#include "readotucommand.h"
+
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ReadOtuCommand::ReadOtuCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
globaldata->newRead();
//if the user changes the input directory command factory will send this info to us in the output parameter
//gets whichever one of the above is set
filename = globaldata->inputFileName;
}
+ */
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ReadOtuCommand::help(){
- try {
- m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
- m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
- m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, relabund, group, order, ordergroup, label and groups.\n");
- m->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");
- m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
- m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
- m->mothurOut("The label parameter is used to read specific labels in your input.\n");
- m->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");
- m->mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile). \n");
- m->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");
- m->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 .rabund file for each group. \n");
- m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
- m->mothurOut("You can use the ordergroup parameter to provide a file containing a list of group names in the order you would like them to appear in your shared file. \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "ReadOtuCommand", "help");
- exit(1);
- }
-}
-
-
-
-//**********************************************************************************************************************
-ReadOtuCommand::~ReadOtuCommand(){}
-//**********************************************************************************************************************
+///**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+ /*
if (globaldata->getFormat() == "shared") {
shared = new SharedCommand(outputDir);
//m->mothurOutEndLine();
}
+ outputTypes = shared->getOutputFiles();
+
+ //set rabund file as new current rabundfile
+ string current = "";
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
+
delete shared;
}
+ */
+
return 0;
}
catch(exception& e) {
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