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currentfile.cpp
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//
// currentfile.cpp
// Mothur
//
// Created by Sarah Westcott on 11/9/17.
// Copyright © 2017 Schloss Lab. All rights reserved.
//
#include "currentfile.h"
/*********************************************************************************************/
set<string> CurrentFile::getCurrentTypes() {
try {
set<string> types;
types.insert("fasta");
types.insert("summary");
types.insert("file");
types.insert("accnos");
types.insert("column");
types.insert("design");
types.insert("group");
types.insert("list");
types.insert("name");
types.insert("oligos");
types.insert("order");
types.insert("ordergroup");
types.insert("phylip");
types.insert("qfile");
types.insert("relabund");
types.insert("sabund");
types.insert("rabund");
types.insert("sff");
types.insert("shared");
types.insert("taxonomy");
types.insert("constaxonomy");
types.insert("contigsreport");
types.insert("tree");
types.insert("flow");
types.insert("biom");
types.insert("count");
types.insert("processors");
return types;
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "getCurrentTypes");
exit(1);
}
}
/*********************************************************************************************/
void CurrentFile::printCurrentFiles(string filename) {
try {
if (filename != "") {
ofstream out;
util.openOutputFile(filename, out);
if (accnosfile != "") { m->mothurOut("accnos=" + accnosfile, out); m->mothurOutEndLine(out); }
if (columnfile != "") { m->mothurOut("column=" + columnfile, out); m->mothurOutEndLine(out); }
if (designfile != "") { m->mothurOut("design=" + designfile, out); m->mothurOutEndLine(out); }
if (fastafile != "") { m->mothurOut("fasta=" + fastafile, out); m->mothurOutEndLine(out); }
if (groupfile != "") { m->mothurOut("group=" + groupfile, out); m->mothurOutEndLine(out); }
if (listfile != "") { m->mothurOut("list=" + listfile, out); m->mothurOutEndLine(out); }
if (namefile != "") { m->mothurOut("name=" + namefile, out); m->mothurOutEndLine(out); }
if (oligosfile != "") { m->mothurOut("oligos=" + oligosfile, out); m->mothurOutEndLine(out); }
if (orderfile != "") { m->mothurOut("order=" + orderfile, out); m->mothurOutEndLine(out); }
if (ordergroupfile != "") { m->mothurOut("ordergroup=" + ordergroupfile, out); m->mothurOutEndLine(out); }
if (phylipfile != "") { m->mothurOut("phylip=" + phylipfile, out); m->mothurOutEndLine(out); }
if (qualfile != "") { m->mothurOut("qfile=" + qualfile, out); m->mothurOutEndLine(out); }
if (rabundfile != "") { m->mothurOut("rabund=" + rabundfile, out); m->mothurOutEndLine(out); }
if (relabundfile != "") { m->mothurOut("relabund=" + relabundfile, out); m->mothurOutEndLine(out); }
if (sabundfile != "") { m->mothurOut("sabund=" + sabundfile, out); m->mothurOutEndLine(out); }
if (sfffile != "") { m->mothurOut("sff=" + sfffile, out); m->mothurOutEndLine(out); }
if (sharedfile != "") { m->mothurOut("shared=" + sharedfile, out); m->mothurOutEndLine(out); }
if (taxonomyfile != "") { m->mothurOut("taxonomy=" + taxonomyfile, out); m->mothurOutEndLine(out); }
if (constaxonomyfile != "") { m->mothurOut("constaxonomy=" + constaxonomyfile, out); m->mothurOutEndLine(out);}
if (contigsreportfile != ""){ m->mothurOut("contigsreport=" + contigsreportfile, out); m->mothurOutEndLine(out);}
if (treefile != "") { m->mothurOut("tree=" + treefile, out); m->mothurOutEndLine(out); }
if (flowfile != "") { m->mothurOut("flow=" + flowfile, out); m->mothurOutEndLine(out); }
if (biomfile != "") { m->mothurOut("biom=" + biomfile, out); m->mothurOutEndLine(out); }
if (countfile != "") { m->mothurOut("count=" + countfile, out); m->mothurOutEndLine(out); }
if (processors != "1") { m->mothurOut("processors=" + processors, out); m->mothurOutEndLine(out); }
if (summaryfile != "") { m->mothurOut("summary=" + summaryfile, out); m->mothurOutEndLine(out); }
if (filefile != "") { m->mothurOut("file=" + filefile, out); m->mothurOutEndLine(out); }
out.close();
}else {
if (accnosfile != "") { m->mothurOut("accnos=" + accnosfile); m->mothurOutEndLine(); }
if (columnfile != "") { m->mothurOut("column=" + columnfile); m->mothurOutEndLine(); }
if (designfile != "") { m->mothurOut("design=" + designfile); m->mothurOutEndLine(); }
if (fastafile != "") { m->mothurOut("fasta=" + fastafile); m->mothurOutEndLine(); }
if (groupfile != "") { m->mothurOut("group=" + groupfile); m->mothurOutEndLine(); }
if (listfile != "") { m->mothurOut("list=" + listfile); m->mothurOutEndLine(); }
if (namefile != "") { m->mothurOut("name=" + namefile); m->mothurOutEndLine(); }
if (oligosfile != "") { m->mothurOut("oligos=" + oligosfile); m->mothurOutEndLine(); }
if (orderfile != "") { m->mothurOut("order=" + orderfile); m->mothurOutEndLine(); }
if (ordergroupfile != "") { m->mothurOut("ordergroup=" + ordergroupfile); m->mothurOutEndLine(); }
if (phylipfile != "") { m->mothurOut("phylip=" + phylipfile); m->mothurOutEndLine(); }
if (qualfile != "") { m->mothurOut("qfile=" + qualfile); m->mothurOutEndLine(); }
if (rabundfile != "") { m->mothurOut("rabund=" + rabundfile); m->mothurOutEndLine(); }
if (relabundfile != "") { m->mothurOut("relabund=" + relabundfile); m->mothurOutEndLine(); }
if (sabundfile != "") { m->mothurOut("sabund=" + sabundfile); m->mothurOutEndLine(); }
if (sfffile != "") { m->mothurOut("sff=" + sfffile); m->mothurOutEndLine(); }
