7 typedef std::vector<Seq *> SeqVectBase;
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9 class SeqVect : public SeqVectBase
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16 // Not implemented; prevent use of copy c'tor and assignment.
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17 SeqVect(const SeqVect &);
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18 SeqVect &operator=(const SeqVect &);
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21 void FromFile(TextFile &File)
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23 FromFASTAFile(File);
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26 void FromFASTAFile(TextFile &File);
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27 void ToFASTAFile(TextFile &File) const;
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29 void ToFile(TextFile &File) const
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34 void PadToMSA(MSA &msa);
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35 void Copy(const SeqVect &rhs);
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37 void StripGapsAndWhitespace();
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40 unsigned Length() const { return (unsigned) size(); }
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41 unsigned GetSeqCount() const { return (unsigned) size(); }
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42 void AppendSeq(const Seq &s);
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43 bool FindName(const char *ptrName, unsigned *ptruIndex) const;
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45 const char *GetSeqName(unsigned uSeqIndex) const;
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46 unsigned GetSeqId(unsigned uSeqIndex) const;
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47 unsigned GetSeqIdFromName(const char *Name) const;
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48 unsigned GetSeqLength(unsigned uSeqIndex) const;
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49 void SetSeqId(unsigned uSeqIndex, unsigned uId);
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50 Seq &GetSeq(unsigned uIndex);
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51 Seq &GetSeqById(unsigned uId);
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52 const Seq &GetSeq(unsigned uIndex) const;
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54 ALPHA GuessAlpha() const;
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58 reference at(size_type i) { return operator[](i); }
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59 const_reference at(size_type i) const { return operator[](i); }
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