+++ /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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