pat's edits of screen.seqs and summary.seqs

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index e9487c519e0d3e0378266eb537d15e28979546dc..98aa7b01862c494018c710ec607f5132d8ce2db1 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -25,7 +25,6 @@ Sequence::Sequence(string newName, string sequence) {
        name = newName;
        if(sequence.find_first_of('-') != string::npos) {
                setAligned(sequence);
-               isAligned = 1;
        }
        setUnaligned(sequence);
        
@@ -33,6 +32,7 @@ Sequence::Sequence(string newName, string sequence) {
 //********************************************************************************************************************
 
 Sequence::Sequence(ifstream& fastaFile){
+       initialize();
        
        string accession;                               //      provided a file handle to a fasta-formatted sequence file, read in the next
        fastaFile >> accession;                 //      accession number and sequence we find...
@@ -131,7 +131,7 @@ void Sequence::setAligned(string sequence){
                        }
                }
        }
-       
+       isAligned = 1;  
 }
 
 //********************************************************************************************************************
@@ -249,11 +249,13 @@ 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 +265,13 @@ 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 +282,19 @@ 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;
+       
+}
+
+//********************************************************************************************************************