changed normalize.shared and sub.sample commands to fix bug in normalize.shared and...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30..47e5ca45cf52c61f8c14ce55c2e3c77dc83003c1 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 
-
 /***********************************************/
 
 class MothurOut {
@@ -21,8 +20,10 @@ class MothurOut {
                static MothurOut* getInstance();
                void setFileName(string);
                
-               void mothurOut(string);
-               void mothurOutEndLine();
+               void mothurOut(string); //writes to cout and the logfile
+               void mothurOutEndLine(); //writes to cout and the logfile
+               void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+               void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
                void mothurOutJustToLog(string);
                void errorOut(exception&, string, string);
                void closeLog();
@@ -39,11 +40,15 @@ class MothurOut {
                vector<string> Treenames;
                map<string, string> names;
                vector<string> namesOfGroups;
-               string saveNextLabel, argv;
+               vector<string> binLabelsInFile;
+               vector<string> currentBinLabels;
+               string saveNextLabel, argv, sharedHeaderMode;
+               bool printedHeaders;
                
                //functions from mothur.h
                //file operations
                vector<unsigned long int> divideFile(string, int&);
+               int divideFile(string, int&, vector<string>&);
                vector<unsigned long int> setFilePosEachLine(string, int&);
                vector<unsigned long int> setFilePosFasta(string, int&);
                string sortFile(string, string);
@@ -65,6 +70,9 @@ class MothurOut {
                void gobble(istream&);
                void gobble(istringstream&);
                map<string, int> readNames(string);
+               int readNames(string, map<string, string>&);
+               int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+               void mothurRemove(string);
                
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
@@ -93,6 +101,7 @@ class MothurOut {
                float ceilDist(float, int);
                float roundDist(float, int);
                unsigned int fromBase36(string);
+               int getRandomIndex(int); //highest
 
                int control_pressed;
                bool executing, runParse, jumble, gui;
@@ -117,6 +126,7 @@ class MothurOut {
                string getOligosFile()          { return oligosfile;            }
                string getAccnosFile()          { return accnosfile;            }
                string getTaxonomyFile()        { return taxonomyfile;          }
+               string getFlowFile()            { return flowfile;                      }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -138,9 +148,11 @@ class MothurOut {
                void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
                void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
+               void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
                void setProcessors(string p)            { processors = p;                                                       }
                
                void printCurrentFiles();
+               bool hasCurrentFiles();
                void clearCurrentFiles();
                
        private:
@@ -169,8 +181,11 @@ class MothurOut {
                        accnosfile = "";
                        taxonomyfile = "";
                        processors = "1";
+                       flowfile = "";
                        gui = false;
-               };
+                       printedHeaders = false;
+                       sharedHeaderMode = "";
+               }
                ~MothurOut();
 
                string logFileName;
@@ -178,7 +193,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
        
                ofstream out;