cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
}else if (globaldata->helpRequest == "parsimony") {
cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
- cout << "The parsimony command parameters are random and iters. No parameters are required." << "\n";
- cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, iters=yourIters)." << "\n";
+ cout << "The parsimony command parameters are random, groups and iters. No parameters are required." << "\n";
+ cout << "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";
+ cout << "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";
+ cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example parsimony(random=out, iters=500)." << "\n";
cout << "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";
cout << "and iters is 1000. The parsimony command output three files: .parsimony, .psummary and .pdistrib, their descriptions are in the manual." << "\n";
}else if (globaldata->helpRequest == "unifrac.weighted") {
cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
cout << "The unifrac.weighted command parameters are groups and iters. No parameters are required." << "\n";
- cout << "The groups paramter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
cout << "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";
cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
}else if (globaldata->helpRequest == "unifrac.unweighted") {
cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
- cout << "The groups paramter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group." << "\n";
+ cout << "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";
cout << "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";
cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
/**************************************************************************************************/
EstOutput Parsimony::getValues(Tree* t) {
try {
+ globaldata = GlobalData::getInstance();
+
data.resize(1,0);
int score = 0;
int lc = t->tree[i].getLChild();
int rc = t->tree[i].getRChild();
- if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
+ int iSize = 0;
+ int rcSize = 0;
+ int lcSize = 0;
+
+ //add in all the groups the users wanted
+ for (it = t->tree[i].pGroups.begin(); it != t->tree[i].pGroups.end(); it++) {
+ if (inUsersGroups(it->first) == true) { iSize++; }
+ }
+
+ //if that leaves no groups give it 1 so it will cause no change to parent
+ if (iSize == 0) { iSize++; }
+
+ //add in all the groups the users wanted
+ for (it = t->tree[rc].pGroups.begin(); it != t->tree[rc].pGroups.end(); it++) {
+
+ if (inUsersGroups(it->first) == true) { rcSize++; }
+ }
+
+ //if that leaves no groups give it 1 so it will cause no change to parent
+ if (rcSize == 0) { rcSize++; }
+
+
+ //add in all the groups the users wanted
+ for (it = t->tree[lc].pGroups.begin(); it != t->tree[lc].pGroups.end(); it++) {
+
+ if (inUsersGroups(it->first) == true) { lcSize++; }
+ }
+
+ //if that leaves no groups give it 1 so it will cause no change to parent
+ if (lcSize == 0) { lcSize++; }
+
+
+ //if you have more groups than either of your kids then theres been a change.
+ if(iSize > rcSize || iSize > lcSize){
score++;
+
}
}
}
/**************************************************************************************************/
+
+bool Parsimony::inUsersGroups(string groupname) {
+ try {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (groupname == globaldata->Groups[i]) { return true; }
+ }
+ return false;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Parsimony class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
#include "treecalculator.h"
#include "treemap.h"
+#include "globaldata.hpp"
/***********************************************************************/
EstOutput getValues(Tree*);
private:
+ GlobalData* globaldata;
EstOutput data;
TreeMap* tmap;
+ bool inUsersGroups(string);
+ map<string, int>::iterator it;
};
/***********************************************************************/
openOutputFile(sumFile, outSum);
distFile = globaldata->getTreeFile() + ".pdistrib";
openOutputFile(distFile, outDist);
+
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }else {
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
//reset randomTree parameter to ""
globaldata->setRandomTree("");
+ //reset groups parameter
+ globaldata->Groups.clear();
return 0;
//if the user only entered invalid groups
if (globaldata->Groups.size() == 0) {
cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- }
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }else {
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
}
-
+
convert(globaldata->getIters(), iters); //how many random trees to generate
unweighted = new Unweighted(tmap);
printUnweightedFile();
printUWSummaryFile();
+ //reset groups parameter
+ globaldata->Groups.clear();
+
delete randT;
return 0;
//reset randomTree parameter to 0
globaldata->setRandomTree("0");
+
//clear out users groups
globaldata->Groups.clear();
projects / mothur.git / commitdiff