added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index d6073d75da3ed630b27b626bbba8615d79b58858..efeb88ce65183135c2a0aaef36d8d3a1c8f432cc 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -76,7 +76,8 @@ Sequence::Sequence(istringstream& fastaString){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
+                       //while (!fastaString.eof())    {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
+            comment = getCommentString(fastaString);
                        
                        int numAmbig = 0;
                        sequence = getSequenceString(fastaString, numAmbig);
@@ -120,7 +121,8 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                                }
                        }
                        
-                       while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
+                       //while (!fastaString.eof())    {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
+            comment = getCommentString(fastaString);
                        
                        int numAmbig = 0;
                        sequence = getSequenceString(fastaString, numAmbig);
@@ -166,8 +168,8 @@ Sequence::Sequence(ifstream& fastaFile){
                                }
                        }
                        
-                       //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){  break;      }       } // get rest of line if there's any crap there
+                       //while (!fastaFile.eof())      {       char c = fastaFile.get(); if (c == 10 || c == 13){  break;      }       } // get rest of line if there's any crap there
+            comment = getCommentString(fastaFile);
                        
                        int numAmbig = 0;
                        sequence = getSequenceString(fastaFile, numAmbig);
@@ -216,9 +218,11 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
                        //read info after sequence name
                        while (!fastaFile.eof())        {       
                 char c = fastaFile.get(); 
-                if (c == 10 || c == 13 || c == -1){  break;    }
+                if (c == 10 || c == 13 || c == -1){   break;   }
                 extraInfo += c;
-            } 
+            }
+            
+            comment = extraInfo;
                        
                        int numAmbig = 0;
                        sequence = getSequenceString(fastaFile, numAmbig);
@@ -261,8 +265,8 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                                }
                        }
                        
-                       //read real sequence
-                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){       break; }       } // get rest of line if there's any crap there
+                       //while (!fastaFile.eof())      {       char c = fastaFile.get(); if (c == 10 || c == 13){       break; }       } // get rest of line if there's any crap there
+            comment = getCommentString(fastaFile);
                        
                        int numAmbig = 0;
                        sequence = getSequenceString(fastaFile, numAmbig);
@@ -360,17 +364,19 @@ string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
 string Sequence::getCommentString(ifstream& fastaFile) {
        try {
                char letter;
-               string sequence = "";
+               string temp = "";
                
                while(fastaFile){
                        letter=fastaFile.get();
-                       if((letter == '\r') || (letter == '\n')){  
+                       if((letter == '\r') || (letter == '\n') || letter == -1){
                                m->gobble(fastaFile);  //in case its a \r\n situation
                                break;
-                       }
+                       }else {
+                temp += letter;
+            }
                }
                
-               return sequence;
+               return temp;
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "getCommentString");
@@ -414,17 +420,19 @@ string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
 string Sequence::getCommentString(istringstream& fastaFile) {
        try {
                char letter;
-               string sequence = "";
+               string temp = "";
                
                while(fastaFile){
                        letter=fastaFile.get();
-                       if((letter == '\r') || (letter == '\n')){  
+                       if((letter == '\r') || (letter == '\n') || letter == -1){  
                                m->gobble(fastaFile);  //in case its a \r\n situation
                                break;
-                       }
+                       }else {
+                temp += letter;
+            }
                }
                
-               return sequence;
+               return temp;
        }
        catch(exception& e) {
                m->errorOut(e, "Sequence", "getCommentString");
@@ -439,6 +447,7 @@ void Sequence::initialize(){
        unaligned = "";
        aligned = "";
        pairwise = "";
+    comment = "";
        
        numBases = 0;
        alignmentLength = 0;
@@ -581,7 +590,7 @@ int Sequence::getNumNs(){
 
 void Sequence::printSequence(ostream& out){
 
-       out << ">" << name << endl;
+       out << ">" << name << comment << endl;
        if(isAligned){
                out << aligned << endl;
        }