X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=58d3ed096eac4e9b3b733adaa31d10b37a068d87;hb=HEAD;hp=8656fd0b5b314084c6fd08cf614288aca2bbc763;hpb=3dba4eab583a0ac8e3638cac5970641c79e661f9;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 8656fd0..58d3ed0 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -16,6 +16,7 @@
 #include "flowdata.h"
 #include "groupmap.h"
 #include "trimoligos.h"
+#include "oligos.h"
 
 class TrimFlowsCommand : public Command {
 public:
@@ -26,7 +27,9 @@ 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"; }
 
@@ -45,42 +48,29 @@ private:
 	int comboStarts;
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
-
-	vector<unsigned long long> getFlowFileBreaks();
-	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
-	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
-	vector<string> outputNames;
+    vector<string> outputNames;
 	set<string> filesToRemove;
-	
-	void getOligos(vector<vector<string> >&);		//a rewrite of what is in trimseqscommand.h
-	
-	bool allFiles;
+    bool allFiles;
 	int processors;
-	int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+	int numFPrimers, numRPrimers, numBarcodes;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
 	int numFlows;
 	float signal, noise;
-	bool fasta;
-	string flowOrder;	
-	
-	string flowFileName, oligoFileName, outputDir;
+	bool fasta, pairedOligos, reorient;
+	string flowOrder, flowFileName, oligoFileName, outputDir;
+    Oligos oligos;
 
-	map<string, int> barcodes;
-	map<string, int> primers;
-	vector<string> revPrimer;
 
-	vector<string> primerNameVector;	//needed here?
-	vector<string> barcodeNameVector;	//needed here?
-
-	map<string, int> combos;			//needed here?
-	map<string, int> groupToIndex;		//needed here?
+	vector<unsigned long long> getFlowFileBreaks();
+	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
+	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+	int getOligos(vector<vector<string> >&);		//a rewrite of what is in trimseqscommand.h
+	
+	
 	
 };
 
-/**************************************************************************************************/
+/**************************************************************************************************
 //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).
@@ -130,8 +120,8 @@ 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 +211,7 @@ 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;
@@ -257,6 +247,6 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 	}
 } 
 #endif
-
+*/
 
 #endif