--- /dev/null
+/*
+ * fastamap.cpp
+ * mothur
+ *
+ * Created by Sarah Westcott on 1/16/09.
+ * Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
+ *
+ */
+
+#include "fastamap.h"
+#include "sequence.hpp"
+
+/*******************************************************************************/
+
+void FastaMap::readFastaFile(string inFileName) {
+ try {
+ ifstream in;
+ m->openInputFile(inFileName, in);
+ string name, sequence, line;
+ sequence = "";
+ string temp;
+ map<string, string>::iterator itName;
+
+
+ while(!in.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ itName = seqmap.find(name);
+ if (itName == seqmap.end()) { seqmap[name] = sequence; }
+ else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ map<string,group>::iterator 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++;
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FastaMap", "readFastaFile");
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+
+void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
+
+ ifstream oldNameFile;
+ m->openInputFile(oldNameFileName, oldNameFile);
+
+ map<string,string> oldNameMap;
+ map<string, string>::iterator itName;
+ string name, list;
+ while(!oldNameFile.eof()){
+ if (m->control_pressed) { break; }
+
+ oldNameFile >> name; m->gobble(oldNameFile);
+ oldNameFile >> list;
+ oldNameMap[name] = list;
+ m->gobble(oldNameFile);
+ }
+ oldNameFile.close();
+
+ ifstream inFASTA;
+ m->openInputFile(inFastaFile, inFASTA);
+ string sequence;
+ while(!inFASTA.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(inFASTA);
+ name = currSeq.getName();
+
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ itName = seqmap.find(name);
+ if (itName == seqmap.end()) { seqmap[name] = sequence; }
+ else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ seqmap[name] = sequence;
+ map<string,group>::iterator 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 = oldNameMap[name];
+ }else { // its a duplicate.
+ data[sequence].names += "," + oldNameMap[name];
+ // data[sequence].groupnumber++;
+ }
+ }
+ m->gobble(inFASTA);
+ }
+
+
+ inFASTA.close();
+}
+
+/*******************************************************************************/
+
+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;
+}
+
+/*******************************************************************************/
+
+string FastaMap::getSequence(string name) {
+
+ map<string,string>::iterator it = seqmap.find(name);
+ if (it == seqmap.end()) { return "not found"; }
+ else { return it->second; }
+
+}
+
+/*******************************************************************************/
+
+void FastaMap::push_back(string name, string seq) {
+
+ map<string,group>::iterator 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].names = name;
+ }else { // its a duplicate.
+ data[seq].names += "," + name;
+ }
+ seqmap[name] = seq;
+}
+
+/*******************************************************************************/
+
+int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
+ return data.size();
+}
+
+/*******************************************************************************/
+
+void FastaMap::printNamesFile(string outFileName){ //prints data
+ try {
+ ofstream outFile;
+ m->openOutputFile(outFileName, outFile);
+
+ // two column file created with groupname and them list of identical sequence names
+ for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
+ outFile << it->second.groupname << '\t' << it->second.names << endl;
+ }
+ outFile.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FastaMap", "printNamesFile");
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+
+void FastaMap::printCondensedFasta(string outFileName){ //prints data
+ try {
+ ofstream out;
+ m->openOutputFile(outFileName, out);
+ //creates a fasta file
+ for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
+ out << ">" << it->second.groupname << endl;
+ out << it->first << endl;
+ }
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FastaMap", "printCondensedFasta");
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+
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