*** empty log message ***

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 7bc8b051f2f7465ee0dd7c030ffd31ca0569ac2c..b59363e13cc92f969145434d1ba8c0fa64573778 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -11,50 +11,29 @@ using namespace std;
 
 #include "sequence.hpp"
 
-//********************************************************************************************************************
-
-Sequence::Sequence(){}
+/***********************************************************************/
 
-//********************************************************************************************************************
-
-Sequence::Sequence(ifstream& fastaFile){
-       
-       string accession;
-       fastaFile >> accession;
-       setName(accession);
+Sequence::Sequence()  {}
 
-       char letter;
-       string sequence;
-       
-       while(fastaFile && letter != '>'){
-       
-               letter = fastaFile.get();
-               
-               if(isalpha(letter)){
-               
-                       sequence += letter;
-                       
-               }
-               
-       }
-       fastaFile.putback(letter);
+/***********************************************************************/
 
-       if(sequence.find_first_of('-') != string::npos){
+Sequence::Sequence(string newName, string sequence) {
+       name = newName;
+       if(sequence.find_first_of('-') != string::npos) {
                setAligned(sequence);
        }
        setUnaligned(sequence);
 }
 
-
 //********************************************************************************************************************
 
-string Sequence::convert2ints(){
+string Sequence::convert2ints() {
        
        if(unaligned == "")     {       /* need to throw an error */    }
        
        string processed;
        
-       for(int i=0;i<unaligned.length();i++){
+       for(int i=0;i<unaligned.length();i++) {
                if(toupper(unaligned[i]) == 'A')                        {       processed += '0';       }
                else if(toupper(unaligned[i]) == 'C')   {       processed += '1';       }
                else if(toupper(unaligned[i]) == 'G')   {       processed += '2';       }
@@ -67,7 +46,7 @@ string Sequence::convert2ints(){
 
 //********************************************************************************************************************
 
-void Sequence::setName(string seqName){
+void Sequence::setName(string seqName) {
        if(seqName[0] == '>')   {       name = seqName.substr(1);       }
        else                                    {       name = seqName;                         }
 }
@@ -76,14 +55,14 @@ void Sequence::setName(string seqName){
 
 void Sequence::setUnaligned(string sequence){
        
-       if(sequence.find_first_of('-') != string::npos){
+       if(sequence.find_first_of('-') != string::npos) {
                string temp = "";
-               for(int j=0;j<sequence.length();j++){
+               for(int j=0;j<sequence.length();j++) {
                        if(isalpha(sequence[j]))        {       temp += sequence[j];    }
                }
                unaligned = temp;
        }
-       else{
+       else {
                unaligned = sequence;
        }
        
@@ -103,7 +82,7 @@ void Sequence::setPairwise(string sequence){
 
 //********************************************************************************************************************
 
-string Sequence::getSeqName(){
+string Sequence::getName(){
        return name;
 }
 
@@ -126,3 +105,20 @@ string Sequence::getUnaligned(){
 }
 
 //********************************************************************************************************************
+
+int Sequence::getLength(){
+       if(unaligned.length() > aligned.length())
+               return unaligned.length();
+       return aligned.length();
+}
+
+//********************************************************************************************************************
+
+void Sequence::printSequence(ostream& out){
+       string toPrint = unaligned;
+       if(aligned.length() > unaligned.length())
+               toPrint = aligned;
+       out << ">" << name << "\n" << toPrint << "\n";
+}
+
+//********************************************************************************************************************