Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / multipleAlign / ProfileBase.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileBase.h b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileBase.h
deleted file mode 100644 (file)
index f022938..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileBase.h
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@@ -1,78 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-/**
- * The reason why we have 2 different types of profiles is because one of them 
- * (ProfileWithSub) has the substitution matrix information already in it. This
- * increases the performance when aligning 2 profile columns.
- */
-#ifndef PROFILEBASE_H
-#define PROFILEBASE_H
-
-#include "../alignment/Alignment.h"
-
-namespace clustalw
-{
-
-class ProfileBase
-{
-    public:
-        /* Functions */
-        ProfileBase(int prfLen, int firstS, int lastS);
-        void calcGapCoeff(SeqArray* seqArray, vector<int>* gaps,  bool useStructPenalties,
-                          vector<char>* gapPenaltyMask, int gapCoef, int lenCoef);
-        const SeqArray* getProfilePtr(){return &profile;};
-        void resetProfile(){for(int i = 0; i < (int)profile.size();i++)
-                            {
-                                profile[i].clear();
-                            }
-                            profile.clear();
-                            };
-        /* Attributes */
-
-    protected:
-        /* Functions */
-        void calcVPenalties(SeqArray* aln, vector<int>* weight); 
-        void calcResidueSpecificPen(SeqArray* aln, vector<int>* weight); 
-        void calcHydrophilicPen(SeqArray* aln, vector<int>* weight); 
-        int localPenalty(int penalty, int n, vector<int>* resWeight, vector<int>* hydWeight,
-                         vector<int>* vWeight);  
-        float percentId(vector<int>* s1, vector<int>* s2);
-
-        /* Attributes */
-        vector<vector<int> > profile;
-
-        /* number of residues used for a window for the variable zone
-           penalties */
-        int vwindow;
-        /* vll is the lower limit for the variable zone penalties
-           (vll < pen < 1.0) */
-        int vll;
-
-        /* "Pascarella and Argos" residue specific gap modification
-           factors. See Table 1 in the ClustalW 1994 NAR paper
-           http://www.ncbi.nlm.nih.gov/pubmed/7984417
-        */
-        string pascarellaRes;
-        vector<int> pascarellaProb;
-
-        vector<vector<int> > vlut;
-        static const int numLetters = 26;
-        float reducedGap;
-        bool nVarPen;
-        bool nHydPen;
-        bool nPrefPen;
-        int gdist;
-        int prfLength;
-        int firstSeq, lastSeq;
-    private:
-        /* Functions */
-
-        /* Attributes */
-
-};
-
-}
-#endif