Merge remote-tracking branch 'origin/master'

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index cbeed469b0b571a66f79238aaac6d758658c0ac0..b0d7c7c18f3852dd40395b0f699749fc885cc14b 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,6 +23,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "screen.seqs";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
        string getDescription()         { return "enables you to keep sequences that fulfill certain user defined criteria"; }
@@ -43,6 +44,7 @@ private:
 
        int screenNameGroupFile(set<string>);
        int screenGroupFile(set<string>);
+    int screenCountFile(set<string>);
        int screenAlignReport(set<string>);
        int screenQual(set<string>);
        int screenTaxonomy(set<string>);
@@ -55,12 +57,11 @@ private:
        #endif
 
        bool abort;
-       string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+       string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile;
        int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
        vector<string> outputNames;
        vector<string> optimize;
        map<string, int> nameMap;
-       int readNames();
        
        int getSummary(vector<unsigned long long>&);
        int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
@@ -107,11 +108,11 @@ struct sumScreenData {
        int count;
        MothurOut* m;
        string goodFName, badAccnosFName, filename;
-    set<string>* badSeqNames;
+    set<string> badSeqNames;
        
        
        sumScreenData(){}
-       sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf, set<string>* bn) {
+       sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf) {
                startPos = s;
                endPos = e;
                minLength = minl;
@@ -124,7 +125,6 @@ struct sumScreenData {
                m = mout;
                start = st;
                end = en;
-               badSeqNames = bn;
                count = 0;
        }
 };
@@ -233,7 +233,7 @@ static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
                                }
                                else{
                                        badAccnosFile << currSeq.getName() << endl;
-                                       pDataArray->badSeqNames->insert(currSeq.getName());
+                                       pDataArray->badSeqNames.insert(currSeq.getName());
                                }
     
                        }