#include "heatmapcommand.h"
-
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+HeatMapCommand::HeatMapCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","sabund","rabund","shared","relabund","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
HeatMapCommand::HeatMapCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+
//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 = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
- m->mothurOut("You must read a list, rabund, sabund, or a list and a group, or a shared before you can use the heatmap.bin command."); m->mothurOutEndLine(); abort = true;
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
+ m->mothurOut("You must read a list, rabund, sabund, or a list and a group, shared, or relabund file before you can use the heatmap.bin command."); m->mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
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; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
m->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 are also separated by dashes.\n");
m->mothurOut("The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n");
m->mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
- m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=F, scale=log10).\n");
+ m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
m->mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
m->mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\n");
int HeatMapCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
format = globaldata->getFormat();
//you are using just a list file and have only one group
rabund = globaldata->rabund;
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;
- if ((format != "list") && (format != "rabund") && (format != "sabund")) {
+ 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))) {
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") { remove(outputNames[i].c_str()); } }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
globaldata->Groups.clear();
delete read; delete heatmap; return 0;
}
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(lookup));
+ string outputFileName = heatmap->getPic(lookup);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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();
- outputNames.push_back(heatmap->getPic(lookup));
+ string outputFileName = heatmap->getPic(lookup);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
globaldata->Groups.clear();
delete read; delete heatmap; return 0;
}
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(lookup));
+ 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]; }
}
//reset groups parameter
globaldata->Groups.clear();
- }else{
+ }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") { remove(outputNames[i].c_str()); } }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
delete rabund; delete read; delete heatmap; return 0;
}
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(rabund));
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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();
- outputNames.push_back(heatmap->getPic(rabund));
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
}
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
delete read; delete heatmap; return 0;
}
rabund = input->getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(rabund));
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
delete rabund; globaldata->rabund = NULL;
}
+ }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") { remove(outputNames[i].c_str()); } } outputTypes.clear();
+ globaldata->Groups.clear();
+ delete read; 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") { remove(outputNames[i].c_str()); } } outputTypes.clear();
+ globaldata->Groups.clear();
+ delete read; 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
+ globaldata->Groups.clear();
+
}
globaldata->rabund = NULL;
delete input; globaldata->ginput = NULL;
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
delete read; delete heatmap; return 0;
}
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
-
+
delete read;
delete heatmap;
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