#include "heatmapcommand.h"
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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, "HeatMapCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string HeatMapCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\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 sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n";
+ helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n";
+ helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n";
+ helpString += "The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\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 are also separated by dashes.\n";
+ helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
+ helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n";
+ helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\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 += "The default value for scale is log10; your other options are log2 and linear.\n";
+ helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\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, "HeatMapCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string HeatMapCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+HeatMapCommand::HeatMapCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(string option){
+HeatMapCommand::HeatMapCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
- labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"groups","line","label","sorted","scale"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//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; }
}
- //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;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["svg"] = 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("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; }
+ }
+
+ it = parameters.find("rabund");
+ //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["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //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["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
}
-
- //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; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
+
+
+ if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ }
}
+
+ //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 = m->hasPath(inputfile); }
+
+ //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; }
}
- //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;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
}
- sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; }
+ string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, numOTU);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontSize);
+
+ sorted = validParameter.validFile(parameters, "sorted", false);
+ if (sorted == "not found") {
+ //if numOTU is used change default
+ if (numOTU != 0) { sorted = "topotu"; }
+ else { sorted = "shared"; }
+ }
scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
- if (abort == false) {
- heatmap = new HeatMap(sorted, scale);
- format = globaldata->getFormat();
- }
+ if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup"); m->mothurOutEndLine(); abort=true; }
}
}
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";
+ m->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";
- 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 (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
+
+ string lastLabel;
+ input = new InputData(inputfile, format);
+
if (format == "sharedfile") {
//you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
- }else if (format == "list") {
+ lastLabel = lookup[0]->getLabel();
+
+ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
//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;
+ rabund = input->getRAbundVector();
+ lastLabel = rabund->getLabel();
+ }else if (format == "relabund") {
+ //you have groups
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ lastLabel = lookupFloat[0]->getLabel();
}
//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") {
+ if (format == "sharedfile") {
//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))) {
+ 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 < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ m->clearGroups();
+ delete input; delete heatmap; return 0;
+ }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lookup);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ string outputFileName = heatmap->getPic(lookup);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
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);
+ 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();
+
+ string outputFileName = heatmap->getPic(lookup);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
+ lastLabel = lookup[0]->getLabel();
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
-
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
- count++;
}
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ m->clearGroups();
+ delete input; delete heatmap; 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
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ 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();
+ string outputFileName = heatmap->getPic(lookup);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+ 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();
+ m->clearGroups();
- }else{
-
- while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
+
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ delete rabund; delete input; delete heatmap; return 0;
+ }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
+ if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
- cout << rabund->getLabel() << '\t' << count << endl;
- heatmap->getPic(rabund);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
-
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = rabund->getLabel();
+
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
- processedLabels.insert(lastRAbund->getLabel());
- userLabels.erase(lastRAbund->getLabel());
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+
+ //restore real lastlabel to save below
+ rabund->setLabel(saveLabel);
}
- if (count != 1) { delete lastRAbund; }
- lastRAbund = rabund;
-
+
+
+ lastLabel = rabund->getLabel();
+ delete rabund;
rabund = input->getRAbundVector();
- count++;
}
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ delete input; delete heatmap; 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(lastRAbund->getLabel()) != 1) {
- cout << ". I will use " << lastRAbund->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 " << lastRAbund->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+
+ if (rabund != NULL) { delete rabund; }
+ rabund = input->getRAbundVector(lastLabel);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+ delete rabund;
}
- delete lastRAbund;
+ }else {
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ m->clearGroups();
+ delete input; delete heatmap; return 0;
+ }
+
+ if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
+
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+ string outputFileName = heatmap->getPic(lookupFloat);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ string outputFileName = heatmap->getPic(lookupFloat);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
+
+ //get next line to process
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
+ m->clearGroups();
+ delete input; delete heatmap; 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++) {
+ 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 {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+ string outputFileName = heatmap->getPic(lookupFloat);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ }
+
+ //reset groups parameter
+ m->clearGroups();
}
+ delete input;
+ delete heatmap;
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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