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

[mothur.git] / taxonomyequalizer.cpp

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
deleted file mode 100644 (file)
index c050726..0000000
--- a/taxonomyequalizer.cpp
+++ /dev/null
@@ -1,155 +0,0 @@
-/*
- *  taxonomyequalizer.cpp
- *  Mothur
- *
- *  Created by westcott on 11/20/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "taxonomyequalizer.h"
-
-/**************************************************************************************************/
-TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir(o) {
-       try {
-               m = MothurOut::getInstance();
-               containsConfidence = false;
-               
-               ifstream inTax;
-               m->openInputFile(tfile, inTax);
-       
-               highestLevel = getHighestLevel(inTax);
-               
-               if (!m->control_pressed) { 
-                       
-                       //if the user has specified a cutoff and it's smaller than the highest level
-                       if ((cutoff != -1) && (cutoff < highestLevel)) { 
-                               highestLevel = cutoff;
-                       }else if (cutoff > highestLevel) {
-                               m->mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
-                               m->mothurOutEndLine();
-                       }
-                       
-                       inTax.close(); 
-                       ifstream in; 
-                       m->openInputFile(tfile, in);
-                       
-                       ofstream out;
-                       equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
-                       m->openOutputFile(equalizedFile, out);
-                       
-       
-                       string name, tax;
-                       while (in) {
-                       
-                               if (m->control_pressed) {  break; }
-                               
-                               in >> name >> tax;   m->gobble(in);
-                               
-                               if (containsConfidence) {  m->removeConfidences(tax);   }
-                               
-                               //is this a taxonomy that needs to be extended?
-                               if (seqLevels[name] < highestLevel) {
-                                       extendTaxonomy(name, tax, highestLevel);
-                               }else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
-                                       truncateTaxonomy(name, tax, highestLevel);
-                               }
-                               
-                               out << name << '\t' << tax << endl;
-                       }
-                       
-                       in.close();
-                       out.close();
-                       
-                       if (m->control_pressed) { m->mothurRemove(equalizedFile);  }
-               }else { inTax.close(); }
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TaxEqualizer", "TaxEqualizer");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-int TaxEqualizer::getHighestLevel(ifstream& in) {
-       try {
-               
-               int level = 0;
-               string name, tax;
-               
-               while (in) {
-                       in >> name >> tax;   m->gobble(in);
-               
-                       //count levels in this taxonomy
-                       int thisLevel = 0;
-                       for (int i = 0; i < tax.length(); i++) {
-                               if (tax[i] == ';') {  thisLevel++;      }
-                       }
-               
-                       //save sequences level
-                       seqLevels[name] = thisLevel;
-       
-                       //is this the longest taxonomy?
-                       if (thisLevel > level) {  
-                               level = thisLevel;  
-                               testTax = tax; //testTax is used to figure out if this file has confidences we need to strip out
-                       } 
-               }
-               
-               int pos = testTax.find_first_of('(');
-
-               //if there are '(' then there are confidences we need to take out
-               if (pos != -1) {  containsConfidence = true;  }
-       
-               return level;
-                                       
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TaxEqualizer", "getHighestLevel");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-void TaxEqualizer::extendTaxonomy(string name, string& tax, int desiredLevel) {
-       try {
-                       
-               //get last taxon
-               tax = tax.substr(0, tax.length()-1);  //take off final ";"
-               int pos = tax.find_last_of(';');
-               string lastTaxon = tax.substr(pos+1);  
-               lastTaxon += ";"; //add back on delimiting char
-               tax += ";";
-               
-               int currentLevel = seqLevels[name];
-               
-               //added last taxon until you get desired level
-               for (int i = currentLevel; i < desiredLevel; i++) {
-                       tax += lastTaxon;
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TaxEqualizer", "extendTaxonomy");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-void TaxEqualizer::truncateTaxonomy(string name, string& tax, int desiredLevel) {
-       try {
-                       
-               int currentLevel = seqLevels[name];
-               tax = tax.substr(0, tax.length()-1);  //take off final ";"
-               
-               //remove a taxon until you get to desired level
-               for (int i = currentLevel; i > desiredLevel; i--) {
-                       tax = tax.substr(0,  tax.find_last_of(';'));
-               }
-               
-               tax += ";";
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TaxEqualizer", "truncateTaxonomy");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-