paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30..fb5b432f549de88a1fa519bc83541649a0882389 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -21,8 +21,10 @@ 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();
@@ -44,6 +46,7 @@ class MothurOut {
                //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 +68,8 @@ 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>&);
                
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
@@ -117,6 +122,7 @@ 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 +144,11 @@ 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:
@@ -169,6 +177,7 @@ class MothurOut {
                        accnosfile = "";
                        taxonomyfile = "";
                        processors = "1";
+                       flowfile = "";
                        gui = false;
                };
                ~MothurOut();
@@ -178,7 +187,7 @@ 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;