made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 52b7322cb1064546fd0f446f63fd61ef61d868fe..3cb26113f8deb8acf3bf28f7040becf2bac7385f 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -9,11 +9,24 @@
 
 #include "tree.h"
 
-
+/*****************************************************************/
+Tree::Tree(string g) {
+       try {
+               globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
+               
+               parseTreeFile();  globaldata->runParse = false;  
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Tree", "Tree - just parse");
+               exit(1);
+       }
+}
 /*****************************************************************/
 Tree::Tree() {
        try {
                globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
                
                if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
 //for(int i = 0; i <   globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }  
@@ -27,7 +40,8 @@ Tree::Tree() {
                        //initialize leaf nodes
                        if (i <= (numLeaves-1)) {
                                tree[i].setName(globaldata->Treenames[i]);
-                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+                               vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+                               tree[i].setGroup(tempGroups);
                                //set pcount and pGroup for groupname to 1.
                                tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
                                tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
@@ -37,12 +51,13 @@ Tree::Tree() {
                        //intialize non leaf nodes
                        }else if (i > (numLeaves-1)) {
                                tree[i].setName("");
-                               tree[i].setGroup("");
+                               vector<string> tempGroups;
+                               tree[i].setGroup(tempGroups);
                        }
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "Tree");
+               m->errorOut(e, "Tree", "Tree");
                exit(1);
        }
 }
@@ -66,15 +81,19 @@ void Tree::addNamesToCounts() {
 
                                
                //go through each leaf and update its pcounts and pgroups
+               
+               //float A = clock();
+
                for (int i = 0; i < numLeaves; i++) {
+
                        string name = tree[i].getName();
-                       
+               
                        map<string, string>::iterator itNames = globaldata->names.find(name);
-                       
-                       if (itNames == globaldata->names.end()) { mothurOut(name + " is not in your name file, please correct."); mothurOutEndLine(); exit(1);  }
+               
+                       if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
                        else {
                                vector<string> dupNames;
-                               splitAtComma(globaldata->names[name], dupNames);
+                               m->splitAtComma(globaldata->names[name], dupNames);
                                
                                map<string, int>::iterator itCounts;
                                int maxPars = 1;
@@ -119,12 +138,23 @@ void Tree::addNamesToCounts() {
                                        }
                                }//end if
                                
-                       }//end else
-               }//end for
+                               //update groups to reflect all the groups this node represents
+                               vector<string> nodeGroups;
+                               map<string, int>::iterator itGroups;
+                               for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+                                       nodeGroups.push_back(itGroups->first);
+                               }
+                               tree[i].setGroup(nodeGroups);
                                
+                       }//end else
+               }//end for              
+               
+               //float B = clock();
+               //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;     
+
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "addNamesToCounts");
+               m->errorOut(e, "Tree", "addNamesToCounts");
                exit(1);
        }
 }
@@ -138,7 +168,7 @@ int Tree::getIndex(string searchName) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "getIndex");
+               m->errorOut(e, "Tree", "getIndex");
                exit(1);
        }
 }
@@ -150,25 +180,31 @@ void Tree::setIndex(string searchName, int index) {
                globaldata->gTreemap->setIndex(searchName, index);
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "setIndex");
+               m->errorOut(e, "Tree", "setIndex");
                exit(1);
        }
 }
 /*****************************************************************/
-void Tree::assembleTree() {
+int Tree::assembleTree() {
        try {
-       
+               //float A = clock();
+
                //if user has given a names file we want to include that info in the pgroups and pcount info.
                if(globaldata->names.size() != 0) {  addNamesToCounts();  }
                
                //build the pGroups in non leaf nodes to be used in the parsimony calcs.
                for (int i = numLeaves; i < numNodes; i++) {
+                       if (m->control_pressed) { return 1; }
+
                        tree[i].pGroups = (mergeGroups(i));
                        tree[i].pcount = (mergeGcounts(i));
                }
+               //float B = clock();
+               //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
+               return 0;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "assembleTree");
+               m->errorOut(e, "Tree", "assembleTree");
                exit(1);
        }
 }
@@ -206,7 +242,7 @@ void Tree::getCopy(Tree* copy) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "getCopy");
+               m->errorOut(e, "Tree", "getCopy");
                exit(1);
        }
 }
@@ -259,7 +295,7 @@ map<string, int> Tree::mergeGroups(int i) {
                return parsimony;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeGroups");
+               m->errorOut(e, "Tree", "mergeGroups");
                exit(1);
        }
 }
@@ -277,14 +313,14 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
                
                //loop through nodes groups removing the ones the user doesn't want
                for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
-                               if (inUsersGroups(it->first, g) != true) {
+                               if (m->inUsersGroups(it->first, g) != true) {
                                        tree[lc].pGroups.erase(it++);
                                }else { it++; }
                }
 
                //loop through nodes groups removing the ones the user doesn't want
                for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
-                               if (inUsersGroups(it->first, g) != true) {
+                               if (m->inUsersGroups(it->first, g) != true) {
                                        tree[rc].pGroups.erase(it++);
                                }else { it++; }
                }
@@ -325,7 +361,7 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
                return parsimony;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeUserGroups");
+               m->errorOut(e, "Tree", "mergeUserGroups");
                exit(1);
        }
 }
@@ -348,7 +384,7 @@ map<string,int> Tree::mergeGcounts(int position) {
                return sum;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeGcounts");
+               m->errorOut(e, "Tree", "mergeGcounts");
                exit(1);
        }
 }
@@ -366,8 +402,8 @@ void Tree::randomLabels(vector<string> g) {
                        //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
                        bool treez, treei;
                
