*/
#include "treegroupscommand.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> TreeGroupCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeGroupCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string TreeGroupCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
+ helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision and label.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
+ helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
+ helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used. If you use a column file the name filename is required. \n";
+ helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
+ helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
+ helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile.\n";
+ helpString += "The default value for calc is jclass-thetayc.\n";
+ helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
+ helpString += validCalculator.printCalc("treegroup");
+ helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
+ helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeGroupCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+TreeGroupCommand::TreeGroupCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-TreeGroupCommand::TreeGroupCommand(string option){
+TreeGroupCommand::TreeGroupCommand(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") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //required parameters
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { abort = true; }
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; }
+ else { inputfile = phylipfile; format = "phylip"; }
columnfile = validParameter.validFile(parameters, "column", true);
- if (columnfile == "not open") { abort = true; }
+ if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { format = "column"; }
+ else { inputfile = columnfile; format = "column"; }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputfile = sharedfile; format = "sharedfile"; }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else { globaldata->setNameFile(namefile); }
- format = globaldata->getFormat();
-
- //error checking on files
- if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+ if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then column, then phylip
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { inputfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { inputfile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
- if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
+ if (namefile == "") {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
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; }
}
- //if the user has not specified any labels use the ones from read.otu
- if(label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
}
calc = validParameter.validFile(parameters, "calc", false);
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
convert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
-
-
- if (abort == false) {
- validCalculator = new ValidCalculators();
-
- if (format == "sharedfile") {
- int i;
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
- }
- }
- }
- }
- }
+ //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(inputfile); //if user entered a file with a path then preserve it
+ }
}
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-void TreeGroupCommand::help(){
- try {
- mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
- mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
- mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\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 allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
- mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
- mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
- mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- mothurOut("Example tree.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-thetayc.\n");
- mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
- validCalculator->printCalc("treegroup", cout);
- mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
- mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "help");
+ m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
}
-
-
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
if (abort == false) {
-
- if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL;}
+ if (format == "sharedfile") { delete input; }
else { delete readMatrix; delete matrix; delete list; }
- delete tmap;
- delete validCalculator;
+ delete tmap;
}
}
int TreeGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (format == "sharedfile") {
+
+ ValidCalculators validCalculator;
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ treeCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ treeCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ treeCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
+ treeCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ treeCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ treeCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ treeCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ treeCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ treeCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ treeCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ treeCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ treeCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ treeCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ treeCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ treeCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ treeCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ treeCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ treeCalculators.push_back(new Lennon());
+ }else if (Estimators[i] == "morisitahorn") {
+ treeCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ treeCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ treeCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ treeCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ treeCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ treeCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ treeCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ treeCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ treeCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ treeCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ treeCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ treeCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ treeCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ treeCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ treeCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ treeCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ treeCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ treeCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ treeCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ treeCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ treeCalculators.push_back(new MemPearson());
+ }
+ }
+ }
+
//if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; }
-
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
lastLabel = lookup[0]->getLabel();
- 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; }
//used in tree constructor
- globaldata->runParse = false;
+ m->runParse = false;
+
+ //create treemap class from groupmap for tree class to use
+ tmap = new TreeMap();
+ tmap->makeSim(m->namesOfGroups);
+
+ //clear globaldatas old tree names if any
+ m->Treenames.clear();
+
+ //fills globaldatas tree names
+ m->Treenames = m->Groups;
+
+ if (m->control_pressed) { return 0; }
//create tree file
makeSimsShared();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}else{
//read in dist file
- filename = globaldata->inputFileName;
+ filename = inputfile;
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
//make treemap
tmap = new TreeMap();
+
+ if (m->control_pressed) { return 0; }
+
tmap->makeSim(list);
- globaldata->gTreemap = tmap;
- globaldata->Groups = tmap->namesOfGroups;
+ m->Groups = tmap->namesOfGroups;
//clear globaldatas old tree names if any
- globaldata->Treenames.clear();
+ m->Treenames.clear();
//fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
+ m->Treenames = m->Groups;
//used in tree constructor
- globaldata->runParse = false;
+ m->runParse = false;
+
+ if (m->control_pressed) { return 0; }
makeSimsDist();
+
+ if (m->control_pressed) { return 0; }
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + "tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre";
+ outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
createTree();
- mothurOut("Tree complete. "); mothurOutEndLine();
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOut("Tree complete. "); m->mothurOutEndLine();
+
}
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
+
+ //set tree file as new current treefile
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
+
+ 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, "TreeGroupCommand", "execute");
+ m->errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
-void TreeGroupCommand::createTree(){
+int TreeGroupCommand::createTree(){
try {
//create tree
- t = new Tree();
+ t = new Tree(tmap);
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
float largest = -1000.0;
-
+
+ if (m->control_pressed) { delete t; return 1; }
+
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
//assemble tree
t->assembleTree();
+ if (m->control_pressed) { delete t; return 1; }
+
//print newick file
t->createNewickFile(outputFile);
//delete tree
delete t;
+
+ if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "createTree");
+ m->errorOut(e, "TreeGroupCommand", "createTree");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "printSims");
+ m->errorOut(e, "TreeGroupCommand", "printSims");
exit(1);
}
}
/***********************************************************/
-void TreeGroupCommand::makeSimsDist() {
+int TreeGroupCommand::makeSimsDist() {
try {
numGroups = list->size();
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[k].push_back(0.0);
}
}
for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
//similairity = -(distance-1)
simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
- simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
+ simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
+
+ if (m->control_pressed) { return 1; }
+
}
-
+ return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "makeSimsDist");
+ m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
exit(1);
}
}
/***********************************************************/
-void TreeGroupCommand::makeSimsShared() {
+int TreeGroupCommand::makeSimsShared() {
try {
-
- //clear globaldatas old tree names if any
- globaldata->Treenames.clear();
-
- //fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
-
- //create treemap class from groupmap for tree class to use
- tmap = new TreeMap();
- tmap->makeSim(globaldata->gGroupmap);
- globaldata->gTreemap = tmap;
-
set<string> processedLabels;
set<string> userLabels = labels;
//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) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
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());
userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
lastLabel = lookup[0]->getLabel();
lookup = input->getSharedRAbundVectors();
}
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
+
//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();
}
}
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]; }
}
for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "makeSimsShared");
+ m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
exit(1);
}
}
/***********************************************************/
-void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
try{
EstOutput data;
vector<SharedRAbundVector*> subset;
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[k].push_back(0.0);
}
}
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
+ outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
for (int k = 0; k < thisLookup.size(); k++) {
for (int l = k; l < thisLookup.size(); l++) {
//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 (treeCalculators[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 = treeCalculators[i]->getValues(subset); //saves the calculator outputs
+ //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
+ if (m->control_pressed) { return 1; }
+
//save values in similarity matrix
simMatrix[k][l] = data[0];
simMatrix[l][k] = data[0];
}
}
}
-
+
+ //createdistance file from simMatrix
+ /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+ ofstream outDist;
+ m->openOutputFile(o, outDist);
+ outDist << simMatrix.size() << endl;
+ for (int k = 0; k < simMatrix.size(); k++) {
+ outDist << thisLookup[k]->getGroup() << '\t';
+ for (int l = 0; l < k; l++) {
+ outDist << (1.0-simMatrix[k][l]) << '\t';
+ }
+ outDist << endl;
+ }
+ outDist.close();*/
+
+
+ if (m->control_pressed) { return 1; }
//creates tree from similarity matrix and write out file
createTree();
+
+ if (m->control_pressed) { return 1; }
}
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "process");
+ m->errorOut(e, "TreeGroupCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff