X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hp=ab8ca91a42b35a9a283a3f9c6f2ee4606a01f7a4;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/trimflowscommand.h b/trimflowscommand.h
index ab8ca91..f5493eb 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -25,9 +25,11 @@ public:
 	
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
-	string getCommandCategory()		{ return "Hidden";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
-	string getCitation() { return "no citation"; }
+    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;
 	
@@ -58,7 +61,7 @@ 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 +69,11 @@ 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?
@@ -83,7 +87,7 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct trimFlowData {
+struct trimFlowData {
 	string flowFileName; 
 	string trimFlowFileName; 
 	string scrapFlowFileName;
@@ -130,7 +134,7 @@ typedef 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;
@@ -220,7 +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;