added debug statements to trim.seqs

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 968ff97221ab7e277dfba48efc01682648998f0f..ac47d79f7d92b113f58dbe421fdbaad892b2b175 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -68,7 +68,7 @@ class MothurOut {
                //map<string, string> names;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
-               string saveNextLabel, argv, sharedHeaderMode;
+               string saveNextLabel, argv, sharedHeaderMode, groupMode;
                bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.h
@@ -174,11 +174,12 @@ class MothurOut {
                string getTaxonomyFile()        { return taxonomyfile;          }
                string getFlowFile()            { return flowfile;                      }
         string getBiomFile()           { return biomfile;                      }
+        string getCountTableFile()     { return counttablefile;        }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
                void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
-               void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }               
+               void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }               
                void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
                void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
                void setNameFile(string f)                      { namefile = getFullPathName(f);                        }       
@@ -197,6 +198,7 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
+        void setCountTableFile(string f)       { counttablefile = getFullPathName(f);  groupMode = "count";    }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
                void printCurrentFiles();
@@ -232,12 +234,14 @@ class MothurOut {
                        processors = "1";
                        flowfile = "";
             biomfile = "";
+            counttablefile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
+            groupMode = "group";
                }
                ~MothurOut();
 
@@ -246,7 +250,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
 
                vector<string> Groups;
                vector<string> namesOfGroups;