changing command name classify.shared to classifyrf.shared

[mothur.git] / refchimeratest.h

diff --git a/refchimeratest.h b/refchimeratest.h
index d4983e05c07ca3b134811f5595290a472af477a4..5ea0801f17f437af48efbc148df9ef04875e3f31 100644 (file)
--- 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;
 };