added errorchecking and help info on new unifrac and treeclimber code

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index ff2c2450bdd35c005c1f29c3be03741a26da834c..4a8325afda1cf2ea95d3aa19ce228e9f4451cc96 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -22,8 +22,30 @@ UnifracWeightedCommand::UnifracWeightedCommand() {
                openOutputFile(sumFile, outSum);
                distFile = globaldata->getTreeFile() + ".wdistrib";
                openOutputFile(distFile, outDist);
-
-               numGroups = tmap->getNumGroups();
+               
+               //if the user has not entered specific groups to analyze then do them all
+               if (globaldata->Groups.size() == 0) {
+                       numGroups = tmap->getNumGroups();
+               }else {
+                       //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) { 
+                               numGroups = tmap->getNumGroups();
+                               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();
+                       }else { numGroups = globaldata->Groups.size(); }
+               }
                
                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                numComp = 0;
@@ -32,7 +54,11 @@ UnifracWeightedCommand::UnifracWeightedCommand() {
                        numComp += i; 
                        for (int l = n; l < numGroups; l++) {
                                //set group comparison labels
-                               groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+                               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]);
+                               }
                        }
                        n++;
                }
@@ -174,6 +200,8 @@ int UnifracWeightedCommand::execute() {
                
                //reset randomTree parameter to 0
                globaldata->setRandomTree("0");
+               //clear out users groups
+               globaldata->Groups.clear();
                
                delete randT;