major change to the tree class to use the count table class instead of tree map....

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index f98620b2ee0bd4cc70bc10d1db908d8de40de995..dc9f121a0e83758d4ecf4977294e8221b3da0712 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -287,17 +287,22 @@ int IndicatorCommand::execute(){
                        string groupfile = ""; 
                        m->setTreeFile(treefile);
                        Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
-                       treeMap = new TreeMap();
+                       ct = new CountTable();
                        bool mismatch = false;
-                               
-                       for (int i = 0; i < m->Treenames.size(); i++) { 
-                               //sanity check - is this a group that is not in the sharedfile?
+            
+            set<string> nameMap;
+            map<string, string> groupMap;
+            set<string> gps;
+            for (int i = 0; i < m->Treenames.size(); i++) { 
+                nameMap.insert(m->Treenames[i]); 
+                //sanity check - is this a group that is not in the sharedfile?
                                if (designfile == "") {
+                    if (i == 0) { gps.insert("Group1"); }
                                        if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
                                                m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
                                                mismatch = true;
                                        }
-                                       treeMap->addSeq(m->Treenames[i], "Group1"); 
+                                       groupMap[m->Treenames[i]] = "Group1"; 
                                }else{
                                        vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
                                        vector<string> myNames = designMap->getNamesSeqs(myGroups);
@@ -308,9 +313,10 @@ int IndicatorCommand::execute(){
                                                        mismatch = true;
                                                }
                                        }
-                                       treeMap->addSeq(m->Treenames[i], "Group1");
+                                       groupMap[m->Treenames[i]] = "Group1";
                                }
-                       }
+            }
+            ct->createTable(nameMap, groupMap, gps);
                        
                        if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
                                        
@@ -318,14 +324,14 @@ int IndicatorCommand::execute(){
                                if (designfile != "") { delete designMap; }
                                if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
                                else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
-                               delete treeMap;
+                               delete ct;
                                return 0;
                        }
                 
                        read = new ReadNewickTree(treefile);
-                       int readOk = read->read(treeMap); 
+                       int readOk = read->read(ct); 
                        
-                       if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
+                       if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete ct; delete read; return 0; }
                        
                        vector<Tree*> T = read->getTrees();
                        
@@ -335,19 +341,18 @@ int IndicatorCommand::execute(){
                                if (designfile != "") { delete designMap; }
                                if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
                                else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
-                               for (int i = 0; i < T.size(); i++) {  delete T[i];  }  delete treeMap; return 0; 
+                               for (int i = 0; i < T.size(); i++) {  delete T[i];  }  delete ct; return 0; 
                        }
             
-                       map<string, string> nameMap;    
-                       T[0]->assembleTree(nameMap);
+                       T[0]->assembleTree();
                                        
                        /***************************************************/
                        //    create ouptut tree - respecting pickedGroups //
                        /***************************************************/
-                       Tree* outputTree = new Tree(m->getNumGroups(), treeMap); 
+                       Tree* outputTree = new Tree(m->getNumGroups(), ct); 
                        
                        outputTree->getSubTree(T[0], m->getGroups());
-                       outputTree->assembleTree(nameMap);
+                       outputTree->assembleTree();
                                
                        //no longer need original tree, we have output tree to use and label
                        for (int i = 0; i < T.size(); i++) {  delete T[i];  } 
@@ -356,14 +361,14 @@ int IndicatorCommand::execute(){
                                if (designfile != "") { delete designMap; }
                                if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
                                else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
-                               delete outputTree; delete treeMap;  return 0; 
+                               delete outputTree; delete ct;  return 0; 
                        }
                        
                        /***************************************************/
                        //              get indicator species values                       //
                        /***************************************************/
                        GetIndicatorSpecies(outputTree);
-                       delete outputTree; delete treeMap;
+                       delete outputTree; delete ct;
                        
                }else { //run with design file only
                        //get indicator species