added getline function to mothur and modified places where we use getline to use...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index e9487c519e0d3e0378266eb537d15e28979546dc..685f0726e6ec5042d32379874e54b83e8a6eff26 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -7,8 +7,6 @@
  *
  */
 
-using namespace std;
-
 #include "sequence.hpp"
 
 /***********************************************************************/
@@ -25,7 +23,6 @@ Sequence::Sequence(string newName, string sequence) {
        name = newName;
        if(sequence.find_first_of('-') != string::npos) {
                setAligned(sequence);
-               isAligned = 1;
        }
        setUnaligned(sequence);
        
@@ -33,10 +30,12 @@ Sequence::Sequence(string newName, string sequence) {
 //********************************************************************************************************************
 
 Sequence::Sequence(ifstream& fastaFile){
+
+       initialize();
+       fastaFile >> name;
+       name = name.substr(1);
        
-       string accession;                               //      provided a file handle to a fasta-formatted sequence file, read in the next
-       fastaFile >> accession;                 //      accession number and sequence we find...
-       setName(accession);
+       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
 
        char letter;
        string sequence;
@@ -52,10 +51,9 @@ Sequence::Sequence(ifstream& fastaFile){
                        if(letter == 'U'){letter = 'T';}
                        sequence += letter;
                }
-               
        }
 
-       if(sequence.find_first_of('-') != string::npos){        //      if there are any gaps in the sequence, assume that it is
+       if((sequence.find_first_of('-') != string::npos) || (sequence.find_first_of('.') != string::npos)) {    //      if there are any gaps in the sequence, assume that it is
                setAligned(sequence);                                                   //      an alignment file
        }
        setUnaligned(sequence);                                                         //      also set the unaligned sequence file
@@ -91,7 +89,7 @@ void Sequence::setName(string seqName) {
 
 void Sequence::setUnaligned(string sequence){
        
-       if(sequence.find_first_of('-') != string::npos) {
+       if(sequence.find_first_of('.') != string::npos || sequence.find_first_of('-') != string::npos) {
                string temp = "";
                for(int j=0;j<sequence.length();j++) {
                        if(isalpha(sequence[j]))        {       temp += sequence[j];    }
@@ -131,7 +129,7 @@ void Sequence::setAligned(string sequence){
                        }
                }
        }
-       
+       isAligned = 1;  
 }
 
 //********************************************************************************************************************
@@ -249,11 +247,13 @@ int Sequence::getStartPos(){
        if(endPos == -1){
                for(int j = 0; j < alignmentLength; j++) {
                        if(aligned[j] != '.'){
-                               startPos = j;
+                               startPos = j + 1;
                                break;
                        }
                }
-       }       
+       }
+       if(isAligned == 0){     startPos = 1;   }
+
        return startPos;
 }
 
@@ -263,11 +263,13 @@ int Sequence::getEndPos(){
        if(endPos == -1){
                for(int j=alignmentLength-1;j>=0;j--){
                        if(aligned[j] != '.'){
-                               endPos = j;
+                               endPos = j + 1;
                                break;
                        }
                }
        }
+       if(isAligned == 0){     endPos = numBases;      }
+       
        return endPos;
 }
 
@@ -278,3 +280,19 @@ bool Sequence::getIsAligned(){
 }
 
 //********************************************************************************************************************
+
+void Sequence::reverseComplement(){
+
+       string temp;
+       for(int i=numBases-1;i>=0;i--){
+               if(unaligned[i] == 'A')         {       temp += 'T';    }
+               else if(unaligned[i] == 'T'){   temp += 'A';    }
+               else if(unaligned[i] == 'G'){   temp += 'C';    }
+               else if(unaligned[i] == 'C'){   temp += 'G';    }
+               else                                            {       temp += 'N';    }
+       }
+       unaligned = temp;
+       
+}
+
+//********************************************************************************************************************