#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
#include "npshannon.h"
#include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
#include "jackknife.h"
#include "geom.h"
#include "qstat.h"
//**********************************************************************************************************************
-CollectCommand::CollectCommand(string option){
+CollectCommand::CollectCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//make sure the user has already run the read.otu command
- if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "CollectCommand");
+ m->errorOut(e, "CollectCommand", "CollectCommand");
exit(1);
}
}
void CollectCommand::help(){
try {
- mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
- mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
- mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
- mothurOut("The collect.single command should be in the following format: \n");
- mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
- mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
+ m->mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
+ m->mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
+ m->mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
+ m->mothurOut("The collect.single command should be in the following format: \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
+ m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
+ m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
validCalculator->printCalc("single", cout);
- mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
+ m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "help");
+ m->errorOut(e, "CollectCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
- if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
- else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+ vector<string> outputNames;
+ string hadShared = "";
+ if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
+ else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+
for (int p = 0; p < inputFileNames.size(); p++) {
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+
if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
globaldata->inputFileName = inputFileNames[p];
-
+
if (inputFileNames.size() > 1) {
- mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
-
+
validCalculator = new ValidCalculators();
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
+ outputNames.push_back(fileNameRoot+"sobs");
}else if (Estimators[i] == "chao") {
cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
+ outputNames.push_back(fileNameRoot+"chao");
}else if (Estimators[i] == "nseqs") {
cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+ outputNames.push_back(fileNameRoot+"nseqs");
}else if (Estimators[i] == "coverage") {
cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
+ outputNames.push_back(fileNameRoot+"coverage");
}else if (Estimators[i] == "ace") {
cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
+ outputNames.push_back(fileNameRoot+"ace");
}else if (Estimators[i] == "jack") {
cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
+ outputNames.push_back(fileNameRoot+"jack");
}else if (Estimators[i] == "shannon") {
cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
+ outputNames.push_back(fileNameRoot+"shannon");
+ }else if (Estimators[i] == "shannoneven") {
+ cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
+ outputNames.push_back(fileNameRoot+"shannoneven");
}else if (Estimators[i] == "npshannon") {
cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
+ outputNames.push_back(fileNameRoot+"np_shannon");
+ }else if (Estimators[i] == "heip") {
+ cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
+ outputNames.push_back(fileNameRoot+"heip");
+ }else if (Estimators[i] == "smithwilson") {
+ cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
+ outputNames.push_back(fileNameRoot+"smithwilson");
}else if (Estimators[i] == "simpson") {
cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
+ outputNames.push_back(fileNameRoot+"simpson");
+ }else if (Estimators[i] == "simpsoneven") {
+ cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
+ outputNames.push_back(fileNameRoot+"simpsoneven");
+ }else if (Estimators[i] == "invsimpson") {
+ cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
+ outputNames.push_back(fileNameRoot+"invsimpson");
}else if (Estimators[i] == "bootstrap") {
cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+ outputNames.push_back(fileNameRoot+"bootstrap");
}else if (Estimators[i] == "geometric") {
cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
+ outputNames.push_back(fileNameRoot+"geometric");
}else if (Estimators[i] == "qstat") {
cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
+ outputNames.push_back(fileNameRoot+"qstat");
}else if (Estimators[i] == "logseries") {
cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
+ outputNames.push_back(fileNameRoot+"logseries");
}else if (Estimators[i] == "bergerparker") {
cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
+ outputNames.push_back(fileNameRoot+"bergerparker");
}else if (Estimators[i] == "bstick") {
cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+ outputNames.push_back(fileNameRoot+"bstick");
}else if (Estimators[i] == "goodscoverage") {
cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
+ outputNames.push_back(fileNameRoot+"goodscoverage");
}else if (Estimators[i] == "efron") {
cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
+ outputNames.push_back(fileNameRoot+"efron");
}else if (Estimators[i] == "boneh") {
cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
+ outputNames.push_back(fileNameRoot+"boneh");
}else if (Estimators[i] == "solow") {
cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
+ outputNames.push_back(fileNameRoot+"solow");
}else if (Estimators[i] == "shen") {
cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
+ outputNames.push_back(fileNameRoot+"shen");
}
}
}
-
//if the users entered no valid calculators don't execute command
- if (cDisplays.size() == 0) { return 0; }
+ if (cDisplays.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
read = new ReadOTUFile(inputFileNames[p]);
read->read(&*globaldata);
-
+
order = globaldata->gorder;
string lastLabel = order->getLabel();
input = globaldata->ginput;
//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;
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete order; globaldata->gorder = NULL;
+ delete validCalculator;
+ globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+ return 0;
+ }
+
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete order; globaldata->gorder = NULL;
+ delete validCalculator;
+ globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+ return 0;
+ }
+
if(allLines == 1 || labels.count(order->getLabel()) == 1){
-
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
delete order;
order = (input->getOrderVector(lastLabel));
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
+
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
order = (input->getOrderVector());
}
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+ return 0;
+ }
+
//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();
}
}
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete order; globaldata->gorder = NULL;
+ delete validCalculator;
+ globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+ return 0;
+ }
delete order;
}
delete validCalculator;
}
-
+ //return to shared mode if you changed above
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "execute");
+ m->errorOut(e, "CollectCommand", "execute");
exit(1);
}
}
return filenames;
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "parseSharedFile");
+ m->errorOut(e, "CollectCommand", "parseSharedFile");
exit(1);
}
}
projects / mothur.git / blobdiff