//**********************************************************************************************************************
-GetRAbundCommand::GetRAbundCommand(string option){
+GetRAbundCommand::GetRAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
else {
//valid paramters for this command
- string Array[] = {"line","label"};
+ string Array[] = {"label","sorted","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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
+ }
+
//make sure the user has already run the read.otu command
- if (globaldata->getListFile() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; }
+ 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...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
+
+ 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") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
if (abort == false) {
- filename = getRootName(globaldata->inputFileName) + "rabund";
- openOutputFile(filename, out);
+ filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
+ m->openOutputFile(filename, out);
}
}
}
catch(exception& e) {
- errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
exit(1);
}
}
void GetRAbundCommand::help(){
try {
- mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
- mothurOut("The get.rabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time.\n");
- mothurOut("The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
- mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels).\n");
- mothurOut("Example get.rabund(line=1-3-5).\n");
- mothurOut("The default value for line and label are all lines in your inputfile.\n");
- mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
+ 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(exception& e) {
- errorOut(e, "GetRAbundCommand", "help");
+ m->errorOut(e, "GetRAbundCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-GetRAbundCommand::~GetRAbundCommand(){
- if (abort == false) { globaldata->gListVector = NULL; }
-}
+GetRAbundCommand::~GetRAbundCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
-
//read first line
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
//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 = labels;
- set<int> userLines = lines;
-
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if (m->control_pressed) { out.close(); remove(filename.c_str()); delete list; globaldata->gListVector = NULL; return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- 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) { 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(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
delete list;
list = input->getListVector(lastLabel);
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
rabund = new RAbundVector();
*rabund = (list->getRAbundVector());
- rabund->print(out);
+
+ if (m->control_pressed) { 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());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
}
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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ 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) {
- delete list;
+ if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
rabund = new RAbundVector();
*rabund = (list->getRAbundVector());
- rabund->print(out);
+
+ if (m->control_pressed) { 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;
}
-
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
out.close();
+
+ globaldata->gListVector = NULL;
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetRAbundCommand", "execute");
+ m->errorOut(e, "GetRAbundCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff