#include "sharedbraycurtis.h"
#include "sharedjackknife.h"
#include "whittaker.h"
-
-
+#include "odum.h"
+#include "canberra.h"
+#include "stricteuclidean.h"
+#include "strictchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "strictpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "strictkulczynski.h"
+#include "speciesprofile.h"
+#include "hamming.h"
//**********************************************************************************************************************
-
+vector<string> CollectSharedCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"freq","label","calc","groups","all","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectSharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectSharedCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"shared"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectSharedCommand::CollectSharedCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedchao"] = tempOutNames;
+ outputTypes["sharedsobs"] = tempOutNames;
+ outputTypes["sharedace"] = tempOutNames;
+ outputTypes["jabund"] = tempOutNames;
+ outputTypes["sorabund"] = tempOutNames;
+ outputTypes["jclass"] = tempOutNames;
+ outputTypes["sorclass"] = tempOutNames;
+ outputTypes["jest"] = tempOutNames;
+ outputTypes["sorest"] = tempOutNames;
+ outputTypes["thetayc"] = tempOutNames;
+ outputTypes["thetan"] = tempOutNames;
+ outputTypes["kstest"] = tempOutNames;
+ outputTypes["whittaker"] = tempOutNames;
+ outputTypes["sharednseqs"] = tempOutNames;
+ outputTypes["ochiai"] = tempOutNames;
+ outputTypes["anderberg"] = tempOutNames;
+ outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynskicody"] = tempOutNames;
+ outputTypes["lennon"] = tempOutNames;
+ outputTypes["morisitahorn"] = tempOutNames;
+ outputTypes["braycurtis"] = tempOutNames;
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["stricteuclidean"] = tempOutNames;
+ outputTypes["strictchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = tempOutNames;
+ outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["hamming"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedchao"] = tempOutNames;
+ outputTypes["sharedsobs"] = tempOutNames;
+ outputTypes["sharedace"] = tempOutNames;
+ outputTypes["jabund"] = tempOutNames;
+ outputTypes["sorabund"] = tempOutNames;
+ outputTypes["jclass"] = tempOutNames;
+ outputTypes["sorclass"] = tempOutNames;
+ outputTypes["jest"] = tempOutNames;
+ outputTypes["sorest"] = tempOutNames;
+ outputTypes["thetayc"] = tempOutNames;
+ outputTypes["thetan"] = tempOutNames;
+ outputTypes["kstest"] = tempOutNames;
+ outputTypes["whittaker"] = tempOutNames;
+ outputTypes["sharednseqs"] = tempOutNames;
+ outputTypes["ochiai"] = tempOutNames;
+ outputTypes["anderberg"] = tempOutNames;
+ outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynskicody"] = tempOutNames;
+ outputTypes["lennon"] = tempOutNames;
+ outputTypes["morisitahorn"] = tempOutNames;
+ outputTypes["braycurtis"] = tempOutNames;
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["stricteuclidean"] = tempOutNames;
+ outputTypes["strictchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = tempOutNames;
+ outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["hamming"] = tempOutNames;
+
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
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 = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
}
globaldata->Groups = Groups;
convert(temp, freq);
temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
- all = isTrue(temp);
+ all = m->isTrue(temp);
if (abort == false) {
- if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
- string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+ if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
format = globaldata->getFormat();
int i;
if (validCalculator->isValidCalculator("shared", Estimators[i]) == true) {
if (Estimators[i] == "sharedchao") {
cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
- outputNames.push_back(fileNameRoot+"shared.chao");
+ outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
}else if (Estimators[i] == "sharedsobs") {
cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
- outputNames.push_back(fileNameRoot+"shared.sobs");
+ outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");
}else if (Estimators[i] == "sharedace") {
cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
- outputNames.push_back(fileNameRoot+"shared.ace");
+ outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace");
}else if (Estimators[i] == "jabund") {
cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
- outputNames.push_back(fileNameRoot+"jabund");
+ outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund");
}else if (Estimators[i] == "sorabund") {
cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
- outputNames.push_back(fileNameRoot+"sorabund");
+ outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund");
}else if (Estimators[i] == "jclass") {
cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
- outputNames.push_back(fileNameRoot+"jclass");
+ outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass");
}else if (Estimators[i] == "sorclass") {
cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
- outputNames.push_back(fileNameRoot+"sorclass");
+ outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass");
}else if (Estimators[i] == "jest") {
cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
- outputNames.push_back(fileNameRoot+"jest");
+ outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest");
}else if (Estimators[i] == "sorest") {
cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
- outputNames.push_back(fileNameRoot+"sorest");
+ outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest");
}else if (Estimators[i] == "thetayc") {
cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
- outputNames.push_back(fileNameRoot+"thetayc");
+ outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc");
}else if (Estimators[i] == "thetan") {
cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
- outputNames.push_back(fileNameRoot+"thetan");
+ outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan");
}else if (Estimators[i] == "kstest") {
cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
- outputNames.push_back(fileNameRoot+"kstest");
+ outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest");
}else if (Estimators[i] == "whittaker") {
cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
- outputNames.push_back(fileNameRoot+"whittaker");
+ outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker");
}else if (Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
- outputNames.push_back(fileNameRoot+"shared.nseqs");
+ outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs");
}else if (Estimators[i] == "ochiai") {
cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
- outputNames.push_back(fileNameRoot+"ochiai");
+ outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai");
}else if (Estimators[i] == "anderberg") {
cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
- outputNames.push_back(fileNameRoot+"anderberg");
+ outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
}else if (Estimators[i] == "skulczynski") {
cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
- outputNames.push_back(fileNameRoot+"kulczynski");
+ outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
}else if (Estimators[i] == "kulczynskicody") {
cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
- outputNames.push_back(fileNameRoot+"kulczynskicody");
+ outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody");
}else if (Estimators[i] == "lennon") {
cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
- outputNames.push_back(fileNameRoot+"lennon");
+ outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon");
}else if (Estimators[i] == "morisitahorn") {
cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
- outputNames.push_back(fileNameRoot+"morisitahorn");
+ outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn");
}else if (Estimators[i] == "braycurtis") {
cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
- outputNames.push_back(fileNameRoot+"braycurtis");
+ outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
+ }else if (Estimators[i] == "odum") {
+ cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+"odum")));
+ outputNames.push_back(fileNameRoot+"odum"); outputTypes["odum"].push_back(fileNameRoot+"odum");
+ }else if (Estimators[i] == "canberra") {
+ cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+"canberra")));
+ outputNames.push_back(fileNameRoot+"canberra"); outputTypes["canberra"].push_back(fileNameRoot+"canberra");
+ }else if (Estimators[i] == "stricteuclidean") {
+ cDisplays.push_back(new CollectDisplay(new StrictEuclidean(), new SharedOneColumnFile(fileNameRoot+"stricteuclidean")));
+ outputNames.push_back(fileNameRoot+"stricteuclidean"); outputTypes["stricteuclidean"].push_back(fileNameRoot+"stricteuclidean");
+ }else if (Estimators[i] == "strictchord") {
+ cDisplays.push_back(new CollectDisplay(new StrictChord(), new SharedOneColumnFile(fileNameRoot+"strictchord")));
+ outputNames.push_back(fileNameRoot+"strictchord"); outputTypes["strictchord"].push_back(fileNameRoot+"strictchord");
+ }else if (Estimators[i] == "hellinger") {
+ cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+"hellinger")));
+ outputNames.push_back(fileNameRoot+"hellinger"); outputTypes["hellinger"].push_back(fileNameRoot+"hellinger");
+ }else if (Estimators[i] == "manhattan") {
+ cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+"manhattan")));
+ outputNames.push_back(fileNameRoot+"manhattan"); outputTypes["manhattan"].push_back(fileNameRoot+"manhattan");
+ }else if (Estimators[i] == "strictpearson") {
+ cDisplays.push_back(new CollectDisplay(new StrictPearson(), new SharedOneColumnFile(fileNameRoot+"strictpearson")));
+ outputNames.push_back(fileNameRoot+"strictpearson"); outputTypes["strictpearson"].push_back(fileNameRoot+"strictpearson");
+ }else if (Estimators[i] == "soergel") {
+ cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+"soergel")));
+ outputNames.push_back(fileNameRoot+"soergel"); outputTypes["soergel"].push_back(fileNameRoot+"soergel");
+ }else if (Estimators[i] == "spearman") {
+ cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+"spearman")));
+ outputNames.push_back(fileNameRoot+"spearman"); outputTypes["spearman"].push_back(fileNameRoot+"spearman");
+ }else if (Estimators[i] == "strictkulczynski") {
+ cDisplays.push_back(new CollectDisplay(new StrictKulczynski(), new SharedOneColumnFile(fileNameRoot+"strictkulczynski")));
+ outputNames.push_back(fileNameRoot+"strictkulczynski"); outputTypes["strictkulczynski"].push_back(fileNameRoot+"strictkulczynski");
+ }else if (Estimators[i] == "speciesprofile") {
+ cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+"speciesprofile")));
+ outputNames.push_back(fileNameRoot+"speciesprofile"); outputTypes["speciesprofile"].push_back(fileNameRoot+"speciesprofile");
+ }else if (Estimators[i] == "hamming") {
+ cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+"hamming")));
+ outputNames.push_back(fileNameRoot+"hamming"); outputTypes["hamming"].push_back(fileNameRoot+"hamming");
}
+
}
}
}
m->mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
m->mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
m->mothurOut("The default value for groups is all the groups in your groupfile.\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");
validCalculator->printCalc("shared", cout);
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ delete order;
+ globaldata->Groups.clear();
+ return 0;
+ }
if(allLines == 1 || labels.count(order->getLabel()) == 1){
-
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
//create collectors curve
cCurve = new Collect(order, cDisplays);
cCurve->getSharedCurve(freq);
delete cCurve;
- 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->getSharedOrderVector(lastLabel);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
//create collectors curve
cCurve = new Collect(order, cDisplays);
cCurve->getSharedCurve(freq);
delete cCurve;
-
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
order = input->getSharedOrderVector();
}
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ globaldata->Groups.clear();
+ return 0;
+ }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
if (needToRun == true) {
if (order != NULL) { delete order; }
order = input->getSharedOrderVector(lastLabel);
-
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
cCurve = new Collect(order, cDisplays);
cCurve->getSharedCurve(freq);
delete cCurve;
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ delete order;
+ globaldata->Groups.clear();
+ return 0;
+ }
+
delete order;
}
projects / mothur.git / blobdiff