X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=fastamap.cpp;h=a1beda31ac5ee82c532676163179197a004f91eb;hb=edec660ee2be477ac1539109d949a60cb7e16243;hp=0e6c22e21f48aec62b4a365db1e2454cd65ce7c9;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d;p=mothur.git

diff --git a/fastamap.cpp b/fastamap.cpp
index 0e6c22e..a1beda3 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -15,31 +15,36 @@ void FastaMap::readFastaFile(ifstream& in) {
 		string name, sequence, line;
 		sequence = "";
 	
-		getline(in, line);
+		in >> line;
 		name = line.substr(1, line.length());  //rips off '>'
 	
 		//read through file
-		while (getline(in, line)) {
-			if (isalnum(line.at(0))){  //if it's a sequence line
-				sequence += line;
-			}
-			else{
+		while (in.eof() != true) {
+			in >> line;
+			if (line != "") {
+				if (isalnum(line.at(0))) {  //if it's a sequence line
+					sequence += line;
+				}
+				else{
 				//input sequence info into map
-				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++;
+					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 = "";
 				}
-				name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
-				sequence = "";
 			}
 		}
 	
 		//store last sequence and name info.
+		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.
@@ -48,7 +53,8 @@ void FastaMap::readFastaFile(ifstream& in) {
 		}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";
@@ -72,25 +78,34 @@ int FastaMap::getGroupNumber(string seq) {	//pass a sequence get the number of i
 	return data[seq].groupnumber;
 }
 /*******************************************************************************/
-void FastaMap::push_back(string seq, string Name) {//sequencename, name
-	data[seq].groupname = Name;
-	data[seq].names = Name;
-}
-/*******************************************************************************/
-void FastaMap::set(string seq, string groupName, string Names) {
-	data[seq].groupname = groupName;
-	data[seq].names = Names;
-}
+string FastaMap::getSequence(string name) {
+	it2 = seqmap.find(name);
+	if (it2 == seqmap.end()) { 	//it's not found
+		return "not found";
+	}else { // found it
+		return it2->second;
+	}
+}	
 /*******************************************************************************/
-void FastaMap::clear() { //clears out data
-	data.clear();
+void FastaMap::push_back(string name, string seq) {
+	it = data.find(seq);
+	if (it == data.end()) { 	//it's unique.
+		data[seq].groupname = name;  //group name will be the name of the first duplicate sequence found.
+		data[seq].groupnumber = 1;
+		data[seq].names = name;
+	}else { // its a duplicate.
+		data[seq].names += "," + name;
+		data[seq].groupnumber++;
+	}
+	
+	seqmap[name] = seq;
 }
 /*******************************************************************************/
-int FastaMap::size(){ //returns datas size which is the number of unique sequences
+int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
 	return data.size();
 }
 /*******************************************************************************/
-void FastaMap::print(ostream& out){ //prints data
+void FastaMap::printNamesFile(ostream& out){ //prints data
 	try {
 		// two column file created with groupname and them list of identical sequence names
 		for (it = data.begin(); it != data.end(); it++) {
@@ -107,3 +122,22 @@ void FastaMap::print(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
+		for (it = data.begin(); it != data.end(); it++) {
+			out << ">" << it->second.groupname << endl;
+			out << it->first << endl;
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/*******************************************************************************/
+