#include "catchallcommand.h"
#include "globaldata.hpp"
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"sabund","label","inputdir","outputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CatchAllCommand::CatchAllCommand(){
+ try {
+ //initialize outputTypes
+
+ //need to determine outputFIles and types
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"sabund"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**************************************************************************************/
CatchAllCommand::CatchAllCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
- allLines = 0;
+ allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; }
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+
+ //initialize outputTypes
+ //need to determine outputFIles and types
+
+
//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 = ""; }
//check for required parameters
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide either a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
+ else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
string label = validParameter.validFile(parameters, "label", false);
//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 = "./"; }
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sabundfile); }
}
}
void CatchAllCommand::help(){
try {
- m->mothurOut("The catchall command interfaces mothur with the catchall program written by ...citation goes here...\n");
- m->mothurOut("For more information about clearcut refer to http://catchall.cac.cornell.edu/ \n");
+ m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
+ m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+ m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("The catchall command should be in the following format: \n");
if (abort == true) { return 0; }
- vector<string> outputNames;
-
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
//get location of catchall
GlobalData* globaldata = GlobalData::getInstance();
- string path = globaldata->argv;
+ path = globaldata->argv;
path = path.substr(0, (path.find_last_of('m')));
path = m->getFullPathName(path);
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
//create catchall input file from mothur's inputfile
string filename = process(sabund);
- sabund->print(cout);
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+ string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+
//run catchall
system(catchAllCommand.c_str());
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv");
+
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
//create catchall input file from mothur's inputfile
string filename = process(sabund);
-
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+ string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+
//run catchall
system(catchAllCommand.c_str());
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv");
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
sabund = (input->getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
+
//create catchall input file from mothur's inputfile
string filename = process(sabund);
-
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+ string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+
//run catchall
system(catchAllCommand.c_str());
-
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv");
+
delete sabund;
}
delete read;
delete input; globaldata->ginput = NULL;
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
//**********************************************************************************************************************
string CatchAllCommand::process(SAbundVector* sabund) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".catchall";
+ string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
filename = m->getFullPathName(filename);
ofstream out;
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