finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 47e5ca45cf52c61f8c14ce55c2e3c77dc83003c1..3019386a64d8947bccfcee23a9705e3b7e5d3898 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -36,10 +36,20 @@ class MothurOut {
                void setReleaseDate(string r) { releaseDate = r; }
                string getVersion() { return version; }
                void setVersion(string r) { version = r; }
-               vector<string> Groups;
+       
+               void addGroup(string g) { Groups.push_back(g); }
+               void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
+               void clearGroups() { Groups.clear(); }
+           int getNumGroups() { return Groups.size(); }
+               vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
+               void addAllGroup(string g) { namesOfGroups.push_back(g); }
+               void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
+               void clearAllGroups() { namesOfGroups.clear(); }
+               int getNumAllGroups() { return namesOfGroups.size(); }
+       
+               vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
                vector<string> Treenames;
                map<string, string> names;
-               vector<string> namesOfGroups;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
@@ -47,12 +57,12 @@ class MothurOut {
                
                //functions from mothur.h
                //file operations
-               vector<unsigned long int> divideFile(string, int&);
+               vector<unsigned long long> divideFile(string, int&);
                int divideFile(string, int&, vector<string>&);
-               vector<unsigned long int> setFilePosEachLine(string, int&);
-               vector<unsigned long int> setFilePosFasta(string, int&);
+               vector<unsigned long long> setFilePosEachLine(string, int&);
+               vector<unsigned long long> setFilePosFasta(string, int&);
                string sortFile(string, string);
-               void appendFiles(string, string);
+               int appendFiles(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
                string hasPath(string);
@@ -195,7 +205,8 @@ class MothurOut {
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
                string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
-       
+               vector<string> Groups;
+               vector<string> namesOfGroups;
                ofstream out;
                
                int mem_usage(double&, double&);