X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fastamap.cpp;fp=fastamap.cpp;h=4f4bf33206d77e437dd32bd2ff14b7f5f1290042;hp=0000000000000000000000000000000000000000;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hpb=bbb5879a7e566935c23d63d42bb945072424b939

diff --git a/fastamap.cpp b/fastamap.cpp
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+++ b/fastamap.cpp
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+/*
+ *  fastamap.cpp
+ *  mothur
+ *
+ *  Created by Sarah Westcott on 1/16/09.
+ *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
+ *
+ */
+
+#include "fastamap.h"
+
+/*******************************************************************************/
+ FastaMap::FastaMap(ifstream& in) {
+	//int numberOfSequences = 0;
+	
+	string name, sequence, line;
+	sequence = "";
+	
+	getline(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{
+			//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++;	
+			}
+			name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
+		}
+	}
+	
+	//store last sequence and name info.
+	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++;	
+	}	
+}
+/*******************************************************************************/
+string FastaMap::getGroupName(string seq) {  //pass a sequence name get its group
+	return data[seq].groupname;
+}
+/*******************************************************************************/
+int FastaMap::getGroupNumber(string seq) {  //pass a sequence name get number of sequence in its group
+	return data[seq].groupnumber;
+}
+/*******************************************************************************/
+string FastaMap::getNames(string seq) {	//pass a sequence get the string of names in the group separated by ','s.
+	return data[seq].names;
+}
+/*******************************************************************************/
+void FastaMap::push_back(string seq, string Name) {//sequencename, name
+	data[seq].groupname = Name;
+	data[seq].groupnumber = 1;
+	data[seq].names = Name;
+}
+/*******************************************************************************/
+void FastaMap::clear() { //clears out data
+	data.clear();
+}
+/*******************************************************************************/
+int FastaMap::size(){ //returns datas size which is the number of unique sequences
+	return data.size();
+}
+/*******************************************************************************/
+void FastaMap::print(ostream&){ //prints data
+
+}
+/*******************************************************************************/