added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / addtargets2.cpp

diff --git a/uchime_src/addtargets2.cpp b/uchime_src/addtargets2.cpp
new file mode 100644 (file)
index 0000000..f3f6377
--- /dev/null
+++ b/uchime_src/addtargets2.cpp
@@ -0,0 +1,38 @@
+#if    UCHIMES\r
+\r
+#include "myutils.h"\r
+#include "chime.h"\r
+#include "ultra.h"\r
+#include <set>\r
+\r
+const float MAX_WORD_COUNT_DROP = 1;\r
+\r
+void SortDescending(const vector<float> &Values, vector<unsigned> &Order);\r
+bool GlobalAlign(const SeqData &Query, const SeqData &Target, string &Path);\r
+double GetFractIdGivenPath(const byte *A, const byte *B, const char *Path);\r
+void USort(const SeqData &Query, const SeqDB &DB, vector<float> &WordCounts,\r
+  vector<unsigned> &Order);\r
+\r
+void AddTargets(SeqDB &DB, const SeqData &Query, set<unsigned> &TargetIndexes)\r
+       {\r
+       const unsigned SeqCount = DB.GetSeqCount();\r
+       if (SeqCount == 0)\r
+               return;\r
+\r
+       vector<float> WordCounts;\r
+       vector<unsigned> Order;\r
+       USort(Query, DB, WordCounts, Order);\r
+       asserta(SIZE(Order) == SeqCount);\r
+       unsigned TopSeqIndex = Order[0];\r
+       float TopWordCount = WordCounts[TopSeqIndex];\r
+       for (unsigned i = 0; i < SeqCount; ++i)\r
+               {\r
+               unsigned SeqIndex = Order[i];\r
+               float WordCount = WordCounts[SeqIndex];\r
+               if (TopWordCount - WordCount > MAX_WORD_COUNT_DROP)\r
+                       return;\r
+               TargetIndexes.insert(SeqIndex);\r
+               }\r
+       }\r
+\r
+#endif\r