removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 308115d844bdf8aa24adf05de9841a60c1708fd8..be7dc79509abbc78aeeb0a66ab45ca57b0d1324a 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -12,9 +12,7 @@
 /***********************************************************************/
 ReadTree::ReadTree() {
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
-               globaldata->gTree.clear();
        }
        catch(exception& e) {
                m->errorOut(e, "ReadTree", "ReadTree");
@@ -22,6 +20,21 @@ ReadTree::ReadTree() {
        }
 }
 /***********************************************************************/
+int ReadTree::AssembleTrees() {
+        try {
+                //assemble users trees
+                for (int i = 0; i < Trees.size(); i++) {
+                        if (m->control_pressed) { return 0;  }
+                        Trees[i]->assembleTree();
+                }
+                return 0;
+        }
+       catch(exception& e) {
+               m->errorOut(e, "ReadTree", "AssembleTrees");
+               exit(1);
+       }
+}
+/***********************************************************************/
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
        
@@ -94,7 +107,7 @@ float ReadTree::readBranchLength(istream& f) {
 /***********************************************************************/
 //This class reads a file in Newick form and stores it in a tree.
 
-int ReadNewickTree::read() {
+int ReadNewickTree::read(TreeMap* tmap) {
        try {
                holder = "";
                int c, error;
@@ -116,23 +129,23 @@ int ReadNewickTree::read() {
                                }
 
                                //make new tree
-                               T = new Tree(); 
+                               T = new Tree(tmap); 
 
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
-                               error = readTreeString(); 
+                               error = readTreeString(tmap); 
                                
                                //save trees for later commands
-                               globaldata->gTree.push_back(T); 
+                               Trees.push_back(T); 
                                m->gobble(filehandle);
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
                        //get right number of seqs from nexus file.
-                       Tree* temp = new Tree();  delete temp;
+                       Tree* temp = new Tree(tmap);  delete temp;
                        
-                       nexusTranslation();  //reads file through the translation and updates treemap
+                       nexusTranslation(tmap);  //reads file through the translation and updates treemap
                        while((c = filehandle.peek()) != EOF) { 
                                // get past comments
                                while ((c = filehandle.peek()) != EOF) {        
@@ -153,15 +166,15 @@ int ReadNewickTree::read() {
                                filehandle.putback(c);  //put back first ( of tree.
                                
                                //make new tree
-                               T = new Tree(); 
+                               T = new Tree(tmap); 
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
                                //read tree info
-                               error = readTreeString(); 
+                               error = readTreeString(tmap); 
                                 
                                //save trees for later commands
-                               globaldata->gTree.push_back(T); 
+                               Trees.push_back(T); 
                        }
                }
                
@@ -178,11 +191,11 @@ int ReadNewickTree::read() {
 }
 /**************************************************************************************************/
 //This function read the file through the translation of the sequences names and updates treemap.
-string ReadNewickTree::nexusTranslation() {
+string ReadNewickTree::nexusTranslation(TreeMap* tmap) {
        try {
                
                holder = "";
-               int numSeqs = globaldata->Treenames.size(); //must save this some when we clear old names we can still know how many sequences there were
+               int numSeqs = m->Treenames.size(); //must save this some when we clear old names we can still know how many sequences there were
                int comment = 0;
                
                // get past comments
@@ -198,7 +211,7 @@ string ReadNewickTree::nexusTranslation() {
                }
                
                //update treemap
-               globaldata->gTreemap->namesOfSeqs.clear();
+               tmap->namesOfSeqs.clear();
                
                /*char c;
                string number, name;
@@ -226,12 +239,12 @@ string ReadNewickTree::nexusTranslation() {
                        name.erase(name.end()-1);  //erase the comma
                        
                        //insert new one with new name
-                       string group = globaldata->gTreemap->getGroup(name);
-                       globaldata->gTreemap->treemap[toString(number)].groupname = group;
-                       globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->getIndex(name);
+                       string group = tmap->getGroup(name);
+                       tmap->treemap[toString(number)].groupname = group;
+                       tmap->treemap[toString(number)].vectorIndex = tmap->getIndex(name);
                        //erase old one.  so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
-                       globaldata->gTreemap->treemap.erase(name);
-                       globaldata->gTreemap->namesOfSeqs.push_back(number);
+                       tmap->treemap.erase(name);
+                       tmap->namesOfSeqs.push_back(number);
                }
                
                return name;
@@ -243,7 +256,7 @@ string ReadNewickTree::nexusTranslation() {
 }
 
 /**************************************************************************************************/
-int ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString(TreeMap* tmap) {
        try {
                
                int n = 0;
@@ -256,7 +269,7 @@ int ReadNewickTree::readTreeString() {
                if(ch == '('){
                        n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 
-                       lc = readNewickInt(filehandle, n, T);
+                       lc = readNewickInt(filehandle, n, T, tmap);
                        if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
        
                        if(filehandle.peek()==','){                                                     
@@ -268,7 +281,7 @@ int ReadNewickTree::readTreeString() {
                        }       
                
                        if(rooted != 1){                                                                
-                               rc = readNewickInt(filehandle, n, T);
+                               rc = readNewickInt(filehandle, n, T, tmap);
                                if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
                                        readSpecialChar(filehandle,')',"right parenthesis");
@@ -313,7 +326,7 @@ int ReadNewickTree::readTreeString() {
 }
 /**************************************************************************************************/
 
-int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
+int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) {
        try {
                
                if (m->control_pressed) { return -1; } 
@@ -326,7 +339,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        //read all children
                        vector<int> childrenNodes;
                        while(f.peek() != ')'){
-                               int child = readNewickInt(f, n, T);
+                               int child = readNewickInt(f, n, T, tmap);
                                if (child == -1) { return -1; } //reports an error in reading
                //cout << "child = " << child << endl;          
                                childrenNodes.push_back(child);
@@ -397,7 +410,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        f.putback(d);
                
                        //set group info
-                       string group = globaldata->gTreemap->getGroup(name);
+                       string group = tmap->getGroup(name);
                        
                        //find index in tree of name
                        int n1 = T->getIndex(name);
@@ -406,16 +419,16 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        if(group == "not found") {
                                m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
                                
-                               globaldata->gTreemap->namesOfSeqs.push_back(name);
-                               globaldata->gTreemap->treemap[name].groupname = "xxx";
+                               tmap->namesOfSeqs.push_back(name);
+                               tmap->treemap[name].groupname = "xxx";
                                
                                map<string, int>::iterator it;
-                               it = globaldata->gTreemap->seqsPerGroup.find("xxx");
-                               if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
-                                       globaldata->gTreemap->namesOfGroups.push_back("xxx");
-                                       globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+                               it = tmap->seqsPerGroup.find("xxx");
+                               if (it == tmap->seqsPerGroup.end()) { //its a new group
+                                       tmap->namesOfGroups.push_back("xxx");
+                                       tmap->seqsPerGroup["xxx"] = 1;
                                }else {
-                                       globaldata->gTreemap->seqsPerGroup["xxx"]++;
+                                       tmap->seqsPerGroup["xxx"]++;
                                }
                                
                                group = "xxx";