#include "sharedbraycurtis.h"
+//**********************************************************************************************************************
+vector<string> HeatMapSimCommand::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 pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ 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, "HeatMapSimCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string HeatMapSimCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label. shared or phylip or column and name are required unless valid current files exist.\n";
+ helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
+ helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
+ helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
+ helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
+ helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+ helpString += validCalculator.printCalc("heat");
+ helpString += "The default value for calc is jclass-thetayc.\n";
+ helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
+ helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
+ helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n";
+ helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
+ helpString += "Example heatmap.sim(phylip=amazonGroups.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, "HeatMapSimCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+HeatMapSimCommand::HeatMapSimCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-HeatMapSimCommand::HeatMapSimCommand(){
+HeatMapSimCommand::HeatMapSimCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
- heatmap = new HeatMapSim();
-
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("heat", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- heatCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- heatCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- heatCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- heatCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- heatCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- heatCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- heatCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- heatCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- heatCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- heatCalculators.push_back(new BrayCurtis());
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+
+ format = "";
+ //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 = ""; }
+
+ //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; }
+ }
+
+ it = parameters.find("shared");
+ //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["shared"] = inputDir + it->second; }
}
}
+
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+
+ //error checking on files
+ if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) {
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { format = "phylip"; inputfile = phylipfile; 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 or phylip or column file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ 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") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jest-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jest-thetayc"; }
+ }
+ m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+
+ if (abort == false) {
+ ValidCalculators validCalculator;
+
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
+ if (Estimators[i] == "jabund") {
+ heatCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ heatCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ heatCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ heatCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ heatCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ heatCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ heatCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ heatCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "morisitahorn") {
+ heatCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ heatCalculators.push_back(new BrayCurtis());
+ }
+ }
+ }
+
+ }
}
-
- //reset calc for next command
- globaldata->setCalc("");
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-HeatMapSimCommand::~HeatMapSimCommand(){
- delete input;
- delete read;
- delete heatmap;
+int HeatMapSimCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ heatmap = new HeatMapSim(outputDir, inputfile);
+
+ if (format == "shared") {
+ runCommandShared();
+ }else{ runCommandDist(); }
+
+ delete heatmap;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); 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(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "execute");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-
-int HeatMapSimCommand::execute(){
+int HeatMapSimCommand::runCommandShared() {
try {
- int count = 1;
-
//if the users entered no valid calculators don't execute command
- if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
+ if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
-
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+ string lastLabel = lookup[0]->getLabel();
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
//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 = globaldata->labels;
- set<int> userLines = globaldata->lines;
-
+ 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) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ //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 input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lookup, heatCalculators);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ 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);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
- lookup = input->getSharedRAbundVectors();
- count++;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+
}
+
+ if (m->control_pressed) { delete input; m->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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+ if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
//reset groups parameter
- globaldata->Groups.clear();
- globaldata->setGroups("");
-
+ m->Groups.clear();
+
+ delete input;
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandDist() {
+ try {
+
+ vector< vector<double> > matrix;
+ vector<string> names;
+ ifstream in;
+
+ //read distance file and create distance vector and names vector
+ if (format == "phylip") {
+ //read phylip file
+ m->openInputFile(phylipfile, in);
+
+ string name;
+ int numSeqs;
+ in >> numSeqs >> name;
+
+ //save name
+ names.push_back(name);
+
+ //resize the matrix and fill with zeros
+ matrix.resize(numSeqs);
+ for(int i = 0; i < numSeqs; i++) {
+ matrix[i].resize(numSeqs, 0.0);
+ }
+
+ //determine if matrix is square or lower triangle
+ //if it is square read the distances for the first sequence
+ char d;
+ bool square;
+ while((d=in.get()) != EOF){
+
+ //is d a number meaning its square
+ if(isalnum(d)){
+ square = true;
+ in.putback(d);
+
+ for(int i=0;i<numSeqs;i++){
+ in >> matrix[0][i];
+ }
+ break;
+ }
+
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ square = false;
+ break;
+ }
+ }
+
+ //read rest of matrix
+ if (square == true) {
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ if (m->control_pressed) { return 0; }
+
+ for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
+ m->gobble(in);
+ }
+ }else {
+ double dist;
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ if (m->control_pressed) { return 0; }
+
+ for(int j=0;j<i;j++){
+ in >> dist;
+ matrix[i][j] = dist; matrix[j][i] = dist;
+ }
+ m->gobble(in);
+ }
+ }
+ in.close();
+ }else {
+ //read names file
+ NameAssignment* nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+
+ //put names in order in vector
+ for (int i = 0; i < nameMap->size(); i++) {
+ names.push_back(nameMap->get(i));
+ }
+
+ //resize matrix
+ matrix.resize(nameMap->size());
+ for (int i = 0; i < nameMap->size(); i++) {
+ matrix[i].resize(nameMap->size(), 0.0);
+ }
+
+ //read column file
+ string first, second;
+ double dist;
+ m->openInputFile(columnfile, in);
+
+ while (!in.eof()) {
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (m->control_pressed) { return 0; }
+
+ map<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::iterator itB = nameMap->find(second);
+
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
+
+ //save distance
+ matrix[itA->second][itB->second] = dist;
+ matrix[itB->second][itA->second] = dist;
+ }
+ in.close();
+
+ delete nameMap;
+ }
+
+
+ string outputFileName = heatmap->getPic(matrix, names);
+ outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
+ outputTypes["svg"].push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
exit(1);
- }
+ }
}
-
//**********************************************************************************************************************
+
+
+
+
+
+