working on readtree

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 2a169d04c542e6c1999fddbe5e6f53612f56ee74..3fa44b50014de39006037771bdc9899f0bc357f3 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -22,7 +22,6 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
                setGroups(); //sets users groups to analyze
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                unweighted = new Unweighted(tmap);
-               counter = 0;
 
        }
        catch(exception& e) {
@@ -44,6 +43,7 @@ int UnifracUnweightedCommand::execute() {
                                
                //get pscores for users trees
                for (int i = 0; i < T.size(); i++) {
+                       counter = 0;
                        unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
                        unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
                                                //column headers
@@ -53,7 +53,6 @@ int UnifracUnweightedCommand::execute() {
                        //get unweighted for users tree
                        rscoreFreq.resize(numComp);  
                        rCumul.resize(numComp);  
-                       validScores.resize(numComp); 
                        utreeScores.resize(numComp);  
                        UWScoreSig.resize(numComp); 
 
@@ -62,9 +61,6 @@ int UnifracUnweightedCommand::execute() {
                        
                        //output scores for each combination
                        for(int k = 0; k < numComp; k++) {
-                               //add users score to valid scores
-                               validScores[k][userData[k]] = userData[k];
-                       
                                //saves users score
                                utreeScores[k].push_back(userData[k]);
                        }
@@ -85,14 +81,14 @@ int UnifracUnweightedCommand::execute() {
                                        }
                                
                                        //add randoms score to validscores
-                                       validScores[k][randomData[k]] = randomData[k];
+                                       validScores[randomData[k]] = randomData[k];
                                }
                        }
                
                for(int a = 0; a < numComp; a++) {
                        float rcumul = 1.0000;
                        //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-                       for (it = validScores[a].begin(); it != validScores[a].end(); it++) { 
+                       for (it = validScores.begin(); it != validScores.end(); it++) { 
                                //make rscoreFreq map and rCumul
                                it2 = rscoreFreq[a].find(it->first);
                                rCumul[a][it->first] = rcumul;
@@ -136,7 +132,7 @@ void UnifracUnweightedCommand::printUnweightedFile() {
                for(int a = 0; a < numComp; a++) {
                        initFile(groupComb[a]);
                        //print each line
-                       for (it = validScores[a].begin(); it != validScores[a].end(); it++) { 
+                       for (it = validScores.begin(); it != validScores.end(); it++) { 
                                data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); 
                                output(data);
                                data.clear();