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[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
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+++ b/website/archive/binaries/mac/src/clustalw/src/alignment/Sequence.cpp
@@ -0,0 +1,239 @@
+/**
+ * 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;
+    }
+}
+
+}
+