//**********************************************************************************************************************
-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;
+ allLines = 1;
+ labels.clear();
+ Groups.clear();
+ Estimators.clear();
+
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","label", "calc","phylip","column","name","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ 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; }
+ }
+
+ 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 = 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 = 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 = 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; }
+ }
+ }
+
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { format = "phylip"; if (outputDir == "") { outputDir += hasPath(phylipfile); } }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { format = "column"; if (outputDir == "") { outputDir += hasPath(columnfile); } }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+
+ //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 heatmap.sim command."); mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); 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 (format == "") { format = "shared"; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ if (format == "shared") {
+ if (outputDir == "") { outputDir += hasPath(globaldata->getSharedFile()); }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { 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;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jest-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jest-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
}
}
+
+ if (abort == false) {
+ validCalculator = new ValidCalculators();
+
+ 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";
+ 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;
+void HeatMapSimCommand::help(){
+ try {
+ mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
+ mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
+ mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
+ mothurOut("With the read.otu command you may use the groups, label and calc parameters. \n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
+ mothurOut("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");
+ mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
+ mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
+ validCalculator->printCalc("heat", cout);
+ mothurOut("The default value for calc is jclass-thetayc.\n");
+ mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
+ mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
+ mothurOut("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");
+ mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
+ mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "help");
+ exit(1);
+ }
}
//**********************************************************************************************************************
+HeatMapSimCommand::~HeatMapSimCommand(){}
+
+//**********************************************************************************************************************
+
int HeatMapSimCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
+ heatmap = new HeatMapSim(outputDir);
+
+ if (format == "shared") {
+ runCommandShared();
+ }else if (format == "phylip") {
+ globaldata->inputFileName = phylipfile;
+ runCommandDist();
+ }else if (format == "column") {
+ globaldata->inputFileName = columnfile;
+ runCommandDist();
+ }
+
+ delete heatmap;
+ delete validCalculator;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandShared() {
+ try {
//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) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+ if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); 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))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
heatmap->getPic(lookup, heatCalculators);
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 ((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();
+ heatmap->getPic(lookup, heatCalculators);
- 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
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//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;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //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);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ heatmap->getPic(lookup, heatCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
globaldata->Groups.clear();
- globaldata->setGroups("");
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
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";
+ 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";
- exit(1);
- }
}
+//**********************************************************************************************************************
+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
+ 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);
+
+ for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
+ gobble(in);
+ }
+ }else {
+ double dist;
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ for(int j=0;j<i;j++){
+ in >> dist;
+ matrix[i][j] = dist; matrix[j][i] = dist;
+ }
+ 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;
+ openInputFile(columnfile, in);
+
+ while (!in.eof()) {
+ in >> first >> second >> dist; gobble(in);
+
+ map<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::iterator itB = nameMap->find(second);
+
+ if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1); }
+ if(itB == nameMap->end()){ cerr << "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;
+ }
+
+ heatmap->getPic(matrix, names); //vector<vector<double>>, vector<string>
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "runCommandDist");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+
+
+
+
+
+
projects / mothur.git / blobdiff