working on readtree

diff --git a/clustercommand.cpp b/clustercommand.cpp
index dc61a6a745eaeddb31a9e573b2b966a1dfde760d..f0ef51f05b846797a42c8e71cacce326db06f4bb 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -106,7 +106,14 @@ int ClusterCommand::execute(){
                else if(rndPreviousDist<cutoff){
                        printData(toString(rndPreviousDist, length-1));
                }
-       
+               
+               //delete globaldata's copy of the sparsematrix and listvector to free up memory
+               SparseMatrix* clearM = NULL;
+               globaldata->setSparseMatrix(clearM);
+               ListVector* clearL = NULL;
+               globaldata->setListVector(clearL);
+
+               
                //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
                if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
                else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }

diff --git a/errorchecking.cpp b/errorchecking.cpp
index ff94c8f4f765a8e0041604416e3b6807b423c05a..b76542aec7907c0cc3ef80b896c5308985c1c73d 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -367,8 +367,8 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                //are you trying to cluster before you have read something                      
-               if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
-                       (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+               if (((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL)) ||
+                       ((commandName == "cluster") && (globaldata->getListVector() == NULL))) {
                                cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
                                errorFree = false;
                } 

diff --git a/readtree.cpp b/readtree.cpp
index 81a7729ffb474294502407eec1c44620bfff3378..4d3bd6daa435e303f236b8ca9dd31385a2df21dd 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -124,7 +124,8 @@ void ReadNewickTree::read() {
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
-                               readTreeString();  
+                               readTreeString(); 
+                               
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
                                gobble(filehandle);
@@ -157,12 +158,12 @@ void ReadNewickTree::read() {
                                numLeaves = T->getNumLeaves();
                                
                                //read tree info
-                               readTreeString();  
+                               readTreeString(); 
+                                
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
                        }
                }
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -272,6 +273,7 @@ void ReadNewickTree::readTreeString() {
                        T->tree[n].setParent(-1);
                        if(lc!=-1){             T->tree[lc].setParent(n);               }
                        if(rc!=-1){             T->tree[rc].setParent(n);               }
+                       cout << "new loop "<< endl;
                }
        
        }
@@ -334,6 +336,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        //adds sequence names that are not in group file to the "xxx" group
                        if(n1 == -1) {
                                cerr << "Name: " << name << " not found in your groupfile and it will be ignored. \n";
+                               
                                globaldata->gTreemap->namesOfSeqs.push_back(name);
                                globaldata->gTreemap->treemap[name].groupname = "xxx";
                                globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
@@ -350,10 +353,13 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                //find index in tree of name
                                n1 = T->getIndex(name);
                                group = "xxx";
+                               numLeaves++;
+                               numNodes = 2*numLeaves - 1;
+                               T->resetTree();
                        }
                        
                        T->tree[n1].setGroup(group);
-               
+                       T->printTree();
                        T->tree[n1].setChildren(-1,-1);
                
                        if(blen == 1){  

diff --git a/readtree.h b/readtree.h
index bee4d94a683966e76922269326728ca2e71bd72f..250b1db898546981b0969b7323095bbedd35a875 100644 (file)
--- a/readtree.h
+++ b/readtree.h
@@ -43,7 +43,7 @@ class ReadTree {
 class ReadNewickTree : public ReadTree {
        
 public:
-       ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle);  } 
+       ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); } 
        ~ReadNewickTree() {};
        void read();
        

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index a540c7444a4b2b67a03ca3be29120138faf43ef5..68f1f928bc52d5c920ac4126bb4fa67fd6ca3783 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -52,7 +52,7 @@ int ReadTreeCommand::execute(){
                for (int i = 0; i < T.size(); i++) {
                        T[i]->assembleTree();
                }
-               
+T[0]->createNewickFile("treeout");             
                return 0;
        }
        catch(exception& e) {

diff --git a/tree.cpp b/tree.cpp
index 642c6658739dd5252b2d61083ce6af2b872785ec..e34253d8cf90fc17b5ca72b0465a6d16a502da4b 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -26,8 +26,6 @@ Tree::Tree() {
                        if (i <= (numLeaves-1)) {
                                tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
                                tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
-                               //the node knows its index
-                               tree[i].setIndex(i);
                                //set pcount and pGroup for groupname to 1.
                                tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
                                tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
@@ -38,8 +36,6 @@ Tree::Tree() {
                        }else if (i > (numLeaves-1)) {
                                tree[i].setName("");
                                tree[i].setGroup("");
-                               //the node knows its index
-                               tree[i].setIndex(i);
                        }
                }
        }
@@ -54,7 +50,43 @@ Tree::Tree() {
 }
 
