moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / treereader.cpp

diff --git a/treereader.cpp b/treereader.cpp
deleted file mode 100644 (file)
index b385d21..0000000
--- a/treereader.cpp
+++ /dev/null
@@ -1,158 +0,0 @@
-//
-//  treereader.cpp
-//  Mothur
-//
-//  Created by Sarah Westcott on 4/11/12.
-//  Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#include "treereader.h"
-#include "readtree.h"
-
-/***********************************************************************/
-
-TreeReader::TreeReader(string tf) : treefile(tf)  { 
-    try {
-        m = MothurOut::getInstance();
-        namefile = "";
-        groupfile = "";
-        readTrees();
-    }
-       catch(exception& e) {
-               m->errorOut(e, "TreeReader", "TreeReader");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-TreeReader::TreeReader(string tf, string gf) : treefile(tf),  groupfile(gf)  { 
-    try {
-        m = MothurOut::getInstance();
-        namefile = "";
-        readTrees();
-    }
-       catch(exception& e) {
-               m->errorOut(e, "TreeReader", "TreeReader");
-               exit(1);
-       }
-}
-/***********************************************************************/
-TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf),  groupfile(gf), namefile(nf)  { 
-    try {
-        m = MothurOut::getInstance();
-        readTrees();
-    }
-       catch(exception& e) {
-               m->errorOut(e, "TreeReader", "TreeReader");
-               exit(1);
-       }
-}
-/***********************************************************************/
-bool TreeReader::readTrees()  { 
-    try {
-        
-        tmap = new TreeMap();
-        if (groupfile != "") {      tmap->readMap(groupfile);        }
-               else{ //fake out by putting everyone in one group
-                       Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
-                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
-               }
-               
-        int numUniquesInName = 0;
-               if (namefile != "") { numUniquesInName = readNamesFile(); }
-               
-               ReadTree* read = new ReadNewickTree(treefile);
-               int readOk = read->read(tmap); 
-               
-               if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine();  delete read; m->control_pressed=true; return 0; }
-               
-               read->AssembleTrees(names);
-               trees = read->getTrees();
-               delete read;
-        
-               //make sure all files match
-               //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
-               int numNamesInTree;
-               if (namefile != "")  {  
-                       if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
-                       else {   numNamesInTree = m->Treenames.size();  }
-               }else {  numNamesInTree = m->Treenames.size();  }
-               
-               
-               //output any names that are in group file but not in tree
-               if (numNamesInTree < tmap->getNumSeqs()) {
-                       for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
-                               //is that name in the tree?
-                               int count = 0;
-                               for (int j = 0; j < m->Treenames.size(); j++) {
-                                       if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
-                                       count++;
-                               }
-                               
-                               if (m->control_pressed) { for (int i = 0; i < trees.size(); i++) { delete trees[i]; } return 0; }
-                               
-                               //then you did not find it so report it 
-                               if (count == m->Treenames.size()) { 
-                                       //if it is in your namefile then don't remove
-                                       map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-                                       
-                                       if (it == nameMap.end()) {
-                                               m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
-                                               tmap->removeSeq(tmap->namesOfSeqs[i]);
-                                               i--; //need this because removeSeq removes name from namesOfSeqs
-                                       }
-                               }
-                       }
-               }
-        
-        return true;
-    }
-       catch(exception& e) {
-               m->errorOut(e, "TreeReader", "readTrees");
-               exit(1);
-       }
-}
-/*****************************************************************/
-int TreeReader::readNamesFile() {
-       try {
-               nameMap.clear();
-        names.clear();
-               int numUniquesInName = 0;
-               
-               ifstream in;
-               m->openInputFile(namefile, in);
-               
-               string first, second;
-               map<string, string>::iterator itNames;
-               
-               while(!in.eof()) {
-                       in >> first >> second; m->gobble(in);
-                       
-                       numUniquesInName++;
-                       
-                       itNames = nameMap.find(first);
-                       if (itNames == nameMap.end()) {  
-                               names[first] = second; 
-                               
-                               //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
-                               vector<string> dupNames;
-                               m->splitAtComma(second, dupNames);
-                               
-                               for (int i = 0; i < dupNames.size(); i++) {     
-                                       nameMap[dupNames[i]] = first; 
-                                       if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); } 
-                               }
-                       }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); nameMap.clear(); names.clear(); namefile = ""; return 1; }                    
-               }
-               in.close();
-               
-               return numUniquesInName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TreeReader", "readNamesFile");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-