* Mothur
*
* Created by Sarah Westcott on 6/2/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
*
*/
#include "getrabundcommand.h"
//**********************************************************************************************************************
-
-GetRAbundCommand::GetRAbundCommand(){
+vector<string> GetRAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","sorted","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- filename = getRootName(globaldata->inputFileName) + "rabund";
+ abort = false; calledHelp = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
- openOutputFile(filename, out);
+ else {
+ //valid paramters for this command
+ string Array[] = {"label","sorted","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+
+ //make sure the user has already run the read.otu command
+ if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+
+ string temp;
+ temp = validParameter.validFile(parameters, "sorted", false); if (temp == "not found") { temp = "T"; }
+ sorted = m->isTrue(temp);
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ if (abort == false) {
+ filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
+ m->openOutputFile(filename, out);
+ }
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetRAbundCommand::help(){
+ try {
+ m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
+ m->mothurOut("The get.rabund command parameters are label and sorted. No parameters are required.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
+ m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n");
+ m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
+ m->mothurOut("Example get.rabund(sorted=F).\n");
+ m->mothurOut("The default value for label is all labels in your inputfile.\n");
+ m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
}
- catch(...) {
- cout << "An unknown error has occurred in the GetRAbundCommand class function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "help");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
-GetRAbundCommand::~GetRAbundCommand(){
-}
+GetRAbundCommand::~GetRAbundCommand(){}
//**********************************************************************************************************************
int GetRAbundCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read first line
read = new ReadOTUFile(globaldata->inputFileName);
input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
- set<string> userLabels = globaldata->labels;
- set<int> userLines = globaldata->lines;
-
+ set<string> userLabels = labels;
- while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; globaldata->gListVector = NULL; return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
- cout << list->getLabel() << '\t' << count << endl;
- rabund = new RAbundVector();
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ rabund = new RAbundVector();
*rabund = (list->getRAbundVector());
- rabund->print(out);
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
+
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(out); }
+
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- cout << lastList->getLabel() << '\t' << count << endl;
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
rabund = new RAbundVector();
- *rabund = (lastList->getRAbundVector());
- rabund->print(out);
+ *rabund = (list->getRAbundVector());
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(out); }
+
delete rabund;
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
}
- if (count != 1) { delete lastList; }
- lastList = list;
+ lastLabel = list->getLabel();
+ delete list;
list = input->getListVector();
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastList->getLabel() << '\t' << count << endl;
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
rabund = new RAbundVector();
- *rabund = (lastList->getRAbundVector());
- rabund->print(out);
+ *rabund = (list->getRAbundVector());
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(out); }
+
delete rabund;
+ delete list;
}
- delete lastList;
-
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
+ m->mothurOutEndLine();
+
out.close();
+
+ globaldata->gListVector = NULL;
+
+ //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); }
+ }
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetRAbundCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetRAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff