X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fastamap.cpp;h=a0652d996fa648a7130928e93c7f3c6b0fae583a;hb=64eee3a595ae53817f52807d7393b22e74e31f56;hp=1cc9abf08da58bad5497079d46185413e0c23ff4;hpb=986663e2220f6b043ee83d1699cfa081dc49cbed;p=mothur.git

diff --git a/fastamap.cpp b/fastamap.cpp
index 1cc9abf..a0652d9 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -8,27 +8,33 @@
  */
 
 #include "fastamap.h"
+#include "sequence.hpp"
 
 /*******************************************************************************/
+
 void FastaMap::readFastaFile(ifstream& in) {
 	try {
 		string name, sequence, line;
 		sequence = "";
-		int c;
+//		int c;
 		string temp;
 		
 		
 		//read through file
-		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; }
+//		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; }
 
 			//store info in map
 			//input sequence info into map
+		while(!in.eof()){
+			Sequence currSeq(in);
+			name = currSeq.getName();
+			sequence = currSeq.getUnaligned();
 			seqmap[name] = sequence;  
 			it = data.find(sequence);
 			if (it == data.end()) { 	//it's unique.
@@ -53,77 +59,27 @@ void FastaMap::readFastaFile(ifstream& in) {
 		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 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 readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
-/*******************************************************************************/
+
 string FastaMap::getGroupName(string seq) {  //pass a sequence name get its group
 	return data[seq].groupname;
 }
+
 /*******************************************************************************/
+
 string FastaMap::getNames(string seq) {	//pass a sequence get the string of names in the group separated by ','s.
 	return data[seq].names;
 }
+
 /*******************************************************************************/
+
 int FastaMap::getGroupNumber(string seq) {	//pass a sequence get the number of identical sequences.
 	return data[seq].groupnumber;
 }
+
 /*******************************************************************************/
+
 string FastaMap::getSequence(string name) {
 	it2 = seqmap.find(name);
 	if (it2 == seqmap.end()) { 	//it's not found
@@ -132,7 +88,9 @@ string FastaMap::getSequence(string name) {
 		return it2->second;
 	}
 }	
+
 /*******************************************************************************/
+
 void FastaMap::push_back(string name, string seq) {
 	it = data.find(seq);
 	if (it == data.end()) { 	//it's unique.
@@ -146,11 +104,15 @@ void FastaMap::push_back(string name, string seq) {
 	
 	seqmap[name] = seq;
 }
+
 /*******************************************************************************/
+
 int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
 	return data.size();
 }
+
 /*******************************************************************************/
+
 void FastaMap::printNamesFile(ostream& out){ //prints data
 	try {
 		// two column file created with groupname and them list of identical sequence names
@@ -167,7 +129,9 @@ void FastaMap::printNamesFile(ostream& out){ //prints data
 		exit(1);
 	}
 }
+
 /*******************************************************************************/
+
 void FastaMap::printCondensedFasta(ostream& out){ //prints data
 	try {
 		//creates a fasta file
@@ -185,5 +149,6 @@ void FastaMap::printCondensedFasta(ostream& out){ //prints data
 		exit(1);
 	}
 }
+
 /*******************************************************************************/