+               bool inUsersGroups(vector<string>, vector<string>); //returns true if any of the strings in first vector are in second vector
         bool inUsersGroups(vector<int>, vector< vector<int> >);
                bool inUsersGroups(string, vector<string>);
         bool inUsersGroups(int, vector<int>);
@@ -158,6 +158,7 @@ class MothurOut {
                void splitAtDash(string&, vector<string>&);
                void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
+        int removeBlanks(vector<string>&);
         vector<string> splitWhiteSpaceWithQuotes(string);
                int removeConfidences(string&);
         string removeQuotes(string);
@@ -165,6 +166,7 @@ class MothurOut {
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
         map<string, vector<string> > parseClasses(string);
+        
                
                //math operation
         double max(vector<double>&); //returns largest value in vector