*/
#include "matrixoutputcommand.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
-
-
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","calc","groups","outputdir","inputdir", "output"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MatrixOutputCommand::MatrixOutputCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = 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 = "";
int i;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
+ if (Estimators[i] == "sharedsobs") {
+ matrixCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ matrixCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ matrixCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
matrixCalculators.push_back(new JAbund());
}else if (Estimators[i] == "sorabund") {
matrixCalculators.push_back(new SorAbund());
matrixCalculators.push_back(new ThetaYC());
}else if (Estimators[i] == "thetan") {
matrixCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ matrixCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ matrixCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ matrixCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ matrixCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ matrixCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ matrixCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ matrixCalculators.push_back(new Lennon());
}else if (Estimators[i] == "morisitahorn") {
matrixCalculators.push_back(new MorHorn());
}else if (Estimators[i] == "braycurtis") {
matrixCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ matrixCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ matrixCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ matrixCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ matrixCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ matrixCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ matrixCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ matrixCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ matrixCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ matrixCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ matrixCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ matrixCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ matrixCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ matrixCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ matrixCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ matrixCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ matrixCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ matrixCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ matrixCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ matrixCalculators.push_back(new MemPearson());
}
}
}
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
//reset groups parameter
globaldata->Groups.clear();
//add new pair of sharedrabunds
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
m->openOutputFile(exportFileName, out);
- outputNames.push_back(exportFileName);
+ outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
printSims(out);
out.close();
projects / mothur.git / blobdiff