*/
#include "catchallcommand.h"
-#include "globaldata.hpp"
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getValidParameters(){
+vector<string> CatchAllCommand::setParameters(){
try {
- string AlignArray[] = {"sabund","shared","label","inputdir","outputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
+ CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-CatchAllCommand::CatchAllCommand(){
- try {
- abort = true; calledHelp = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ m->errorOut(e, "CatchAllCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredParameters(){
+string CatchAllCommand::getHelpString(){
try {
- string AlignArray[] = {"sabund","shared","or"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n";
+ helpString += "For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n";
+ helpString += "The catchall executable must be in the same folder as your mothur executable. \n";
+ helpString += "If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n";
+ helpString += "The catchall command parameters are shared, sabund and label. shared or sabund is required. \n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The catchall command should be in the following format: \n";
+ helpString += "catchall(sabund=yourSabundFile) \n";
+ helpString += "Example: catchall(sabund=abrecovery.fn.sabund) \n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
+ m->errorOut(e, "CatchAllCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredFiles(){
+CatchAllCommand::CatchAllCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+ m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
exit(1);
}
}
/**************************************************************************************/
CatchAllCommand::CatchAllCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
+
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"shared","sabund","label","inputdir","outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+ else { m->setSabundFile(sabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
-
- //check for shared file loaded during read.otu
- if (sharedfile == "") {
- if (globaldata->getSharedFile() != "") { sharedfile = globaldata->getSharedFile(); }
- }
+ else { m->setSharedFile(sharedfile); }
string label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
- if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for the catchall command."); m->mothurOutEndLine(); abort=true; }
-
+ if ((sharedfile == "") && (sabundfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); 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"){
exit(1);
}
}
-//**********************************************************************************************************************
-
-void CatchAllCommand::help(){
- try {
- 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 the same folder as your mothur executable. \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 shared, sabund and label. shared or 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");
- m->mothurOut("catchall(sabund=yourSabundFile) \n");
- m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int CatchAllCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get location of catchall
- GlobalData* globaldata = GlobalData::getInstance();
- path = globaldata->argv;
+ path = m->argv;
path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
+ savedOutputDir = outputDir;
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
outputDir = m->getFullPathName(outputDir);
vector<string> inputFileNames;
- if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); }
+ if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); }
else { inputFileNames.push_back(sabundfile); }
for (int p = 0; p < inputFileNames.size(); p++) {
//run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete input; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete input; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//run catchall
system(catchAllCommand.c_str());
- remove(filename.c_str());
+ m->mothurRemove(filename);
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
out.close();
delete input;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } return 0; }
}
if (sharedfile == "") {
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+ string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
summaryfilename = m->getFullPathName(summaryfilename);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}else { //combine summaries
}
string summaryfilename = combineSummmary(sumNames);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
-
- globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");
}
m->mothurOutEndLine();
try {
ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+ string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
//open combined file
m->openOutputFile(combineFileName, out);
numLines = thisFilesLines.size();
temp.close();
- remove(outputNames[i].c_str());
+ m->mothurRemove(outputNames[i]);
}
//for each label
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
groups.push_back(lookup[i]->getGroup());
}
projects / mothur.git / blobdiff