1 //uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
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8 // Gap penalty scores are negative
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9 // (i.e., are scores, not penalties).
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12 const char *SubstMxName;
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13 const float * const *SubstMx;
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22 // Global internal gaps
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29 // Global terminal gaps
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41 void SetLocal(float Open, float Ext);
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42 void Init2(const float * const *Mx, float Open, float Ext);
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43 void Init4(const float * const *Mx, float Open, float Ext, float TermOpen, float TermExt);
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44 void Init(const AlnParams &AP, const HSPData &HSP, unsigned LA, unsigned LB);
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45 void InitFromCmdLine(bool Nucleo);
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46 void SetMxFromCmdLine(bool Nucleo);
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47 void SetPenalties(const string &OpenStr, const string &ExtStr);
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48 float GetLocalOpen() const;
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49 float GetLocalExt() const;
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50 bool GetIsNucleo() const;
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54 const char *GetType() const;
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59 const float OBVIOUSLY_WRONG_PENALTY = 1000.0;
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61 #endif // alnparams_h
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