#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"
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; }
}
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
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");
vector<string> outputNames;
+ string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
- else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+ 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(); return 0; }
+ 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]));
+ if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
globaldata->inputFileName = inputFileNames[p];
if (inputFileNames.size() > 1) {
}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");
}
//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);
set<string> userLabels = labels;
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
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);
- int error = cCurve->getCurve(freq);
+ cCurve->getCurve(freq);
delete cCurve;
- if (error == 1) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- delete input; globaldata->ginput = NULL;
- delete read;
- delete order; globaldata->gorder = NULL;
- delete validCalculator;
- globaldata->Groups.clear();
- return 0;
- }
-
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
order = (input->getOrderVector(lastLabel));
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
- int error = cCurve->getCurve(freq);
+ cCurve->getCurve(freq);
delete cCurve;
- if (error == 1) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- delete input; globaldata->ginput = NULL;
- delete read;
- delete order; globaldata->gorder = NULL;
- delete validCalculator;
- globaldata->Groups.clear();
- return 0;
- }
- m->mothurOut(order->getLabel()); m->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;
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
- int error = cCurve->getCurve(freq);
+ cCurve->getCurve(freq);
delete cCurve;
- if (error == 1) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ 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(); }
input = globaldata->ginput;
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
- string sharedFileRoot = getRootName(filename);
+ string sharedFileRoot = m->getRootName(filename);
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
for (int i = 0; i < lookup.size(); i++) {
RAbundVector rav = lookup[i]->getRAbundVector();
- openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
}
projects / mothur.git / blobdiff