X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readfasta.cpp;h=fcac6bd276406119fd35415ba56f491b62958a3c;hp=e1f22ce228bbb729ce24a75a10d507f243d2179c;hb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;hpb=544469443afe44920bdf279aefd26d29534cabaf

diff --git a/readfasta.cpp b/readfasta.cpp
index e1f22ce..fcac6bd 100644
--- a/readfasta.cpp
+++ b/readfasta.cpp
@@ -12,18 +12,7 @@
 #include <fstream>
 
 /*******************************************************************************/
-ReadFasta::ReadFasta(string file) : ReadSeqs(file) {
-	try {
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-}
+ReadFasta::ReadFasta(string file) : ReadSeqs(file) {}
 /*******************************************************************************/
 ReadFasta::~ReadFasta(){
 	//for(int i = 0; i < sequencedb.getNumSeqs(); i++)
@@ -31,7 +20,8 @@ ReadFasta::~ReadFasta(){
 }
 /*******************************************************************************/
 void ReadFasta::read() {
-	string name = "";
+	try {
+	/*string name = "";
 	string sequence = "";
 	string temp;
 	int count = 0;
@@ -61,12 +51,104 @@ void ReadFasta::read() {
 			
 	}
 	Sequence newSequence(name, sequence);
-	sequencedb.add(newSequence);
+	sequencedb.add(newSequence); */
+
+		string name, sequence, line;
+		sequence = "";
+		int c;
+		string temp;
+		
+		
+		//read through file
+		while ((c = filehandle.get()) != EOF) {
+			name = ""; sequence = ""; 
+			//is this a name
+			if (c == '>') { 
+				name = readName(filehandle); 
+				sequence = readSequence(filehandle); 
+			}else {  cout << "Error fasta in your file. Please correct." << endl; }
 
-	filehandle.close();
+			//input sequence info into sequencedb
+			Sequence newSequence(name, sequence);
+			sequencedb.add(newSequence);
+			
+			//takes care of white space
+			gobble(filehandle);
+		}
+
+		filehandle.close();
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ReadFasta class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ReadFasta class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
 }
 
 /*********************************************************************************/
 SequenceDB* ReadFasta::getDB() {
 	return &sequencedb;
 }
+/*******************************************************************************/
+string ReadFasta::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 ReadFasta class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ReadFasta class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/*******************************************************************************/
+string ReadFasta::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 ReadFasta class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ReadFasta class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/*******************************************************************************/
+