6 // Gap penalty scores are negative
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7 // (i.e., are scores, not penalties).
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10 const char *SubstMxName;
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11 const float * const *SubstMx;
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20 // Global internal gaps
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27 // Global terminal gaps
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39 void SetLocal(float Open, float Ext);
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40 void Init2(const float * const *Mx, float Open, float Ext);
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41 void Init4(const float * const *Mx, float Open, float Ext, float TermOpen, float TermExt);
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42 void Init(const AlnParams &AP, const HSPData &HSP, unsigned LA, unsigned LB);
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43 void InitFromCmdLine(bool Nucleo);
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44 void SetMxFromCmdLine(bool Nucleo);
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45 void SetPenalties(const string &OpenStr, const string &ExtStr);
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46 float GetLocalOpen() const;
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47 float GetLocalExt() const;
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48 bool GetIsNucleo() const;
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52 const char *GetType() const;
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57 const float OBVIOUSLY_WRONG_PENALTY = 1000.0;
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59 #endif // alnparams_h
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