//**********************************************************************************************************************
-MatrixOutputCommand::MatrixOutputCommand(string option){
+MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
- else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
+ if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
}
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
- if ((output != "lt") && (output != "square")) { mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); mothurOutEndLine(); output = "lt"; }
+ if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
//if the user has not specified any labels use the ones from read.otu
if (label == "") {
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+ m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
exit(1);
}
}
void MatrixOutputCommand::help(){
try {
- mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
- mothurOut("The dist.shared command parameters are groups, calc, output 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 used.\n");
- mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
- mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
- mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
- mothurOut("The default value for groups is all the groups in your groupfile.\n");
- mothurOut("The default value for calc is jclass and thetayc.\n");
+ m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The dist.shared command parameters are groups, calc, output and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
+ m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+ m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
+ m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass and thetayc.\n");
validCalculator->printCalc("matrix", cout);
- mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ m->mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "help");
+ m->errorOut(e, "MatrixOutputCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
//if the users entered no valid calculators don't execute command
- if (matrixCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
+ if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
set<string> processedLabels;
set<string> userLabels = labels;
- 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;}
numGroups = lookup.size();
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
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();
}
}
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//reset groups parameter
globaldata->Groups.clear();
+
+ 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, "MatrixOutputCommand", "execute");
+ m->errorOut(e, "MatrixOutputCommand", "execute");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "printSims");
+ m->errorOut(e, "MatrixOutputCommand", "printSims");
exit(1);
}
}
exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
openOutputFile(exportFileName, out);
+ outputNames.push_back(exportFileName);
+
printSims(out);
out.close();
}
catch(exception& e) {
- errorOut(e, "MatrixOutputCommand", "process");
+ m->errorOut(e, "MatrixOutputCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff