X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=refchimeratest.h;h=5ea0801f17f437af48efbc148df9ef04875e3f31;hp=d4983e05c07ca3b134811f5595290a472af477a4;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/refchimeratest.h b/refchimeratest.h
index d4983e0..5ea0801 100644
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,13 +16,22 @@
 class RefChimeraTest {
 	
 public:
-	RefChimeraTest(vector<Sequence>&);
+	RefChimeraTest(){};
+    RefChimeraTest(vector<Sequence>&, bool);
 	int printHeader(ofstream&);
-	int analyzeQuery(string, string, ofstream&);
+    int analyzeQuery(string, string, ofstream&);
 	int getClosestRefIndex();
+    string getClosestRefAlignment();
+    string getQueryAlignment();
+
 private:
-	int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
-	int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
+	int getAlignedMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
+    int analyzeAlignedQuery(string, string, ofstream&);
+    int analyzeUnalignedQuery(string, string, ofstream&);
+    double alignQueryToReferences(string, string, string&, string&, double&);
+    int getUnalignedDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
+
+    int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
 	int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
 	string stitchBimera(int, int, int);
 	string stitchTrimera(int, int, int, int, int);
@@ -33,8 +42,11 @@ private:
 	int numRefSeqs;
 	int alignLength;
 	int bestMatch;
+    string bestRefAlignment;
+    string bestQueryAlignment;
 	//ofstream chimeraReportFile;
-	
+	bool aligned;
+    
 	MothurOut* m;
 };