reworked the classifiers summary file added groupfile option to classify.seqs, added...

[mothur.git] / rawtrainingdatamaker.cpp

diff --git a/rawtrainingdatamaker.cpp b/rawtrainingdatamaker.cpp
deleted file mode 100644 (file)
index 362cdb7..0000000
--- a/rawtrainingdatamaker.cpp
+++ /dev/null
@@ -1,188 +0,0 @@
-/*
- *  rawTrainingDataMaker.cpp
- *  Mothur
- *
- *  Created by westcott on 4/21/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "rawtrainingdatamaker.h"
-
-/**************************************************************************************************/
-
-RawTrainingDataMaker::RawTrainingDataMaker(){
-       try {
-               m = MothurOut::getInstance();
-               numNodes = 1;
-               numSeqs = 0;
-               tree.push_back(rawTaxNode("Root"));
-               tree[0].rank = "Root";
-               maxLevel = 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "RawTrainingDataMaker");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-
-RawTrainingDataMaker::RawTrainingDataMaker(string tfile){
-       try {
-               m = MothurOut::getInstance();
-               numNodes = 1;
-               numSeqs = 0;
-               tree.push_back(rawTaxNode("Root"));
-               tree[0].rank = "Root";
-               maxLevel = 0;
-               
-               ifstream in;
-               openInputFile(tfile, in);
-               
-               //read in users taxonomy file and add sequences to tree
-               string name, tax;
-               while(!in.eof()){
-                       in >> name >> tax; gobble(in);
-                       
-                       addSeqToTree(name, tax);
-               }
-               in.close();
-       
-               assignRank(0);
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "RawTrainingDataMaker");
-               exit(1);
-       }
-}
-
-/**************************************************************************************************/
-
-string RawTrainingDataMaker::getNextTaxon(string& heirarchy){
-       try {
-               string currentLevel = "";
-               if(heirarchy != ""){
-                       int pos = heirarchy.find_first_of(';');
-                       currentLevel=heirarchy.substr(0,pos);
-                       if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
-                       else { heirarchy = ""; }
-               }
-               return currentLevel;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "getNextTaxon");
-               exit(1);
-       }
-}
-
-/**************************************************************************************************/
-
-int RawTrainingDataMaker::addSeqToTree(string seqName, string seqTaxonomy){
-       try {
-               numSeqs++;
-               
-               map<string, int>::iterator childPointer;
-               
-               int currentNode = 0;
-               string taxon;
-               
-               while(seqTaxonomy != ""){
-                       
-                       if (m->control_pressed) { return 0; }
-                       
-                       //somehow the parent is getting one too many accnos
-                       //use print to reassign the taxa id
-                       taxon = getNextTaxon(seqTaxonomy);
-                       
-                       childPointer = tree[currentNode].children.find(taxon);
-                       
-                       if(childPointer != tree[currentNode].children.end()){   //if the node already exists, move on
-                               currentNode = childPointer->second;
-                       }else{                                                                                  //otherwise, create it
-                               tree.push_back(rawTaxNode(taxon));
-                               numNodes++;
-                               tree[currentNode].children[taxon] = numNodes-1;
-                               tree[numNodes-1].parent = currentNode;
-                               
-                               currentNode = tree[currentNode].children[taxon];
-                       }
-               }
-
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "addSeqToTree");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-
-void RawTrainingDataMaker::assignRank(int index){
-       try {
-               map<string,int>::iterator it;
-                               
-               string ranks[9] = { "Root","Domain","Kingdom","Phylum","Class","Order","Family","Genus","Species" };
-               
-               for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
-                       tree[it->second].level = tree[index].level + 1;
-                       
-                       if (tree[it->second].level > 8) { 
-                               tree[it->second].rank = ("unknown" + toString(tree[it->second].level));
-                       }else {
-                               tree[it->second].rank = ranks[tree[it->second].level];
-                       }
-                                               
-                       //save maxLevel for binning the unclassified seqs
-                       if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; } 
-                       
-                       assignRank(it->second);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "assignRank");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-
-void RawTrainingDataMaker::print(ofstream& out){
-       try {
-               //string temp = tree[0].name +" " + tree[0].rank;
-               //sanityCheck[temp] = temp;
-               
-               out << "0" << "*" << tree[0].name << "*" << tree[0].parent << "*" << tree[0].level << "*" << tree[0].rank << endl;
-               print(0, out);
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "print");
-               exit(1);
-       }
-}
-
-/**************************************************************************************************/
-
-void RawTrainingDataMaker::print(int i, ofstream& out){
-       try {
-               map<string,int>::iterator it;
-               for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
-                       //string temp = tree[it->second].name + " " + tree[it->second].rank;
-                       
-                       //map<string, string>::iterator itSan;
-                       //itSan = sanityCheck.find(temp);
-                       
-                       //if (itSan == sanityCheck.end()) {
-                               out << it->second << "*" << tree[it->second].name << "*" << tree[it->second].parent << "*" << tree[it->second].level << "*" << tree[it->second].rank << endl;
-                               //sanityCheck[temp] = temp;
-                       //}
-                       print(it->second, out);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RawTrainingDataMaker", "print");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-
-
-