Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / alignment / Sequence.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/alignment/Sequence.cpp b/website/archive/binaries/mac/src/clustalw/src/alignment/Sequence.cpp
deleted file mode 100644 (file)
index a309081..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/alignment/Sequence.cpp
+++ /dev/null
@@ -1,239 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include <algorithm>
-#include "Sequence.h"
-
-using namespace std;
-
-namespace clustalw
-{
-
-/**
- * 
- * @param seq 
- * @param name 
- * @param title 
- * @return 
- */
-Sequence::Sequence(string& seq, string& name, string& title)
-{
-    copyStringIntoVector(&_sequence, &seq);
-    encodeSequence();
-    _name = name;
-    _title = title;
-    identifier = utilityObject->getUniqueSequenceIdentifier();
-}
-
-Sequence::Sequence(std::string& seq, std::string& name, std::string& title, unsigned long id)
-{
-    copyStringIntoVector(&_sequence, &seq);
-    encodeSequence();
-    _name = name;
-    _title = title;
-    identifier = id;
-}
-
-/**
- * This is an overloaded contructor that is used to construct a seq object from an
- * encoded sequenced instead of a string.
- * @param encodedSequence 
- * @param name 
- * @param title 
- * @param id The unique identifier from the previous sequence!!!
- * @return 
- */
-Sequence::Sequence(std::vector<int>* encodedSequence, std::string& name, std::string& title,
-                   unsigned long id)
-{
-    _encodedSequence = *encodedSequence;
-    _name = name;
-    _title = title;
-    identifier = id;        
-}
-
-/**
- * 
- */
-void Sequence::encodeSequence()
-{
-     /* code seq as ints .. use gapPos2 for gap */
-    std::vector<char>::iterator it;
-
-    _encodedSequence.push_back(0);
-    
-    for(it = _sequence.begin(); it != _sequence.end(); ++it) 
-    {
-        if (*it == '-')
-        {
-            _encodedSequence.push_back(userParameters->getGapPos2());
-        }
-        else
-        {
-            _encodedSequence.push_back(userParameters->resIndex(
-                                   userParameters->getAminoAcidCodes(), *it));
-        }
-    }
-}
-
-/**
- * 
- * @param _vectorTo 
- * @param _stringFrom 
- */
-void Sequence::copyStringIntoVector(vector<char>* _vectorTo, string* _stringFrom)
-{
-    _vectorTo->clear();
-
-    for(int i = 0; i < (int)_stringFrom->size(); i++)
-    {
-        _vectorTo->push_back(_stringFrom->at(i));
-    }
-    
-    if(_vectorTo->size() != _stringFrom->size())
-    {
-        std::cerr << "Error: In function copyStringIntoVector. Strings different length!\n";
-        exit(1);
-    }
-}
-
-/**
- * 
- */
-void Sequence::printSequence()
-{
-    std::cout << "This is the sequence and the encoded sequence " << _name << std::endl;
-    
-    std::vector<char>::iterator itChar;    
-    for(itChar = _sequence.begin(); itChar != _sequence.end(); ++itChar)
-    {
-        cout << *itChar;
-    } 
-    cout << std::endl;
-        
-    std::vector<int>::iterator itInt;
-    for(itInt = _encodedSequence.begin(); itInt != _encodedSequence.end(); ++itInt)
-    {
-        cout << "  " << *itInt;
-    } 
-    cout << std::endl;
-}
-
-/**
- * 
- */
-void Sequence::checkIntegrity()
-{
-    // The sequences should be the same length.
-    if(_sequence.size() != _encodedSequence.size())
-    {
-        std::cerr << "Error: _sequence is not same size as _encodedSequence\n";
-        exit(1);
-    }
-}
-
-/**
- * 
- * @return the encoded sequence, this is what is used in the pairwise!
- */
-std::vector<int>* Sequence::getSequence()
-{
-    return &_encodedSequence;
-}
-
-/**
- * 
- * @return 
- */
-std::string Sequence::getName()
-{
-    return _name;
-}
-
-/**
- * 
- * @return 
- */
-std::string Sequence::getTitle()
-{
-    return _title;
-}
-
-/**
- * 
- * @return 
- */
-bool Sequence::isEmpty()
-{
-    if(_sequence.size() == 0)
-    {
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-   
-}
-
-/**
- * 
- * @return 
- */
-bool Sequence::checkDNAFlag()
-// check if DNA or Protein
-// The decision is based on counting all A,C,G,T,U or N.
-// If >= 85% of all characters (except -) are as above => DNA 
-{
-    int c, numResidues, numBases;
-    float ratio;
-    string dna_codes = "ACGTUN";
-
-    numResidues = numBases = 0;
-    
-    vector<char>::iterator seqIterator = _sequence.begin();
-    
-    while (seqIterator != _sequence.end())
-    {
-        if (*seqIterator != '-')
-        {
-            numResidues++;
-            if (*seqIterator == 'N')
-            {
-                numBases++;
-            }
-            else
-            {
-                c = userParameters->resIndex(dna_codes, *seqIterator);
-                if (c >= 0)
-                {
-                    numBases++;
-                }
-            }
-        }
-        seqIterator++;
-    }
-    
-    if ((numBases == 0) || (numResidues == 0))
-    {
-        return false;
-    }
-    ratio = (float)numBases / (float)numResidues;
-
-    if (ratio >= 0.85)
-    {
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-}
-