X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=uchime_src%2Fgetparents.cpp;fp=uchime_src%2Fgetparents.cpp;h=d82f9028b25f1ff9c37f8ec100970df5d687c511;hb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;hp=0000000000000000000000000000000000000000;hpb=aa23898d895a8c04cc4582a8809343df0aef6622;p=mothur.git

diff --git a/uchime_src/getparents.cpp b/uchime_src/getparents.cpp
new file mode 100644
index 0000000..d82f902
--- /dev/null
+++ b/uchime_src/getparents.cpp
@@ -0,0 +1,89 @@
+#include "myutils.h"
+#include "chime.h"
+#include "ultra.h"
+#include <set>
+
+void AddTargets(Ultra &U, const SeqData &Query, set<unsigned> &TargetIndexes);
+
+void GetChunkInfo(unsigned L, unsigned &Length, vector<unsigned> &Los)
+	{
+	Los.clear();
+
+	if (L <= opt_minchunk)
+		{
+		Length = L;
+		Los.push_back(0);
+		return;
+		}
+
+	Length = (L - 1)/opt_chunks + 1;
+	if (Length < opt_minchunk)
+		Length = opt_minchunk;
+
+	unsigned Lo = 0;
+	for (;;)
+		{
+		if (Lo + Length >= L)
+			{
+			Lo = L - Length - 1;
+			Los.push_back(Lo);
+			return;
+			}
+		Los.push_back(Lo);
+		Lo += Length;
+		}
+	}
+
+void GetCandidateParents(Ultra &U, const SeqData &QSD, float AbQ,
+  vector<unsigned> &Parents)
+	{
+	Parents.clear();
+
+	set<unsigned> TargetIndexes;
+
+	unsigned QL = QSD.L;
+
+	SeqData QuerySD = QSD;
+
+	unsigned ChunkLength;
+	vector<unsigned> ChunkLos;
+	GetChunkInfo(QL, ChunkLength, ChunkLos);
+	unsigned ChunkCount = SIZE(ChunkLos);
+	for (unsigned ChunkIndex = 0; ChunkIndex < ChunkCount; ++ChunkIndex)
+		{
+		unsigned Lo = ChunkLos[ChunkIndex];
+		asserta(Lo + ChunkLength <= QL);
+
+		const byte *Chunk = QSD.Seq + Lo;
+
+	// THIS MESSES UP --self!!
+		//char Prefix[32];
+		//sprintf(Prefix, "%u|", Lo);
+		//string ChunkLabel = string(Prefix) + string(QSD.Label);
+
+		//QuerySD.Label = ChunkLabel.c_str();
+		QuerySD.Seq = Chunk;
+		QuerySD.L = ChunkLength;
+
+		AddTargets(U, QuerySD, TargetIndexes);
+
+		Lo += ChunkLength;
+		}
+
+	for (set<unsigned>::const_iterator p = TargetIndexes.begin();
+	  p != TargetIndexes.end(); ++p)
+		{
+		unsigned TargetIndex = *p;
+		bool Accept = true;
+		if (AbQ > 0.0f)
+			{
+			const char *TargetLabel = U.GetSeedLabel(TargetIndex);
+			float AbT = GetAbFromLabel(string(TargetLabel));
+			if (AbT > 0.0f && AbT < opt_abskew*AbQ)
+				Accept = false;
+			}
+
+		if (Accept)
+			Parents.push_back(TargetIndex);
+		}
+	}