fixed problem with class.fy.seqs where group totals did not add up. added constructo...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 3bd80a87fde16f95d1bf1f8ae9369c0f962eb181..71dd3a925fab8eb7771803c6db557dfb9d10200b 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -10,14 +10,11 @@
 #include "sequence.hpp"
 
 /***********************************************************************/
-
 Sequence::Sequence(){
        m = MothurOut::getInstance();
        initialize();
 }
-
 /***********************************************************************/
-
 Sequence::Sequence(string newName, string sequence) {
        try {
                m = MothurOut::getInstance();
@@ -33,22 +30,33 @@ Sequence::Sequence(string newName, string sequence) {
                exit(1);
        }                       
 }
+/***********************************************************************/
+Sequence::Sequence(string newName, string sequence, string justUnAligned) {
+       try {
+               m = MothurOut::getInstance();
+               initialize();   
+               name = newName;
+               
+               //setUnaligned removes any gap characters for us
+               setUnaligned(sequence);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "Sequence");
+               exit(1);
+       }                       
+}
+
 //********************************************************************************************************************
 //this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
 Sequence::Sequence(istringstream& fastaString){
        try {
                m = MothurOut::getInstance();
-       int pid;
-       MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-       cout << pid << " after mothur instance " << &name << endl;
+       
                initialize();
-       cout << "after mothur initialize" << endl;
                fastaString >> name;
-       cout << pid << " after name "  << name << endl;
                name = name.substr(1);
-
                string sequence;
-cout << pid << " name = "  << name << endl;            
+       
                //read comments
                while ((name[0] == '#') && fastaString) { 
                        while (!fastaString.eof())      {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
@@ -61,13 +69,11 @@ cout << pid << " name = "  << name << endl;
                                name = "";
                                break;
                        }
-                       cout << pid << "in while comment" << endl;      
                }
-       cout << pid << "after mothur comment" << endl;  
-               while (!fastaString.eof())      {       char c = fastaString.get(); cout << pid << " char = " << int(c) << endl; if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
-       cout << pid << " after mothur name" << endl;    
+               
+               while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+               
                sequence = getSequenceString(fastaString);              
-       cout << pid << " after mothur sequence" << endl;        
                setAligned(sequence);   
                //setUnaligned removes any gap characters for us                                                
                setUnaligned(sequence);         
@@ -77,6 +83,44 @@ cout << pid << " name = "  << name << endl;
                exit(1);
        }                                                               
 }
+//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
+Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
+       try {
+               m = MothurOut::getInstance();
+       
+               initialize();
+               fastaString >> name;
+               name = name.substr(1);
+               string sequence;
+       
+               //read comments
+               while ((name[0] == '#') && fastaString) { 
+                       while (!fastaString.eof())      {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
+                       sequence = getCommentString(fastaString);
+                       
+                       if (fastaString) {  
+                               fastaString >> name;  
+                               name = name.substr(1);  
+                       }else { 
+                               name = "";
+                               break;
+                       }
+               }
+               
+               while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+               
+               sequence = getSequenceString(fastaString);              
+               
+               //setUnaligned removes any gap characters for us                                                
+               setUnaligned(sequence);         
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "Sequence");
+               exit(1);
+       }                                                               
+}
+
 
 //********************************************************************************************************************
 //this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
@@ -116,6 +160,44 @@ Sequence::Sequence(ifstream& fastaFile){
                exit(1);
        }                                                       
 }
+//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
+Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
+       try {
+               m = MothurOut::getInstance();
+               initialize();
+               fastaFile >> name;
+               name = name.substr(1);
+               string sequence;
+               
+               //read comments
+               while ((name[0] == '#') && fastaFile) { 
+                       while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
+                       sequence = getCommentString(fastaFile);
+                       
+                       if (fastaFile) {  
+                               fastaFile >> name;  
+                               name = name.substr(1);  
+                       }else { 
+                               name = "";
+                               break;
+                       }
+               }
+               
+               //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
+               
+               sequence = getSequenceString(fastaFile);                
+               
+               //setUnaligned removes any gap characters for us                                                
+               setUnaligned(sequence); 
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "Sequence");
+               exit(1);
+       }                                                       
+}
+
 //********************************************************************************************************************
 string Sequence::getSequenceString(ifstream& fastaFile) {
        try {
@@ -169,11 +251,10 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
        try {
                char letter;
                string sequence = "";   
-int pid;
-MPI_Comm_rank(MPI_COMM_WORLD, &pid);           
+               
                while(!fastaFile.eof()){
                        letter= fastaFile.get();
-       cout << pid << '\t' << letter << endl;
+       
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;
@@ -322,7 +403,8 @@ string Sequence::getName(){
 //********************************************************************************************************************
 
 string Sequence::getAligned(){
-       return aligned;
+       if(isAligned == 0)      { return unaligned; }
+       else                            {  return aligned;  }
 }
 
 //********************************************************************************************************************
@@ -451,5 +533,4 @@ void Sequence::reverseComplement(){
        aligned = temp;
        
 }
-
-//********************************************************************************************************************
+/**************************************************************************************************/