diff BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.cpp @ 1:bec36315bd12 default tip

Deleted selected files

--- a/BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-//
-//  sequenceUtils.cpp
-//  BEDTools
-//
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Contains common functions for manipulating DNA sequences.
-//
-//  Acknowledgment: I am grateful to Michael Stromberg for the code below to
-//                  reverse complement a sequence.
-
-#include "sequenceUtils.h"
-
-// Performs an in-place sequence reversal
-void reverseSequence(string &seq) {
-    std::reverse(seq.begin(), seq.end());
-}
-
-// Performs an in-place reverse complement conversion
-void reverseComplement(string &seq) {
-
-    // reverse the sequence
-    reverseSequence(seq);
-
-    // swap the bases
-    for(unsigned int i = 0; i < seq.length(); i++) {
-        switch(seq[i]) {
-            case 'A':
-                seq[i] = 'T';
-                break;
-            case 'C':
-                seq[i] = 'G';
-                break;
-            case 'G':
-                seq[i] = 'C';
-                break;
-            case 'T':
-                seq[i] = 'A';
-                break;
-            case 'a':
-                seq[i] = 't';
-                break;
-            case 'c':
-                seq[i] = 'g';
-                break;
-            case 'g':
-                seq[i] = 'c';
-                break;
-            case 't':
-                seq[i] = 'a';
-                break;
-            default:
-                break;
-        }
-    }
-}
-
-
-void toLowerCase(std::string &seq)
-{
-    const int length = seq.length();
-    for(int i=0; i < length; ++i)
-    {
-        seq[i] = std::tolower(seq[i]);
-    }
-}
-
-
-void toUpperCase(std::string &seq)
-{
-    const int length = seq.length();
-    for(int i=0; i < length; ++i)
-    {
-        seq[i] = std::toupper(seq[i]);
-    }
-}
-
-
-void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other)
-{
-    // swap the bases
-    for(unsigned int i = 0; i < seq.length(); i++) {
-        switch(seq[i]) {
-            case 'A':
-            case 'a':
-                a++;
-                break;
-            case 'C':
-            case 'c':
-                c++;
-                break;
-            case 'G':
-            case 'g':
-                g++;
-                break;
-            case 'T':
-            case 't':
-                t++;
-                break;
-            case 'N':
-            case 'n':
-                n++;
-                break;
-            default:
-                other++;
-                break;
-        }
-    }    
-}
-
-
-int countPattern(const string &seq, const string &pattern)
-{
-    // swap the bases
-    int patternLength = pattern.size();
-    int patternCount = 0;
-    for(unsigned int i = 0; i < seq.length(); i++) {
-        if (seq.substr(i,patternLength) == pattern) {
-            patternCount++;
-        }
-    }
-    return patternCount;
-}
-        
-