//**********************************************************************************************************************
-HeatMapSimCommand::HeatMapSimCommand(string option){
+HeatMapSimCommand::HeatMapSimCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
labels.clear();
Groups.clear();
Estimators.clear();
-
+
//allow user to run help
if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
it = parameters.find("column");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["column"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; if (outputDir == "") { outputDir += hasPath(phylipfile); } }
+ else { format = "phylip"; if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { format = "column"; if (outputDir == "") { outputDir += hasPath(columnfile); } }
+ else { format = "column"; if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
//error checking on files
- if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
- if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
+ if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
}
if (format == "") { format = "shared"; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if (format == "shared") {
- if (outputDir == "") { outputDir += hasPath(globaldata->getSharedFile()); }
+ if (outputDir == "") { outputDir += m->hasPath(globaldata->getSharedFile()); }
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; }
}
else {
if (calc == "default") { calc = "jest-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
}
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
+ m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
exit(1);
}
}
void HeatMapSimCommand::help(){
try {
- mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
- mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
- mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
- mothurOut("With the read.otu command you may use the groups, label and calc parameters. \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 group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n");
- mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
- mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n");
- 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 heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
+ m->mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
+ m->mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
+ m->mothurOut("With the read.otu command you may use the groups, label and calc parameters. \n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
+ 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 is also separated by dashes.\n");
+ m->mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
+ m->mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\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");
validCalculator->printCalc("heat", cout);
- mothurOut("The default value for calc is jclass-thetayc.\n");
- mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
- mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
- mothurOut("Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n");
- mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
- mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ m->mothurOut("The default value for calc is jclass-thetayc.\n");
+ m->mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
+ m->mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
+ m->mothurOut("Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n");
+ m->mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
+ m->mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "help");
+ m->errorOut(e, "HeatMapSimCommand", "help");
exit(1);
}
}
delete heatmap;
delete validCalculator;
-
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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) {
- errorOut(e, "HeatMapSimCommand", "execute");
+ m->errorOut(e, "HeatMapSimCommand", "execute");
exit(1);
}
}
int HeatMapSimCommand::runCommandShared() {
try {
//if the users entered no valid calculators don't execute command
- if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
+ if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
- if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0;}
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
//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 (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
+
//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) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
+
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- heatmap->getPic(lookup, heatCalculators);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
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);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- heatmap->getPic(lookup, heatCalculators);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
}
+
+ if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); 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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
+ if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); return 0; }
+
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- heatmap->getPic(lookup, heatCalculators);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
+ if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); return 0; }
//reset groups parameter
globaldata->Groups.clear();
return 0;
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "runCommandShared");
+ m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
exit(1);
}
}
//read distance file and create distance vector and names vector
if (format == "phylip") {
//read phylip file
- openInputFile(phylipfile, in);
+ m->openInputFile(phylipfile, in);
string name;
int numSeqs;
in >> name;
names.push_back(name);
- for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
- gobble(in);
+ if (m->control_pressed) { return 0; }
+
+ for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
+ m->gobble(in);
}
}else {
double dist;
in >> name;
names.push_back(name);
+ if (m->control_pressed) { return 0; }
+
for(int j=0;j<i;j++){
in >> dist;
matrix[i][j] = dist; matrix[j][i] = dist;
}
- gobble(in);
+ m->gobble(in);
}
}
in.close();
//read column file
string first, second;
double dist;
- openInputFile(columnfile, in);
+ m->openInputFile(columnfile, in);
while (!in.eof()) {
- in >> first >> second >> dist; gobble(in);
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (m->control_pressed) { return 0; }
map<string, int>::iterator itA = nameMap->find(first);
map<string, int>::iterator itB = nameMap->find(second);
}
- heatmap->getPic(matrix, names); //vector<vector<double>>, vector<string>
+ outputNames.push_back(heatmap->getPic(matrix, names)); //vector<vector<double>>, vector<string>
return 0;
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "runCommandDist");
+ m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
exit(1);
}
}
projects / mothur.git / blobdiff