string Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
globaldata->newRead();
//check for required parameters
- listfile = validParameter->validFile(parameters, "list", true);
+ listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
- sabundfile = validParameter->validFile(parameters, "sabund", true);
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
- rabundfile = validParameter->validFile(parameters, "rabund", true);
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
- sharedfile = validParameter->validFile(parameters, "shared", true);
+ sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); }
- groupfile = validParameter->validFile(parameters, "group", true);
+ groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else {
globaldata->setGroupFile(groupfile);
groupMap = new GroupMap(groupfile);
groupMap->readMap();
+ globaldata->gGroupmap = groupMap;
}
//you are doing a list and group shared
//you have not given a file
if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
- cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; abort = true;
+ mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter->validFile(parameters, "line", false);
+ line = validParameter.validFile(parameters, "line", false);
if (line == "not found") { line = ""; }
else {
if(line != "all") { splitAtDash(line, lines); allLines = 0; }
globaldata->lines = lines;
}
- label = validParameter->validFile(parameters, "label", false);
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { splitAtDash(label, labels); allLines = 0; }
globaldata->allLines = allLines;
//make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- orderfile = validParameter->validFile(parameters, "order", true);
+ orderfile = validParameter.validFile(parameters, "order", true);
if (orderfile == "not open") { abort = true; }
else if (orderfile == "not found") { orderfile = ""; }
else { globaldata->setOrderFile(orderfile); }
- delete validParameter;
if (abort == false) {
//gets whichever one of the above is set
filename = globaldata->inputFileName;
- read = new ReadOTUFile(filename);
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
exit(1);
}
}
void ReadOtuCommand::help(){
try {
- cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
- cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
- cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
- cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
- cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
- cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
- cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
- cout << "The label and line parameters are used to read specific lines in your input." << "\n";
- cout << "The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
- cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n";
- cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file" << "\n";
- cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
- cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+ mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
+ mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
+ mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n");
+ mothurOut("The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
+ mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
+ mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
+ mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
+ mothurOut("The label and line parameters are used to read specific lines in your input.\n");
+ mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n");
+ mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). \n");
+ mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
+ mothurOut("and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. \n");
+ mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReadOtuCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
ReadOtuCommand::~ReadOtuCommand(){
- if (abort == false) { delete read; }
-}
+ }
//**********************************************************************************************************************
if (abort == true) { return 0; }
- read->read(&*globaldata);
if (globaldata->getFormat() == "shared") {
- groupMap->readMap();
- //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
- globaldata->gGroupmap = groupMap;
shared = new SharedCommand();
- shared->execute();
-
- parselist = new ParseListCommand();
- parselist->execute();
-
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
- globaldata->setSharedFile(getRootName(filename) + "shared");
+ int okay = shared->execute();
+ delete shared;
+
+ //problem with shared
+ if (okay == 1) {
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile("");
+ }else{
+
+ //change format to shared to speed up commands
+ globaldata->setFormat("sharedfile");
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile(getRootName(filename) + "shared");
+ }
}
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReadOtuCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff