fixed some bugs

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 0848363be7cf4099cbb50cb58a3d11623eecc78f..1cc9abf08da58bad5497079d46185413e0c23ff4 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -14,54 +14,100 @@ void FastaMap::readFastaFile(ifstream& in) {
        try {
                string name, sequence, line;
                sequence = "";
-       
-               in >> line;
-               name = line.substr(1, line.length());  //rips off '>'
-       
+               int c;
+               string temp;
+               
+               
                //read through file
-               while (!in.eof()) {
-                       in >> line;
+               while ((c = in.get()) != EOF) {
+                       name = ""; sequence = ""; 
+                       //is this a name
+                       if (c == '>') { 
+                               name = readName(in); 
+                               sequence = readSequence(in); 
+                       }else {  cout << "Error fasta in your file. Please correct." << endl; }
 
-                       if (line[0] != '>') {  //if it's a sequence line
-                               sequence += line;
-                       }
-                       else{
+                       //store info in map
                        //input sequence info into map
-                               seqmap[name] = sequence;  
-
-                               it = data.find(sequence);
-                               if (it == data.end()) {         //it's unique.
-                                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-                                       data[sequence].groupnumber = 1;
-                                       data[sequence].names = name;
-                               }else { // its a duplicate.
-                                       data[sequence].names += "," + name;
-                                       data[sequence].groupnumber++;
-                               }
-                               name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
-                               sequence = "";
-                       }
+                       seqmap[name] = sequence;  
+                       it = data.find(sequence);
+                       if (it == data.end()) {         //it's unique.
+                               data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+                               data[sequence].groupnumber = 1;
+                               data[sequence].names = name;
+                       }else { // its a duplicate.
+                               data[sequence].names += "," + name;
+                               data[sequence].groupnumber++;
+                       }       
                        
                        gobble(in);
                }
-               it = data.find(sequence);
-               if (it == data.end()) {         //it's unique.
-                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-                       data[sequence].groupnumber = 1;
-                       data[sequence].names = name;
-               }else { // its a duplicate.
-                       data[sequence].names += "," + name;
-                       data[sequence].groupnumber++;
+                                       
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+/*******************************************************************************/
+string FastaMap::readName(ifstream& in) {
+       try{
+               string name = "";
+               int c;
+               string temp;
+               
+               while ((c = in.get()) != EOF) {
+                       //if c is not a line return
+                       if (c != 10) {
+                               name += c;
+                       }else { break;  }
                }
+                       
+               return name;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the FastaMap class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/*******************************************************************************/
+string FastaMap::readSequence(ifstream& in) {
+       try{
+               string sequence = "";
+               string line;
+               int pos, c;
                
+               while (!in.eof()) {
+                       //save position in file in case next line is a new name.
+                       pos = in.tellg();
+                       line = "";
+                       in >> line;                     
+                       //if you are at a new name
+                       if (line[0] == '>') {
+                               //put file pointer back since you are now at a new name
+                               in.seekg(pos, ios::beg);
+                               c = in.get();  //because you put it back to a newline char
+                               break;
+                       }else {  sequence += line;      }
+               }
                        
+               return sequence;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the FastaMap class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
 }
@@ -124,7 +170,7 @@ void FastaMap::printNamesFile(ostream& out){ //prints data
 /*******************************************************************************/
 void FastaMap::printCondensedFasta(ostream& out){ //prints data
        try {
-               // two column file created with groupname and them list of identical sequence names
+               //creates a fasta file
                for (it = data.begin(); it != data.end(); it++) {
                        out << ">" << it->second.groupname << endl;
                        out << it->first << endl;