X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=b7fbf4342b821d1f6eb6dbb7094d94c3e85d19a3;hb=d71a31a60542608595ce1278cc4a3398479cec7f;hp=0dc1cd977c9b106b4986e2cb839939cae7541db2;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 0dc1cd9..b7fbf43 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,6 +26,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
 	string getDescription()		{ return "trim.flows"; }
@@ -49,7 +50,8 @@ private:
 	vector<unsigned long long> getFlowFileBreaks();
 	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
 	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
 	vector<string> outputNames;
 	set<string> filesToRemove;
 	
@@ -58,7 +60,7 @@ private:
 	bool allFiles;
 	int processors;
 	int numFPrimers, numRPrimers;
-	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
 	int numFlows;
 	float signal, noise;
 	bool fasta;
@@ -66,10 +68,11 @@ private:
 	
 	string flowFileName, oligoFileName, outputDir;
 
-
 	map<string, int> barcodes;
 	map<string, int> primers;
 	vector<string> revPrimer;
+    vector<string> linker;
+    vector<string> spacer;
 
 	vector<string> primerNameVector;	//needed here?
 	vector<string> barcodeNameVector;	//needed here?
@@ -130,7 +133,7 @@ struct trimFlowData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){ 
 	trimFlowData* pDataArray;