#include "makegroupcommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> MakeGroupCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "groups","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MakeGroupCommand::MakeGroupCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MakeGroupCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","groups"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MakeGroupCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(string option) {
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
- //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 = ""; }
-
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(fastaFileName, fastaFileNames);
+ m->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(fastaFileNames[i]);
+ string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
ifstream in;
- int ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+ int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastaFileNames[i] = tryPath;
}
}
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
- }else{ filename += getRootName(getSimpleName(fastaFileNames[i])); }
+ }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); }
}
- filename += "groups";
+ //prevent giantic file name
+ if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
+ else { filename += "groups"; }
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
+ //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 = ""; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
- else { splitAtDash(groups, groupsNames); }
+ else { m->splitAtDash(groups, groupsNames); }
if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
try {
if (abort == true) { return 0; }
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
+
+ filename = outputDir + filename;
+
ofstream out;
- openOutputFile(filename, out);
+ m->openOutputFile(filename, out);
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (m->control_pressed) { out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
ifstream in;
- openInputFile(fastaFileNames[i], in);
+ m->openInputFile(fastaFileNames[i], in);
while (!in.eof()) {
- Sequence seq(in, "no align"); gobble(in);
+ Sequence seq(in, "no align"); m->gobble(in);
- if (m->control_pressed) { in.close(); out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(filename.c_str()); return 0; }
if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
}
out.close();
m->mothurOutEndLine();
- m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine();
+ m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
return 0;
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