if (sharedfile != "") { m->mothurOut("shared=" + sharedfile); m->mothurOutEndLine(); }
if (taxonomyfile != "") { m->mothurOut("taxonomy=" + taxonomyfile); m->mothurOutEndLine(); }
if (constaxonomyfile != "") { m->mothurOut("constaxonomy=" + constaxonomyfile); m->mothurOutEndLine();}
if (contigsreportfile != ""){ m->mothurOut("contigsreport=" + contigsreportfile); m->mothurOutEndLine();}
if (treefile != "") { m->mothurOut("tree=" + treefile); m->mothurOutEndLine(); }
if (flowfile != "") { m->mothurOut("flow=" + flowfile); m->mothurOutEndLine(); }
if (biomfile != "") { m->mothurOut("biom=" + biomfile); m->mothurOutEndLine(); }
if (countfile != "") { m->mothurOut("count=" + countfile); m->mothurOutEndLine(); }
if (processors != "1") { m->mothurOut("processors=" + processors); m->mothurOutEndLine(); }
if (summaryfile != "") { m->mothurOut("summary=" + summaryfile); m->mothurOutEndLine(); }
if (filefile != "") { m->mothurOut("file=" + filefile); m->mothurOutEndLine(); }
}
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "printCurrentFiles");
exit(1);
}
}
/*********************************************************************************************/
bool CurrentFile::hasCurrentFiles() {
try {
bool hasCurrent = false;
if (accnosfile != "") { return true; }
if (columnfile != "") { return true; }
if (designfile != "") { return true; }
if (fastafile != "") { return true; }
if (groupfile != "") { return true; }
if (listfile != "") { return true; }
if (namefile != "") { return true; }
if (oligosfile != "") { return true; }
if (orderfile != "") { return true; }
if (ordergroupfile != "") { return true; }
if (phylipfile != "") { return true; }
if (qualfile != "") { return true; }
if (rabundfile != "") { return true; }
if (relabundfile != "") { return true; }
if (sabundfile != "") { return true; }
if (sfffile != "") { return true; }
if (sharedfile != "") { return true; }
if (taxonomyfile != "") { return true; }
if (constaxonomyfile != "") { return true; }
if (contigsreportfile != ""){ return true; }
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
if (countfile != "") { return true; }
if (summaryfile != "") { return true; }
if (filefile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "hasCurrentFiles");
exit(1);
}
}
/*********************************************************************************************/
void CurrentFile::clearCurrentFiles() {
try {
phylipfile = "";
filefile = "";
columnfile = "";
listfile = "";
rabundfile = "";
sabundfile = "";
namefile = "";
groupfile = "";
designfile = "";
orderfile = "";
treefile = "";
sharedfile = "";
ordergroupfile = "";
contigsreportfile = "";
constaxonomyfile = "";
relabundfile = "";
fastafile = "";
qualfile = "";
sfffile = "";
oligosfile = "";
accnosfile = "";
taxonomyfile = "";
flowfile = "";
biomfile = "";
countfile = "";
summaryfile = "";
unsigned concurentThreadsSupported = std::thread::hardware_concurrency();
if (concurentThreadsSupported < 1) { concurentThreadsSupported = 1; } //in case thread errors
processors = toString(concurentThreadsSupported);
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "clearCurrentFiles");
exit(1);
}
}
/*********************************************************************************************/
int CurrentFile::setProcessors(string p) {
try {
if (!util.isInteger(p)) {
unsigned concurentThreadsSupported = std::thread::hardware_concurrency();
if (concurentThreadsSupported < 1) { concurentThreadsSupported = 1; } //in case thread errors
processors = toString(concurentThreadsSupported);
m->mothurOut("[ERROR]: " + p + " is not an integer. Setting processors to " + toString(processors) + "\n");
}else { processors = p; m->mothurOut("\nUsing " + toString(processors) + " processors.\n"); }
int numProcessors = 1;
util.mothurConvert(p, numProcessors);
return numProcessors;
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "clearCurrentFiles");
exit(1);
}
}
/*********************************************************************************************/
void CurrentFile::setDefaultPath(string pathname) {
try {
if (pathname != "") { //add / to name if needed
string lastChar = pathname.substr(pathname.length()-1);
if (lastChar != PATH_SEPARATOR) { pathname += PATH_SEPARATOR; }
}
defaultPath = util.getFullPathName(pathname);
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "setDefaultPath");
exit(1);
}
}
/*********************************************************************************************/
void CurrentFile::setTestFilePath(string pathname) {
try {
if (pathname != "") {
//add / to name if needed
string lastChar = pathname.substr(pathname.length()-1);
if (lastChar != PATH_SEPARATOR) { pathname += PATH_SEPARATOR; }
}
testFilePath = util.getFullPathName(pathname);
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "setTestFilePath");
exit(1);
}
}
/*********************************************************************************************/
void CurrentFile::setBlastPath(string pathname) {
try {
if (pathname != "") {
//add / to name if needed
string lastChar = pathname.substr(pathname.length()-1);
if (lastChar != PATH_SEPARATOR) { pathname += PATH_SEPARATOR; }
}
blastPath = util.getFullPathName(pathname);
}
catch(exception& e) {
m->errorOut(e, "CurrentFile", "setDefaultPath");
exit(1);
}
}
/*********************************************************************************************/