X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=169b43512375aef99a22029b35425d87d6360afb;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=fb47874f8e1ff619a015b66b1f60952aafd61eb0;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index fb47874..169b435 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,19 +20,25 @@ class AlignCommand : public Command {
 	
 public:
 	AlignCommand(string);	
+	AlignCommand();
 	~AlignCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute(); 
 	void help();	
 	
 private:
 	struct linePair {
 		unsigned long int start;
-		int numSeqs;
-		linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	bool MPIWroteAccnos;
+	map<string, vector<string> > outputTypes;
 	
 	AlignmentDB* templateDB;
 	Alignment* alignment;
@@ -50,8 +56,10 @@ private:
 	float match, misMatch, gapOpen, gapExtend, threshold;
 	int processors, kmerSize;
 	vector<string> candidateFileNames;
+	vector<string> outputNames;
 	
-	bool abort, flip;
+	bool abort, flip, calledHelp;
+
 };
 
 #endif