+++ /dev/null
-/*
- * parselistcommand.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/2/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "parselistcommand.h"
-
-//**********************************************************************************************************************
-ParseListCommand::ParseListCommand(){
- try {
- globaldata = GlobalData::getInstance();
-
- //read in group map info.
- //groupMap = new GroupMap(globaldata->getGroupFile());
- //groupMap->readMap();
- groupMap = globaldata->gGroupmap;
-
- //fill filehandles with neccessary ofstreams
- int i;
- ofstream* temp;
- SharedListVector* templist;
- for (i=0; i<groupMap->getNumGroups(); i++) {
- temp = new ofstream;
- templist = new SharedListVector();
- filehandles[groupMap->namesOfGroups[i]] = temp;
- mapOfLists[groupMap->namesOfGroups[i]] = templist;
- }
-
- //set fileroot
- fileroot = getRootName(globaldata->getListFile());
-
- //clears file before we start to write to it below
- for (int i=0; i<groupMap->getNumGroups(); i++) {
- remove((fileroot + groupMap->namesOfGroups[i] + ".list").c_str());
- }
-
- }
- catch(exception& e) {
- errorOut(e, "ParseListCommand", "ParseListCommand");
- exit(1);
- }
-
-}
-/***********************************************************************/
-void ParseListCommand::parse(int index, SharedListVector* list) {
- try {
- string member, bin, groupName;
- bin = list->get(index);
-
- while (bin.find_first_of(',') != -1) {//while you still have sequences
- member = bin.substr(0,bin.find_first_of(','));
- if ((bin.find_first_of(',')+1) <= bin.length()) { //checks to make sure you don't have comma at end of string
- bin = bin.substr(bin.find_first_of(',')+1, bin.length());
- }
-
- groupName = groupMap->getGroup(member);
- if (groupName != "not found") {
- listGroups[groupName] = listGroups[groupName] + "," + member; //adds prefix to the correct group.
- }else {
- mothurOut("Error: Sequence '" + toString(member) + "' was not found in the group file, please correct\n");
- }
- }
-
- //save last name after comma
- groupName = groupMap->getGroup(bin);
- if (groupName != "not found") {
- listGroups[groupName] = listGroups[groupName] + "," + bin; //adds prefix to the correct group.
- }else {
- mothurOut("Error: Sequence '" + toString(bin) + "' was not found in the group file, please correct\n");
- }
- }
- catch(exception& e) {
- errorOut(e, "ParseListCommand", "parse");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-int ParseListCommand::execute(){
- try{
-
- int count = 1;
-
- //read in listfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
- list = globaldata->gSharedList;
- string lastLabel = list->getLabel();
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = globaldata->labels;
- set<int> userLines = globaldata->lines;
-
- //parses and sets each groups listvector
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lastLabel) == 1){
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- process(list);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- userLines.erase(count);
- }
-
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- delete list;
- list = input->getSharedListVector(lastLabel);
-
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- process(list);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
-
- lastLabel = list->getLabel();
-
- delete list;
- list = input->getSharedListVector();
- count++;
- }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
- needToRun = true;
- }else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
- }
- }
-
- //run last line if you need to
- if (needToRun == true) {
- delete list;
- list = input->getSharedListVector(lastLabel);
-
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- process(list);
- delete list;
- }
-
- globaldata->gSharedList = NULL;
- //delete list vectors to fill with parsed data
- for (it2 = mapOfLists.begin(); it2 != mapOfLists.end(); it2++) {
- delete it2->second;
- }
- for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
- delete it2->second;
- }
-
- delete input; globaldata->ginput = NULL;
- delete read;
-
-
- return 0;
- }
- catch(exception& e) {
- errorOut(e, "ParseListCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-ParseListCommand::~ParseListCommand(){
-
-
-}
-//**********************************************************************************************************************
-void ParseListCommand::process(SharedListVector* thisList) {
- try {
- string seq;
-
- for(int i=0; i<thisList->size(); i++) {
- parse(i, thisList); //parses data[i] list of sequence names
- for (it=listGroups.begin(); it != listGroups.end(); it++) { //loop through map and set new list vectors
- seq = it->second;
- seq = seq.substr(1, seq.length()); //rips off extra comma
- mapOfLists[it->first]->push_back(seq); //sets new listvector for each group
- }
- listGroups.clear();
- }
- //prints each new list file
- for (int i=0; i<groupMap->getNumGroups(); i++) {
- openOutputFileAppend(fileroot + groupMap->namesOfGroups[i] + ".list", *(filehandles[groupMap->namesOfGroups[i]]));
- mapOfLists[groupMap->namesOfGroups[i]]->setLabel(thisList->getLabel());
- mapOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
- mapOfLists[groupMap->namesOfGroups[i]]->clear();
- (*(filehandles[groupMap->namesOfGroups[i]])).close();
- }
-
- }
- catch(exception& e) {
- errorOut(e, "ParseListCommand", "process");
- exit(1);
- }
-}
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