fixed parsimony with groups and worked on unifrac.unweighted with groups

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index f7ad5253bb019f785ff01dd36317219b61db4c24..73eab59683b6f8ff379823ff9ab2d23c4620875f 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -16,10 +16,10 @@ UnifracWeightedCommand::UnifracWeightedCommand() {
                
                T = globaldata->gTree;
                tmap = globaldata->gTreemap;
-               weightedFile = globaldata->getTreeFile() + ".weighted";
-               openOutputFile(weightedFile, out);
+               //weightedFile = globaldata->getTreeFile() + ".weighted";
+               //openOutputFile(weightedFile, out);
                //column headers
-               out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+               //out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 
                sumFile = globaldata->getTreeFile() + ".wsummary";
                openOutputFile(sumFile, outSum);
@@ -78,17 +78,11 @@ int UnifracWeightedCommand::execute() {
                                                //copy T[i]'s info.
                                                randT->getCopy(T[i]);
                                                 
-                                               if (globaldata->Groups.size() != 0) {
-                                                       //create a random tree with same topology as T[i], but different labels
-                                                       randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
-                                                       //get wscore of random tree
-                                                       randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
-                                               }else {
-                                                       //create a random tree with same topology as T[i], but different labels
-                                                       randT->assembleRandomUnifracTree(tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
-                                                       //get wscore of random tree
-                                                       randomData = weighted->getValues(randT, tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
-                                               }
+                                               //create a random tree with same topology as T[i], but different labels
+                                               randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
+                                               //get wscore of random tree
+                                               randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
+                                               
                                                //save scores
                                                rScores[count].push_back(randomData[0]);
                                                validScores[count][randomData[0]] = randomData[0];
@@ -113,7 +107,7 @@ int UnifracWeightedCommand::execute() {
                                WScoreSig.push_back((iters-index)/(float)iters);
                        }
                        
-                       out << "Tree# " << i << endl;
+                       //out << "Tree# " << i << endl;
                        //printWeightedFile();
                        
                        //clear data
@@ -247,6 +241,9 @@ void UnifracWeightedCommand::setGroups() {
                //if the user has not entered specific groups to analyze then do them all
                if (globaldata->Groups.size() == 0) {
                        numGroups = tmap->getNumGroups();
+                       for (int i=0; i < numGroups; i++) { 
+                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                       }
                }else {
                        if (globaldata->getGroups() != "all") {
                                //check that groups are valid
@@ -261,33 +258,36 @@ void UnifracWeightedCommand::setGroups() {
                                //if the user only entered invalid groups
                                if (globaldata->Groups.size() == 0) { 
                                        numGroups = tmap->getNumGroups();
+                                       for (int i=0; i < numGroups; i++) { 
+                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                       }
                                        cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
                                }else if (globaldata->Groups.size() == 1) { 
                                        cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
                                        numGroups = tmap->getNumGroups();
                                        globaldata->Groups.clear();
+                                       for (int i=0; i < numGroups; i++) { 
+                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                       }
                                }else { numGroups = globaldata->Groups.size(); }
                        }else { //users wants all groups
                                numGroups = tmap->getNumGroups();
                                globaldata->Groups.clear();
                                globaldata->setGroups("");
+                               for (int i=0; i < numGroups; i++) { 
+                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                               }
                        }
                }
                
                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                numComp = 0;
-               int n = 1;
-               for (int i=1; i<numGroups; i++) { 
+               for (int i=0; i<numGroups; i++) { 
                        numComp += i; 
-                       for (int l = n; l < numGroups; l++) {
+                       for (int l = i+1; l < numGroups; l++) {
                                //set group comparison labels
-                               if (globaldata->Groups.size() != 0) {
-                                       groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
-                               }else {
-                                       groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
-                               }
+                               groupComb.push_back(globaldata->Groups[i]+globaldata->Groups[l]);
                        }
-                       n++;
                }
        }
        catch(exception& e) {