X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fastamap.cpp;h=a0652d996fa648a7130928e93c7f3c6b0fae583a;hb=df82ee669d7eb9ae9a1a334339dfab7961cb16c6;hp=ebfecedb860bafb6385ca2f75a3752702354498b;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git

diff --git a/fastamap.cpp b/fastamap.cpp
index ebfeced..a0652d9 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -8,43 +8,47 @@
  */
 
 #include "fastamap.h"
+#include "sequence.hpp"
 
 /*******************************************************************************/
+
 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;
-			if (line != "") {
-				if (isalnum(line.at(0))) {  //if it's a sequence line
-					sequence += line;
-				}
-				else{
-				//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 = "";
-				}
-			}
+//		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.
+				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);
 		}
-	
-			
+					
 	}
 	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";
@@ -55,19 +59,27 @@ void FastaMap::readFastaFile(ifstream& in) {
 		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
@@ -76,7 +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.
@@ -90,11 +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
@@ -111,10 +129,12 @@ void FastaMap::printNamesFile(ostream& out){ //prints data
 		exit(1);
 	}
 }
+
 /*******************************************************************************/
+
 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;
@@ -129,5 +149,6 @@ void FastaMap::printCondensedFasta(ostream& out){ //prints data
 		exit(1);
 	}
 }
+
 /*******************************************************************************/