X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=inline;f=aligncommand.h;h=1410626a42e3a407289f18565dd0e64a3d4d3cd4;hb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;hp=1167c938708bcce7bb54755229bfceef00379822;hpb=b45e6f3d505a212cebad5ca22e2611b1466bca48;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 1167c93..1410626 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,7 +20,12 @@ 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();	
 	
@@ -33,6 +38,7 @@ private:
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	bool MPIWroteAccnos;
+	map<string, vector<string> > outputTypes;
 	
 	AlignmentDB* templateDB;
 	Alignment* alignment;
@@ -50,6 +56,7 @@ private:
 	float match, misMatch, gapOpen, gapExtend, threshold;
 	int processors, kmerSize;
 	vector<string> candidateFileNames;
+	vector<string> outputNames;
 	
 	bool abort, flip;
 };