//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(){
+HeatMapCommand::HeatMapCommand(string option){
try {
globaldata = GlobalData::getInstance();
- heatmap = new HeatMap();
- format = globaldata->getFormat();
- util = new SharedUtil();
+ 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() == "")) {
+ mothurOut("You must read a list, or a list and a group, or a shared before you can use the heatmap.bin command."); mothurOutEndLine(); 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 != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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";
+ errorOut(e, "HeatMapCommand", "HeatMapCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void HeatMapCommand::help(){
+ try {
+ mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
+ mothurOut("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");
+ 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 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");
+ mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
+ mothurOut("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");
+ mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels).\n");
+ mothurOut("Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used.\n");
+ mothurOut("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");
+ mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
+ mothurOut("The heatmap.bin command outputs a .svg file for each line or label you specify.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapCommand", "help");
exit(1);
- }
+ }
}
+
//**********************************************************************************************************************
HeatMapCommand::~HeatMapCommand(){
- delete input;
- delete read;
- delete heatmap;
- delete util;
+ if (abort == false) {
+ delete read;
+ delete heatmap;
+ }
}
//**********************************************************************************************************************
int HeatMapCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
int count = 1;
-
+ string lastLabel;
+
if (format == "sharedfile") {
//you have groups
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else if (format == "shared") {
- //you are using a list and a groupfile
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
+ lastLabel = lookup[0]->getLabel();
}else if (format == "list") {
//you are using just a list file and have only one group
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
- ordersingle = globaldata->gorder;
- input = globaldata->ginput;
+ rabund = globaldata->rabund;
+ lastLabel = rabund->getLabel();
+ 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") {
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
- globaldata->setGroups("");
-
-
- while(order != 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(order->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- heatmap->getPic(order);
-
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ heatmap->getPic(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
+ heatmap->getPic(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
-
+
+ lastLabel = lookup[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
+ 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++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
}else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
- count++;
}
+
+ //run last line if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ heatmap->getPic(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+
//reset groups parameter
globaldata->Groups.clear();
}else{
- while(ordersingle != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->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 << ordersingle->getLabel() << '\t' << count << endl;
- heatmap->getPic(ordersingle);
+ mothurOut(rabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ heatmap->getPic(rabund);
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+ userLines.erase(count);
}
- ordersingle = (input->getOrderVector());
+ if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+ mothurOut(rabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
+ heatmap->getPic(rabund);
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+ }
+
+
+
+ lastLabel = rabund->getLabel();
+ delete 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++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+ mothurOut(rabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
+ heatmap->getPic(rabund);
+ delete rabund; globaldata->rabund = NULL;
+ }
+
}
+ delete input; globaldata->ginput = NULL;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "HeatMapCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff