#include "readotucommand.h"
//**********************************************************************************************************************
-ReadOtuCommand::ReadOtuCommand(string option){
+ReadOtuCommand::ReadOtuCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
+
globaldata->newRead();
//if the user changes the input directory command factory will send this info to us in the output parameter
//you have not given a file
if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
- mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
+ m->mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
}
globaldata->allLines = allLines;
-
+
orderfile = validParameter.validFile(parameters, "order", true);
if (orderfile == "not open") { abort = true; }
else if (orderfile == "not found") { orderfile = ""; }
else { globaldata->setOrderFile(orderfile); }
-
+
if (abort == false) {
//gets whichever one of the above is set
filename = globaldata->inputFileName;
}
-
}
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
exit(1);
}
}
void ReadOtuCommand::help(){
try {
- 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, label and groups.\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 label parameter is used to read specific labels 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) 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 .rabund file for each group. \n");
- mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
- mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
+ 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 or summary.shared 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, group, order, 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("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "help");
+ m->errorOut(e, "ReadOtuCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
- }
-
+ReadOtuCommand::~ReadOtuCommand(){}
//**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
if (abort == true) { return 0; }
-
+
if (globaldata->getFormat() == "shared") {
shared = new SharedCommand(outputDir);
globaldata->setListFile("");
globaldata->setGroupFile("");
globaldata->setSharedFile("");
- }else{
-
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
+ }else { //shared command outputs the filenames
+ //m->mothurOutEndLine();
+ //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
+ //m->mothurOutEndLine();
}
+
delete shared;
}
return 0;
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "execute");
+ m->errorOut(e, "ReadOtuCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff