added errorchecking and help info on new unifrac and treeclimber code

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 8adff2d896f811d46e80b806acf45261d759c69b..77069443c2fd26a0cebbabf4dd661e1d37288030 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -23,6 +23,23 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
                distFile = globaldata->getTreeFile() + ".uwdistrib";
                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; 
+                       }               
+               }
+
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                unweighted = new Unweighted(tmap);
 
@@ -93,6 +110,8 @@ int UnifracUnweightedCommand::execute() {
                                outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
                        }
                        
+                       saveRandomScores(); //save all random scores for unweighted file
+                       
                        //find the signifigance of the score
                        float rcumul = 0.0000;
                        for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
@@ -105,8 +124,7 @@ int UnifracUnweightedCommand::execute() {
                        //save the signifigance of the users score for printing later
                        UWScoreSig.push_back(rCumul[userData[0]]);
                        
-                       saveRandomScores(); //save all random scores for unweighted file
-               
+                       
                        //clear random data
                        rscoreFreq.clear();  //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
                        rCumul.clear();
@@ -207,15 +225,14 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 /***********************************************************/
 void UnifracUnweightedCommand::saveRandomScores() {
        try {
-               //update total map with new random scores
                for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
                        //does this score already exist in the total map
                        it2 = totalrscoreFreq.find(it->first);
                        //if yes then add them
                        if (it2 != totalrscoreFreq.end()) { 
-                               it2->second += it->second;
+                               totalrscoreFreq[it->first] += rscoreFreq[it->first];
                        }else{ //its a new score
-                               totalrscoreFreq[it->first] = 1;
+                               totalrscoreFreq[it->first] = rscoreFreq[it->first];
                        }
                }
        }