#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"
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(); 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];
}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);
//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;
- m->mothurOut(order->getLabel()); m->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;
- 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;
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(); }
projects / mothur.git / blobdiff