Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / StemCandidate.hpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/StemCandidate.hpp b/binaries/src/mafft/extensions/mxscarna_src/StemCandidate.hpp
deleted file mode 100644 (file)
index e1678d6..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/StemCandidate.hpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/////////////////////////////////////////////////////////////
-// StemCandidate.hpp
-// Profile Stem Candidate calcurated by profile base pairing
-// probability matrix 
-////////////////////////////////////////////////////////////
-
-#ifndef __STEMCANDIDATE_HPP__
-#define __STEMCANDIDATE_HPP__
-
-#include <string>
-#include <vector>
-
-using namespace std;
-
-namespace MXSCARNA {
-class StemCandidate {
-private:
-    int numSeq;                      /* the number of sequences in the profile */
-    int length;                      /* length of profile stem candidate of fixed length */
-    int position;                    /* 5' start position of SC in profile */
-    int distance;
-    std::vector<std::string> substr; /* profile base string of SC */
-    std::vector<std::string> rvstr;  /* profile base string of stem partner of SC */
-    int rvposition;                  /* 3' end position of stem partner of SC */
-    int rvscnumber;                  /* SC number of stem partner */
-    int contPos;                            /* previous stem that corresponds continuous stem and has position -1. */
-    int beforePos;                  /* most recent stem that doesn't overlap to SC and has position -len. */
-    float score;                     /* score of the sum of base pairing probability matrix */
-    std::vector<float> baseScore;
-    float stacking;                  /* the mean of stacking energy */
-    float stemStacking;              /* the mean of 1-continuous stacking energy */
-
-public:
-    StemCandidate() : numSeq(0), length(0), position(0), distance(0), 
-                      rvposition(0), rvscnumber(0), contPos(-1), beforePos(0),
-                      score(0), stacking(0), stemStacking(0) {}
-    StemCandidate(int numSeq, int length) : numSeq(numSeq), length(length), 
-                                           substr(numSeq), rvstr(numSeq), 
-                                           contPos(-1) { }
-
-    void SetNumSeq(int num) { numSeq = num; }
-    void SetLength(int len) { length = len; }
-    void SetNumSubstr(int num) {
-        substr.resize(num);
-       for(int i = 0; i < num; i++) {
-           string &tmpStr = substr[i];
-           tmpStr = "";
-           substr[i] = tmpStr;
-       }
-    }
-    void SetNumRvstr(int num) {
-        rvstr.resize(num);
-       
-       for(int i = 0; i < num; i++) {
-           string &tmpStr = rvstr[i];
-           tmpStr = "";
-           rvstr[i] = tmpStr;
-       }
-    }
-    void SetPosition(int pos) { position = pos; }
-
-    void AddSubstr(int num, char word) {
-       std::string &tmpStr = substr[num];
-       tmpStr += word;
-       substr[num] = tmpStr;
-    }
-
-    void AddRvstr(int num, char word) {
-       std::string &tmpStr = rvstr[num];
-       tmpStr += word;
-       rvstr[num] = tmpStr;
-    }
-
-    void AddBaseScore(float score) {
-        baseScore.push_back(score);
-    }
-
-    void SetRvposition(int pos) { rvposition = pos; }
-    void SetRvscnumber(int num) { rvscnumber = num; }
-    void SetContPos(int pos) { contPos = pos; }
-    void SetBeforePos(int pos) { beforePos = pos; }
-    void SetDistance(int d) { distance = d; }
-    void SetScore(float s) { score = s; }
-    void AddScore(float s) { score += s; }
-    void SetStacking(float s) { stacking = s; }
-    void AddStacking(float s) { stacking += s; }
-    void SetStemStacking(float s) { stemStacking = s; }
-    int  GetNumSeq() const { return numSeq; }
-    int  GetLength() const { return length; }
-    int  GetPosition() const { return position; }
-    
-    string GetSubstr(int num) const { 
-       const std::string &tmpStr = substr[num];
-       return tmpStr;
-    }
-    string GetRvstr(int num) const {
-       const std::string &tmpStr = rvstr[num];
-       return tmpStr;
-    }
-    float GetBaseScore(int i) const  {
-        return baseScore[i];
-    }
-    int GetRvposition() const {
-       return rvposition;
-    }
-    int GetRvscnumber() const {
-       return rvscnumber;
-    }
-    int GetContPos() const {
-       return contPos;
-    }
-    int GetBeforePos() const {
-       return beforePos;
-    }
-    int GetDistance() const {
-        return distance;
-    }
-    float GetScore() const {
-       return score;
-    }
-    float GetStacking() const  {
-       return stacking;
-    }
-    float GetStemStacking() const {
-       return stemStacking;
-    }
-};
-}
-#endif // __STEMCANDIDATE_HPP__