#include "parsimonycommand.h"
/***********************************************************/
-ParsimonyCommand::ParsimonyCommand(string option) {
+ParsimonyCommand::ParsimonyCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
Groups.clear();
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
//are you trying to use parsimony without reading a tree or saying you want random distribution
if (randomtree == "") {
if (globaldata->gTree.size() == 0) {
- mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); mothurOutEndLine(); abort = true; }
+ m->mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); m->mothurOutEndLine(); abort = true; }
}
//if the user changes the output directory command factory will send this info to us in the output parameter
if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); }
output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString);
+ outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony");
sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary";
openOutputFile(sumFile, outSum);
+ outputNames.push_back(sumFile);
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
getUserInput();
if(outputDir == "") { outputDir += hasPath(randomtree); }
output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString);
+ outputNames.push_back(outputDir+ getSimpleName(randomtree));
}
//set users groups to analyze
}
catch(exception& e) {
- errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
exit(1);
}
}
void ParsimonyCommand::help(){
try {
- mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
- mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n");
- mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n");
- mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
- mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
- mothurOut("Example parsimony(random=out, iters=500).\n");
- mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n");
- mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
+ m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
+ m->mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n");
+ m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
+ m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
+ m->mothurOut("Example parsimony(random=out, iters=500).\n");
+ m->mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n");
+ m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
}
catch(exception& e) {
- errorOut(e, "ParsimonyCommand", "help");
+ m->errorOut(e, "ParsimonyCommand", "help");
exit(1);
}
}
//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, "ParsimonyCommand", "execute");
+ m->errorOut(e, "ParsimonyCommand", "execute");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "ParsimonyCommand", "printParsimonyFile");
+ m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
exit(1);
}
}
try {
//column headers
outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
- mothurOut("Tree#\tGroups\tParsScore\tParsSig"); mothurOutEndLine();
+ m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
if (UScoreSig[a][i] > (1/(float)iters)) {
outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
- mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
}else {
outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
- mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
}
}
}
outSum.close();
}
catch(exception& e) {
- errorOut(e, "ParsimonyCommand", "printUSummaryFile");
+ m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
exit(1);
}
}
//create treemap
tmap = new TreeMap();
- mothurOut("Please enter the number of groups you would like to analyze: ");
+ m->mothurOut("Please enter the number of groups you would like to analyze: ");
cin >> numGroups;
- mothurOutJustToLog(toString(numGroups)); mothurOutEndLine();
+ m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
int num, count;
count = 1;
numEachGroup.resize(numGroups, 0);
for (int i = 1; i <= numGroups; i++) {
- mothurOut("Please enter the number of sequences in group " + toString(i) + ": ");
+ m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": ");
cin >> num;
- mothurOutJustToLog(toString(num)); mothurOutEndLine();
+ m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
//set tmaps seqsPerGroup
tmap->seqsPerGroup[toString(i)] = num;
}
catch(exception& e) {
- errorOut(e, "ParsimonyCommand", "getUserInput");
+ m->errorOut(e, "ParsimonyCommand", "getUserInput");
exit(1);
}
}
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