*/
#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; calledHelp = true;
+ 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){
+MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"label","calc","groups"};
+ string Array[] = {"label","calc","groups","outputdir","inputdir", "output"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(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 = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
- else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
+ if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
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; }
}
+ output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
+ if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+
//if the user has not specified any labels use the ones from read.otu
if (label == "") {
allLines = globaldata->allLines;
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
if (abort == false) {
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());
}
}
}
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+ m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
exit(1);
}
}
void MatrixOutputCommand::help(){
try {
- mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
- mothurOut("The dist.shared command parameters are groups, calc and label. No parameters are required.\n");
- mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
- mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
- mothurOut("The default value for groups is all the groups in your groupfile.\n");
- mothurOut("The default value for calc is jclass and thetayc.\n");
+ m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The dist.shared command parameters are groups, calc, output and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
+ m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+ m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
+ m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass and thetayc.\n");
validCalculator->printCalc("matrix", cout);
- mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ m->mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "help");
+ m->errorOut(e, "MatrixOutputCommand", "help");
exit(1);
}
}
int MatrixOutputCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
- if (matrixCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
+ if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
set<string> processedLabels;
set<string> userLabels = labels;
- if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0;}
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
numGroups = lookup.size();
+
+ if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
//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) { 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){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors();
}
+ 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;
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 (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++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
+ 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();
+
+ 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, "MatrixOutputCommand", "execute");
+ m->errorOut(e, "MatrixOutputCommand", "execute");
exit(1);
}
}
void MatrixOutputCommand::printSims(ostream& out) {
try {
- //output column headers
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //output num seqs
out << simMatrix.size() << endl;
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < m; n++) {
- out << simMatrix[m][n] << '\t';
+ if (output == "lt") {
+ for (int m = 0; m < simMatrix.size(); m++) {
+ out << lookup[m]->getGroup() << '\t';
+ for (int n = 0; n < m; n++) {
+ out << simMatrix[m][n] << '\t';
+ }
+ out << endl;
+ }
+ }else{
+ for (int m = 0; m < simMatrix.size(); m++) {
+ out << lookup[m]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[m].size(); n++) {
+ out << simMatrix[m][n] << '\t';
+ }
+ out << endl;
}
- out << endl;
}
-
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "printSims");
+ m->errorOut(e, "MatrixOutputCommand", "printSims");
exit(1);
}
}
/***********************************************************/
-void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
+int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
EstOutput data;
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int p = 0; p < simMatrix.size(); p++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[p].push_back(0.0);
}
}
if (k != l) { //we dont need to similiarity of a groups to itself
//get estimated similarity between 2 groups
+ if (m->control_pressed) { return 0; }
+
subset.clear(); //clear out old pair of sharedrabunds
//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 = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
- openOutputFile(exportFileName, out);
+ exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ m->openOutputFile(exportFileName, out);
+ outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
+
printSims(out);
out.close();
}
-
+ return 0;
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "process");
+ m->errorOut(e, "MatrixOutputCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff