X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=refchimeratest.h;h=5ea0801f17f437af48efbc148df9ef04875e3f31;hp=6b648fb9703d255a690fec9924dd439efd28df17;hb=615301e57c25e241356a9c2380648d117709458d;hpb=5e5253ff472de3c6349e562d2580873287be0c65

diff --git a/refchimeratest.h b/refchimeratest.h
index 6b648fb..5ea0801 100644
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,12 +16,22 @@
 class RefChimeraTest {
 	
 public:
-	RefChimeraTest(vector<Sequence>&, string);
-	int analyzeQuery(string, string);
+	RefChimeraTest(){};
+    RefChimeraTest(vector<Sequence>&, bool);
+	int printHeader(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);
@@ -32,8 +42,11 @@ private:
 	int numRefSeqs;
 	int alignLength;
 	int bestMatch;
-	ofstream chimeraReportFile;
-	
+    string bestRefAlignment;
+    string bestQueryAlignment;
+	//ofstream chimeraReportFile;
+	bool aligned;
+    
 	MothurOut* m;
 };