globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Groups.clear();
Estimators.clear();
else {
//valid paramters for this command
- string AlignArray[] = {"groups","line","label", "calc"};
+ string AlignArray[] = {"groups","label", "calc"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
//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 {
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 == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
void HeatMapSimCommand::help(){
try {
mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n");
- mothurOut("The heatmap.sim command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time.\n");
+ mothurOut("The heatmap.sim command parameters are groups, calc and label. No parameters are required.\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 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.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels).\n");
- mothurOut("Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund).\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 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");
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 line or label you specify.\n");
+ mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
if (abort == true) { return 0; }
- int count = 1;
-
//if the users entered no valid calculators don't execute command
if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); 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;
- set<int> userLines = lines;
-
//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(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
heatmap->getPic(lookup, heatCalculators);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
if ((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);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
//prevent memory leak
//get next line to process
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //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);