added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 12de987e231247a4fb195aef20054bd94dacd375..2a6ba2de6316eb24ff281d703f8e27d4c94a45a3 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -65,7 +65,7 @@ class MothurOut {
        
                vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
                vector<string> Treenames;
-               map<string, string> names;
+               //map<string, string> names;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
@@ -73,6 +73,7 @@ class MothurOut {
                
                //functions from mothur.h
                //file operations
+        bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
                vector<unsigned long long> divideFile(string, int&);
                int divideFile(string, int&, vector<string>&);
                vector<unsigned long long> setFilePosEachLine(string, int&);
@@ -138,7 +139,7 @@ class MothurOut {
                int getRandomIndex(int); //highest
 
                int control_pressed;
-               bool executing, runParse, jumble, gui;
+               bool executing, runParse, jumble, gui, mothurCalling;
                
                //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
                string getPhylipFile()          { return phylipfile;            }
@@ -219,6 +220,7 @@ class MothurOut {
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
+            mothurCalling = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();