#include "getsharedotucommand.h"
-//**********************************************************************************************************************
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
if (groups == "not found") { groups = ""; }
else {
userGroups = "unique." + groups;
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
if (groups == "not found") { groups = ""; }
else {
userGroups = groups;
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
unique = false;
}
int error = groupMap->readMap();
if (error == 1) { delete groupMap; return 0; }
+ if (m->control_pressed) { delete groupMap; return 0; }
+
globaldata->gGroupmap = groupMap;
if (Groups.size() == 0) {
if (fastafile != "") {
ifstream inFasta;
- openInputFile(fastafile, inFasta);
+ m->openInputFile(fastafile, inFasta);
while(!inFasta.eof()) {
- Sequence seq(inFasta); gobble(inFasta);
+ if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
if (seq.getName() != "") { seqs.push_back(seq); }
}
inFasta.close();
set<string> userLabels = labels;
ifstream in;
- openInputFile(listfile, in);
+ m->openInputFile(listfile, in);
//as long as you are not at the end of the file or done wih the lines you want
while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ if (lastlist != NULL) { delete lastlist; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ delete groupMap; return 0;
+ }
+
list = new ListVector(in);
if(allLines == 1 || labels.count(list->getLabel()) == 1){
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
m->mothurOut(lastlist->getLabel());
if (lastlist != NULL) { delete lastlist; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
/***********************************************************/
-void GetSharedOTUCommand::process(ListVector* shared) {
+int GetSharedOTUCommand::process(ListVector* shared) {
try {
map<string, string> fastaMap;
ofstream outNames;
string outputFileNames;
- if (outputDir == "") { outputDir += hasPath(listfile); }
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
if (output != "accnos") {
- outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
}else {
- outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
}
- openOutputFile(outputFileNames, outNames);
+ m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
int num = 0;
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
+ if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
bool uniqueOTU = true;
//find group
string seqGroup = groupMap->getGroup(name);
if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + toString(i+1)));
+ namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
}else { namesOfSeqsInThisBin.push_back(name); }
if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
//get last name
string seqGroup = groupMap->getGroup(names);
if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((names + "\t" + seqGroup + "\t" + toString(i+1)));
+ namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
}else { namesOfSeqsInThisBin.push_back(names); }
if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
if (fastafile != "") {
if (output != "accnos") {
- string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('\t'));
- seqName = seqName.substr(0,seqName.find_last_of('\t'));
+ string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
+ seqName = seqName.substr(0,seqName.find_last_of('|'));
fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later
}else {
fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
}else {
m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
outputNames.push_back(outputFileNames);
+ if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+ else { outputTypes["accnos"].push_back(outputFileNames); }
}
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
- if (outputDir == "") { outputDir += hasPath(fastafile); }
- string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+ if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+ string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
ofstream outFasta;
- openOutputFile(outputFileFasta, outFasta);
- outputNames.push_back(outputFileFasta);
+ m->openOutputFile(outputFileFasta, outFasta);
+ outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
for (int k = 0; k < seqs.size(); k++) {
+ if (m->control_pressed) { outFasta.close(); return 0; }
+
//if this is a sequence we want, output it
it = fastaMap.find(seqs[k].getName());
if (it != fastaMap.end()) {
outFasta.close();
}
-
+
+ return 0;
}
catch(exception& e) {
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