-                       treez = inUsersGroups(tree[z].getGroup(), g);
-                       treei = inUsersGroups(tree[i].getGroup(), g);
+                       treez = m->inUsersGroups(tree[z].getGroup(), g);
+                       treei = m->inUsersGroups(tree[i].getGroup(), g);
                        
                        if ((treez == true) && (treei == true)) {
                                //switches node i and node z's info.
@@ -375,7 +411,7 @@ void Tree::randomLabels(vector<string> g) {
                                tree[z].pGroups = (tree[i].pGroups);
                                tree[i].pGroups = (lib_hold);
                                
-                               string zgroup = tree[z].getGroup();
+                               vector<string> zgroup = tree[z].getGroup();
                                tree[z].setGroup(tree[i].getGroup());
                                tree[i].setGroup(zgroup);
                                
@@ -390,11 +426,11 @@ void Tree::randomLabels(vector<string> g) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomLabels");
+               m->errorOut(e, "Tree", "randomLabels");
                exit(1);
        }
 }
-/**************************************************************************************************/
+/**************************************************************************************************
 
 void Tree::randomLabels(string groupA, string groupB) {
        try {
@@ -420,7 +456,7 @@ void Tree::randomLabels(string groupA, string groupB) {
                }
        }               
        catch(exception& e) {
-               errorOut(e, "Tree", "randomLabels");
+               m->errorOut(e, "Tree", "randomLabels");
                exit(1);
        }
 }
@@ -436,7 +472,7 @@ void Tree::randomBlengths()  {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomBlengths");
+               m->errorOut(e, "Tree", "randomBlengths");
                exit(1);
        }
 }
@@ -447,7 +483,9 @@ void Tree::assembleRandomUnifracTree(vector<string> g) {
 }
 /*************************************************************************************************/
 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
-       randomLabels(groupA, groupB);
+
+       vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+       randomLabels(temp);
        assembleTree();
 }
 
@@ -491,7 +529,7 @@ void Tree::randomTopology() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomTopology");
+               m->errorOut(e, "Tree", "randomTopology");
                exit(1);
        }
 }
@@ -503,7 +541,7 @@ void Tree::print(ostream& out) {
                out << ";" << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "print");
+               m->errorOut(e, "Tree", "print");
                exit(1);
        }
 }
@@ -515,7 +553,7 @@ void Tree::printForBoot(ostream& out) {
                out << ";" << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "printForBoot");
+               m->errorOut(e, "Tree", "printForBoot");
                exit(1);
        }
 }
@@ -525,10 +563,10 @@ void Tree::printForBoot(ostream& out) {
 void Tree::createNewickFile(string f) {
        try {
                int root = findRoot();
-               //filename = getRootName(globaldata->getTreeFile()) + "newick";
+               //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
                filename = f;
 
-               openOutputFile(filename, out);
+               m->openOutputFile(filename, out);
                
                printBranch(root, out, "branch");
                
@@ -537,7 +575,7 @@ void Tree::createNewickFile(string f) {
                out.close();
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "createNewickFile");
+               m->errorOut(e, "Tree", "createNewickFile");
                exit(1);
        }
 }
@@ -556,7 +594,7 @@ int Tree::findRoot() {
                return -1;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "findRoot");
+               m->errorOut(e, "Tree", "findRoot");
                exit(1);
        }
 }
@@ -584,7 +622,9 @@ void Tree::printBranch(int node, ostream& out, string mode) {
                                }
                        }
                }else { //you are a leaf
-                       out << tree[node].getGroup(); 
+                       string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+                       
+                       out << leafGroup; 
                        if (mode == "branch") {
                                //if there is a branch length then print it
                                if (tree[node].getBranchLength() != -1) {
@@ -600,7 +640,7 @@ void Tree::printBranch(int node, ostream& out, string mode) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "printBranch");
+               m->errorOut(e, "Tree", "printBranch");
                exit(1);
        }
 }
@@ -624,7 +664,7 @@ void Tree::parseTreeFile() {
        try {
                string filename = globaldata->getTreeFile();
                ifstream filehandle;
-               openInputFile(filename, filehandle);
+               m->openInputFile(filename, filehandle);
                int c, comment;
                comment = 0;
                int done = 1;
@@ -694,9 +734,13 @@ void Tree::parseTreeFile() {
                        }
                }
                filehandle.close();
+               
+               //for (int i = 0; i < globaldata->Treenames.size(); i++) {
+//cout << globaldata->Treenames[i] << endl; }
+//cout << globaldata->Treenames.size() << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "parseTreeFile");
+               m->errorOut(e, "Tree", "parseTreeFile");
                exit(1);
        }
 }
@@ -760,7 +804,7 @@ int Tree::readTreeString(ifstream& filehandle)      {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "readTreeString");
+               m->errorOut(e, "Tree", "readTreeString");
                exit(1);
        }
 }