6 static AlnParams g_AP;
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7 static bool g_APInitDone = false;
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9 bool GlobalAlign(const SeqData &Query, const SeqData &Target, PathData &PD)
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13 g_AP.InitFromCmdLine(true);
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14 g_APInitDone = true;
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17 ViterbiFast(Query.Seq, Query.L, Target.Seq, Target.L, g_AP, PD);
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21 bool GlobalAlign(const SeqData &Query, const SeqData &Target, string &Path)
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24 GlobalAlign(Query, Target, PD);
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25 Path = string(PD.Start);
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29 bool GlobalAlign(const SeqData &Query, const SeqData &Target, const AlnParams &/*AP*/,
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30 const AlnHeuristics &AH, HSPFinder &/*HF*/, float /*MinFractId*/, float &/*HSPId*/, PathData &PD)
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34 bool Found = GlobalAlign(Query, Target, Path);
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37 unsigned n = SIZE(Path);
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39 memcpy(PD.Front, Path.c_str(), n);
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40 PD.Start = PD.Front;
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