#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;
+ //initialize outputTypes
+ 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) {
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 = "";
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");
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 ((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]; }
}
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());
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;
}
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()); } }
+ 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();
- outputNames.push_back(heatmap->getPic(lookupFloat));
+ string outputFileName = heatmap->getPic(lookupFloat);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
processedLabels.insert(lookupFloat[0]->getLabel());
userLabels.erase(lookupFloat[0]->getLabel());
lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(lookupFloat));
+ 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->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;
}
lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
- outputNames.push_back(heatmap->getPic(lookupFloat));
+ 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]; }
}
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;
}