X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=refchimeratest.cpp;h=c084bffd40c94ef9c14a43d05de39e768dc96bea;hp=3685ed1ea56e482a08641ca6eb5e20fb23b53de0;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=23f4ffb61f28ec1e6b837633f77f7c6a81c46352

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 3685ed1..c084bff 100644
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -24,7 +24,8 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, bool aligned) : aligned(a
 	referenceSeqs.resize(numRefSeqs);
 	referenceNames.resize(numRefSeqs);
 	for(int i=0;i<numRefSeqs;i++){
-		referenceSeqs[i] = refs[i].getAligned();
+		if (aligned) { referenceSeqs[i] = refs[i].getAligned(); }
+        else { referenceSeqs[i] = refs[i].getUnaligned(); }
 		referenceNames[i] = refs[i].getName();
 	}
 	
@@ -117,10 +118,10 @@ int RefChimeraTest::analyzeUnalignedQuery(string queryName, string querySeq, ofs
     vector<string> queryAlign(numRefSeqs);
     vector<string> refAlign(numRefSeqs);
 
-    vector<vector<int> > leftDiffs(numRefSeqs, 0);
-    vector<vector<int> > rightDiffs(numRefSeqs, 0);
-    vector<vector<int> > leftMaps(numRefSeqs, 0);
-    vector<vector<int> > rightMaps(numRefSeqs, 0);
+    vector<vector<int> > leftDiffs(numRefSeqs);
+    vector<vector<int> > rightDiffs(numRefSeqs);
+    vector<vector<int> > leftMaps(numRefSeqs);
+    vector<vector<int> > rightMaps(numRefSeqs);
     
     int bestRefIndex = -1;
     int bestRefDiffs = numeric_limits<int>::max();
@@ -128,7 +129,7 @@ int RefChimeraTest::analyzeUnalignedQuery(string queryName, string querySeq, ofs
     
     for(int i=0;i<numRefSeqs;i++){
         double length = 0;
-        int diffs = alignQueryToReferences(querySeq, referenceSeqs[i], queryAlign[i], refAlign[i], length);
+        double diffs = alignQueryToReferences(querySeq, referenceSeqs[i], queryAlign[i], refAlign[i], length);
         if(diffs < bestRefDiffs){
             bestRefDiffs = diffs;
             bestRefLength = length;
@@ -324,7 +325,7 @@ double RefChimeraTest::alignQueryToReferences(string query, string reference, st
         		
 		int end = refLength - 1;
         int maxRow = 0;
-        double maxRowValue = -100000000000;
+        double maxRowValue = -2147483647;
         for(int i=0;i<queryLength;i++){
             if(alignMatrix[i][end] > maxRowValue){
                 maxRow = i;
@@ -334,7 +335,7 @@ double RefChimeraTest::alignQueryToReferences(string query, string reference, st
         
         end = queryLength - 1;
         int maxColumn = 0;
-        double maxColumnValue = -100000000000;
+        double maxColumnValue = -2147483647;
 
         for(int j=0;j<refLength;j++){
             if(alignMatrix[end][j] > maxColumnValue){