X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=284c9a5ac1a0bd5c90dca6b4854b725d6b428023;hb=af9291809910b6ddf617490ed5c16254b77b449f;hp=007b6d6302d4062c09c62d9017fa663f3a902072;hpb=5d00ef3e809832f08efdd691a9eace8ac20feb07;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 007b6d6..284c9a5 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,7 +23,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "screen.seqs";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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 +45,7 @@ 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 +58,11 @@ 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 +109,11 @@ 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;
@@ -124,14 +126,13 @@ struct sumScreenData {
 		m = mout;
 		start = st;
 		end = en;
-		badSeqNames = bn;
 		count = 0;
 	}
 };
 
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){ 
 	sumData* pDataArray;
@@ -233,7 +234,7 @@ static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
 				}
 				else{
 					badAccnosFile << currSeq.getName() << endl;
-					pDataArray->badSeqNames->insert(currSeq.getName());
+					pDataArray->badSeqNames.insert(currSeq.getName());
 				}
     
 			}