fixed unweighted command

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8caeba754ff1461ae31ad2b97eaf3d6455223368..ccb5aa2705f8c621ec8d8aac801c43506c110bd6 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1625,7 +1625,7 @@
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
@@ -1950,6 +1950,7 @@
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = Mothur;
+                               SDKROOT = macosx10.6;
                        };
                        name = Debug;
                };
@@ -2048,7 +2049,7 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,

diff --git a/readtree.cpp b/readtree.cpp
index e8aeacc4431688ca0dfc8f94bf546c1fea2a91dd..308115d844bdf8aa24adf05de9841a60c1708fd8 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -217,7 +217,7 @@ string ReadNewickTree::nexusTranslation() {
                        
                        if (lastChar == ',') {  name.erase(name.end()-1); } //erase the comma
                        */      
-               cout << "numseqs = " << numSeqs << endl;
+               
                string number, name;
                for(int i=0;i<numSeqs;i++){
                        

diff --git a/unweighted.cpp b/unweighted.cpp
index 08e83ec5ba4ccbbbefe36163c25d1075fb05a883..a75ddc54058f878f63c579a4834754cb3890a374 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -199,14 +199,14 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
                                m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
                        }else{
-                               
+                               //cout << "trying to get root" << endl; 
                                //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
                                getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
-                               
+                               //cout << "here" << endl;       
                                for(int i=0;i<t->getNumNodes();i++){
                                        
                                        if (m->control_pressed) {  return data; }
-                                       
+                                       //cout << i << endl;    
                                        //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
                                        //pcountSize = 2, not unique to one group
                                        //pcountSize = 1, unique to one group
@@ -497,17 +497,18 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) { 
        try {
                //you are a leaf so get your parent
-               int index = t->tree[index].getParent();
+               int index = t->tree[v].getParent();
                
                if (includeRoot) { 
                        rootForGrouping[grouping].clear();
                }else {
+                       
                        //my parent is a potential root
                        rootForGrouping[grouping].insert(index);
                        
                        //while you aren't at root
                        while(t->tree[index].getParent() != -1){
-                               
+                               //cout << index << endl;        
                                if (m->control_pressed) {  return 0; }
                                
                                //am I the root for this grouping? if so I want to stop "early"