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 1caa1fe5814679a86e8026f1ec7a54d228dee44e..0f34d0296020b8a3ebcf457084c10a80e25c27bb 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -82,6 +82,7 @@ class MothurOut {
                vector<unsigned long long> setFilePosFasta(string, int&);
                string sortFile(string, string);
                int appendFiles(string, string);
+        int appendBinaryFiles(string, string);
         int appendFilesWithoutHeaders(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
@@ -97,6 +98,8 @@ class MothurOut {
                int openOutputFileAppend(string, ofstream&);
         int openOutputFileBinaryAppend(string, ofstream&);
                int openInputFile(string, ifstream&);
+        int openInputFileBinary(string, ifstream&);
+        int openInputFileBinary(string, ifstream&, string);
                int openInputFile(string, ifstream&, string); //no error given
     
         bool checkLocations(string&, string);  //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location.  Returns false if cant be found. If found completes name with location
@@ -129,7 +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>);
@@ -143,6 +146,7 @@ class MothurOut {
         bool isLabelEquivalent(string, string);
         string getSimpleLabel(string);
         string findEdianness();
+        string mothurGetpid(int);
        
                
                //string manipulation
@@ -154,6 +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);
@@ -161,6 +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