X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hp=8656fd0b5b314084c6fd08cf614288aca2bbc763;hb=615301e57c25e241356a9c2380648d117709458d;hpb=3dba4eab583a0ac8e3638cac5970641c79e661f9

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 8656fd0..f5493eb 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,7 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
 	string getDescription()		{ return "trim.flows"; }
 
@@ -49,7 +51,8 @@ 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;
 	
@@ -58,9 +61,7 @@ private:
 	bool allFiles;
 	int processors;
 	int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    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;
@@ -71,6 +72,8 @@ private:
 	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?
@@ -131,7 +134,7 @@ 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;
@@ -221,7 +224,7 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 				
 				flowData.printFlows(trimFlowFile);
 				
-				if(pDataArray->fasta)	{	currSeq.printSequence(fastaFile);	}
+				if(pDataArray->fasta)	{	currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);	}
 				
 				if(pDataArray->allFiles){
 					ofstream output;