 /*****************************************************************/
+void Tree::resetTree(){
+try {
+               numLeaves = globaldata->gTreemap->getNumSeqs();
+               numNodes = 2*numLeaves - 1;
+               
+               tree.resize(numNodes);
 
+               //initialize tree with correct number of nodes, name and group info.
+               for (int i = 0; i < numNodes; i++) {
+                       //initialize leaf nodes
+                       if (i <= (numLeaves-1)) {
+                               tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
+                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
+                               //set pcount and pGroup for groupname to 1.
+                               tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+                               tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+                               //Treemap knows name, group and index to speed up search
+                               globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+       
+                       //intialize non leaf nodes
+                       }else if (i > (numLeaves-1)) {
+                               tree[i].setName("");
+                               tree[i].setGroup("");
+                       }
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+
+}
+/*****************************************************************/
 int Tree::getIndex(string searchName) {
        try {
                //Treemap knows name, group and index to speed up search
@@ -157,7 +189,7 @@ map<string, int> Tree::mergeGroups(int i) {
        try {
                int lc = tree[i].getLChild();
                int rc = tree[i].getRChild();
-               
+cout << i << lc << rc << endl;
                //set parsimony groups to left child
                map<string,int> parsimony = tree[lc].pGroups;
                

diff --git a/tree.h b/tree.h
index d6a3b556f09ca251a2cbad64e07c0187dd50e6b4..828b03868e9703f57e83d5e9b10117d260a44e52 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -24,6 +24,7 @@ public:
        
        
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
+       void resetTree(); //this is needed to allow user to omit names from the group file
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
        void assembleRandomUnifracTree(string, string);

diff --git a/treemap.cpp b/treemap.cpp
index 6314eb04d04006ba5c57808f6927bddec89d6a00..9eb8330ad1917a26441b8c22527b50652dbd011a 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -47,7 +47,7 @@ void TreeMap::readMap() {
 
 int TreeMap::getNumGroups() {
                        
-       return seqsPerGroup.size();     
+       return namesOfGroups.size();    
                
 }
 /************************************************************/

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 2a169d04c542e6c1999fddbe5e6f53612f56ee74..3fa44b50014de39006037771bdc9899f0bc357f3 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -22,7 +22,6 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
                setGroups(); //sets users groups to analyze
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                unweighted = new Unweighted(tmap);
-               counter = 0;
 
        }
        catch(exception& e) {
@@ -44,6 +43,7 @@ int UnifracUnweightedCommand::execute() {
                                
                //get pscores for users trees
                for (int i = 0; i < T.size(); i++) {
+                       counter = 0;
                        unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
                        unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
                                                //column headers
@@ -53,7 +53,6 @@ int UnifracUnweightedCommand::execute() {
                        //get unweighted for users tree
                        rscoreFreq.resize(numComp);  
                        rCumul.resize(numComp);  
-                       validScores.resize(numComp); 
                        utreeScores.resize(numComp);  
                        UWScoreSig.resize(numComp); 
 
@@ -62,9 +61,6 @@ int UnifracUnweightedCommand::execute() {
                        
                        //output scores for each combination
                        for(int k = 0; k < numComp; k++) {
-                               //add users score to valid scores
-                               validScores[k][userData[k]] = userData[k];
-                       
                                //saves users score
                                utreeScores[k].push_back(userData[k]);
                        }
@@ -85,14 +81,14 @@ int UnifracUnweightedCommand::execute() {
                                        }
                                
                                        //add randoms score to validscores
-                                       validScores[k][randomData[k]] = randomData[k];
+                                       validScores[randomData[k]] = randomData[k];
                                }
                        }
                
                for(int a = 0; a < numComp; a++) {
                        float rcumul = 1.0000;
                        //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-                       for (it = validScores[a].begin(); it != validScores[a].end(); it++) { 
+                       for (it = validScores.begin(); it != validScores.end(); it++) { 
                                //make rscoreFreq map and rCumul
                                it2 = rscoreFreq[a].find(it->first);
                                rCumul[a][it->first] = rcumul;
@@ -136,7 +132,7 @@ void UnifracUnweightedCommand::printUnweightedFile() {
                for(int a = 0; a < numComp; a++) {
                        initFile(groupComb[a]);
                        //print each line
-                       for (it = validScores[a].begin(); it != validScores[a].end(); it++) { 
+                       for (it = validScores.begin(); it != validScores.end(); it++) { 
                                data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); 
                                output(data);
                                data.clear();