//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(){
+HeatMapCommand::HeatMapCommand(string option){
try {
globaldata = GlobalData::getInstance();
- heatmap = new HeatMap();
- format = globaldata->getFormat();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","line","label","sorted","scale"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
+ cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap.bin command." << endl; abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if ((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; }
+
+ scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
+
+ if (abort == false) {
+ heatmap = new HeatMap(sorted, scale);
+ format = globaldata->getFormat();
+ }
+ }
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void HeatMapCommand::help(){
+ try {
+ cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
+ cout << "The heatmap.bin command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
+ cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n";
+ cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
+ cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+ cout << "The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file." << "\n";
+ cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
+ cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMapCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
HeatMapCommand::~HeatMapCommand(){
- delete input;
+
delete read;
delete heatmap;
}
int HeatMapCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
int count = 1;
+ RAbundVector* lastRAbund;
+ vector<SharedRAbundVector*> lastLookup;
if (format == "sharedfile") {
//you have groups
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ lastLookup = lookup;
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
rabund = globaldata->rabund;
+ lastRAbund = globaldata->rabund;
input = globaldata->ginput;
}
+ //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 = labels;
+ set<int> userLines = lines;
+
if (format != "list") {
- while(lookup[0] != NULL){
+ //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) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
cout << lookup[0]->getLabel() << '\t' << count << endl;
heatmap->getPic(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
}
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup);
+
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ }
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
+
//get next line to process
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;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
//reset groups parameter
globaldata->Groups.clear();
}else{
- while(rabund != NULL){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
cout << rabund->getLabel() << '\t' << count << endl;
heatmap->getPic(rabund);
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+ userLines.erase(count);
}
- delete rabund;
+ if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
+
+ cout << lastRAbund->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastRAbund);
+
+ processedLabels.insert(lastRAbund->getLabel());
+ userLabels.erase(lastRAbund->getLabel());
+ }
+
+ if (count != 1) { delete lastRAbund; }
+ lastRAbund = rabund;
+
rabund = input->getRAbundVector();
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(lastRAbund->getLabel()) != 1) {
+ cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastRAbund->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastRAbund);
+ }
+
+ delete lastRAbund;
+
}
- globaldata->setGroups("");
+ delete input;
return 0;
}
catch(exception& e) {