Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / postProcessings.cpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/postProcessings.cpp b/binaries/src/mafft/extensions/mxscarna_src/postProcessings.cpp
deleted file mode 100644 (file)
index 1028630..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/postProcessings.cpp
+++ /dev/null
@@ -1,91 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////////////
-// postProcessings.cpp
-// 
-// several post process functions after aligning two profile stem candidate sequences
-//////////////////////////////////////////////////////////////////////////////////////
-
-#include <iostream>
-#include "scarna.hpp"
-#include "StemCandidate.hpp"
-#include <vector>
-#include <string>
-
-using namespace::MXSCARNA;
-
-void printStructure(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2);
-
-void removeConflicts(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2)
-{
-    int size = matchPSCS1->size();
-    
-    std::vector<int> found(size, 0);
-    for(int k = size - 1; k >= 0; k--) {
-       int i    = matchPSCS1->at(k);
-       int i_rv = pscs1->at(i).GetRvscnumber();
-       int j    = matchPSCS2->at(k);
-       int j_rv = pscs2->at(j).GetRvscnumber();
-       
-       found[k] = 0;
-       
-       for(int m = size - 1; m >= 0; m--) {
-           if ( (matchPSCS1->at(m) == i_rv) && (matchPSCS2->at(m) == j_rv) ) {
-               found[k] = 1;
-               break;
-           }
-       }
-    }
-
-    int pt = 0;
-    for(int k = 0; k < size; k++) {
-       matchPSCS1->at(pt) = matchPSCS1->at(k);
-       matchPSCS2->at(pt) = matchPSCS2->at(k);
-       if(found[k] == 1) ++pt; 
-    }
-
-    matchPSCS1->resize(pt);
-    matchPSCS2->resize(pt);
-    
-    //printStructure (pscs1, pscs2, matchPSCS1, matchPSCS2);
-}
-
-void printStructure(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2)
-{
-    int size = matchPSCS1->size();
-    int len  = WORDLENGTH;
-    std::vector<char> structure1(100, '.');
-    std::vector<char> structure2(100, '.');
-    for(int k = 0; k < size; k++) {
-       int i    = matchPSCS1->at(k);
-       int pos1 = pscs1->at(i).GetPosition();
-       int j    = matchPSCS2->at(k);
-       int pos2 = pscs2->at(j).GetPosition();
-       for(int l = 0; l < len; l++) {
-           if(pscs1->at(i).GetDistance() > 0) {
-               structure1[pos1 + l] = '(';
-           }
-           else {
-               structure1[pos1 + l] = ')';
-           }
-       
-           if(pscs2->at(j).GetDistance() > 0) {
-               structure2[pos2 + l] = '(';
-           }
-           else {
-               structure2[pos2 + l] = ')';
-           }
-       }
-       /*
-       std::cout << i << "\t" << pscs1->at(i).GetLength() << "\t" << pscs1->at(i).GetPosition() << "\t" << pscs1->at(i).GetRvposition() << "\t" << pscs1->at(i).GetDistance()  << "\t" << pscs1->at(i).GetContPos() << "\t" << pscs1->at(i).GetBeforePos() << "\t" << pscs1->at(i).GetRvscnumber() << endl;
-       */
-    }
-    size = structure1.size();
-    for(int k = 0; k < size; k++) {
-       std::cout << structure1[k];
-    }
-    std::cout << endl;
-    for(int k = 0; k < size; k++) {
-       std::cout << structure2[k];
-    }
-    std::cout << endl;
-}
-