X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;fp=treemap.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=c228162aab1d511af3fc5318aaf3e5eb5b39610c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
deleted file mode 100644
index c228162..0000000
--- a/treemap.cpp
+++ /dev/null
@@ -1,325 +0,0 @@
-/*
- *  treemap.cpp
- *  Mothur
- *
- *  Created by Sarah Westcott on 1/26/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "treemap.h"
-
-/************************************************************/
-
- TreeMap::TreeMap(string filename) {
-	m = MothurOut::getInstance();
-	groupFileName = filename;
-	m->openInputFile(filename, fileHandle);
-}
-
-/************************************************************/
- TreeMap::~TreeMap(){}
-/************************************************************/
-int TreeMap::readMap(string gf) {
-    
-    groupFileName = gf;
-	m->openInputFile(gf, fileHandle);
-    
-    string seqName, seqGroup;
-    int error = 0;
-    
-    while(fileHandle){
-        fileHandle >> seqName;       m->gobble(fileHandle);	//read from first column
-        fileHandle >> seqGroup;			//read from second column
-        
-        if (m->control_pressed) {  fileHandle.close();  return 1; }
-        
-        setNamesOfGroups(seqGroup);
-        
-        map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
-        if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
-        else {
-            namesOfSeqs.push_back(seqName);
-            treemap[seqName].groupname = seqGroup;	//store data in map
-            
-            it2 = seqsPerGroup.find(seqGroup);
-            if (it2 == seqsPerGroup.end()) { //if it's a new group
-                seqsPerGroup[seqGroup] = 1;
-            }else {//it's a group we already have
-                seqsPerGroup[seqGroup]++;
-            }				
-        }
-        
-        m->gobble(fileHandle);
-    }
-    fileHandle.close();
-    
-    return error;
-}
-
-/************************************************************/
-int TreeMap::readMap() {
-		string seqName, seqGroup;
-		int error = 0;
-		
-		while(fileHandle){
-			fileHandle >> seqName;      	 m->gobble(fileHandle); //read from first column
-			fileHandle >> seqGroup;			//read from second column
-			
-			if (m->control_pressed) {  fileHandle.close();  return 1; }
-			
-			setNamesOfGroups(seqGroup);
-					
-			map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
-			if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
-			else {
-				namesOfSeqs.push_back(seqName);
-				treemap[seqName].groupname = seqGroup;	//store data in map
-				
-				it2 = seqsPerGroup.find(seqGroup);
-				if (it2 == seqsPerGroup.end()) { //if it's a new group
-					seqsPerGroup[seqGroup] = 1;
-				}else {//it's a group we already have
-					seqsPerGroup[seqGroup]++;
-				}				
-			}
-			
-			m->gobble(fileHandle);
-		}
-		fileHandle.close();
-	
-
-		return error;
-}
-/************************************************************/
-void TreeMap::addSeq(string seqName, string seqGroup) {
-	
-		namesOfSeqs.push_back(seqName);
-		setNamesOfGroups(seqGroup);
-					
-		treemap[seqName].groupname = seqGroup;	//store data in map
-			
-		it2 = seqsPerGroup.find(seqGroup);
-		if (it2 == seqsPerGroup.end()) { //if it's a new group
-			seqsPerGroup[seqGroup] = 1;
-		}else {//it's a group we already have
-			seqsPerGroup[seqGroup]++;
-		}
-}
-/************************************************************/
-void TreeMap::removeSeq(string seqName) {
-	
-	//erase name from namesOfSeqs
-	for (int i = 0; i < namesOfSeqs.size(); i++) {
-		if (namesOfSeqs[i] == seqName)  {
-			namesOfSeqs.erase(namesOfSeqs.begin()+i);
-			break;
-		}
-	}
-	
-	//decrement sequences in this group
-	string group = treemap[seqName].groupname;
-	seqsPerGroup[group]--;
-	
-	//remove seq from treemap
-	it = treemap.find(seqName);
-	treemap.erase(it);
-}
-/************************************************************/
-
-int TreeMap::getNumGroups() {
-			
-	return namesOfGroups.size();	
-		
-}
-/************************************************************/
-
-int TreeMap::getNumSeqs() {
-			
-	return namesOfSeqs.size();	
-		
-}
-
-/************************************************************/
-
-string TreeMap::getGroup(string sequenceName) {
-			
-	it = treemap.find(sequenceName);
-	if (it != treemap.end()) { //sequence name was in group file
-		return it->second.groupname;	
-	}else {
-		return "not found";
-	}
-		
-}
-/************************************************************/
-void TreeMap::setIndex(string seq, int index) {
-	it = treemap.find(seq);
-	if (it != treemap.end()) { //sequence name was in group file
-		treemap[seq].vectorIndex = index;	
-	}else {
-		treemap[seq].vectorIndex = index;
-		treemap[seq].groupname = "not found";
-	}
-}
-/************************************************************/
-int TreeMap::getIndex(string seq) {
-	
-	it = treemap.find(seq);
-	// if it is a valid sequence name then return index
-	if (it != treemap.end()) { return treemap[seq].vectorIndex; }
-	// if not return error code
-	else { return -1; }
-	
-}
-/************************************************************/
-
-void TreeMap::setNamesOfGroups(string seqGroup) {
-			int i, count;
-			count = 0;
-			for (i=0; i<namesOfGroups.size(); i++) {
-				if (namesOfGroups[i] != seqGroup) {
-					count++; //you have not found this group
-				}else {
-					break; //you already have it
-				}
-			}
-			if (count == namesOfGroups.size()) {
-				namesOfGroups.push_back(seqGroup); //new group
-			}
-}
-/************************************************************/
-bool TreeMap::isValidGroup(string groupname) {
-	try {
-		for (int i = 0; i < namesOfGroups.size(); i++) {
-			if (groupname == namesOfGroups[i]) { return true; }
-		}
-		
-		return false;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "isValidGroup");
-		exit(1);
-	}
-}
-/***********************************************************************/
-
-void TreeMap::print(ostream& output){
-	try {
-		
-		for(it = treemap.begin(); it != treemap.end(); it++){
-			output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "print");
-		exit(1);
-	}
-}
-
-/************************************************************/
-void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
-	try {
-		//set names of groups
-		namesOfGroups = ThisnamesOfGroups;
-		
-		//set names of seqs to names of groups
-		namesOfSeqs = ThisnamesOfGroups;
-		
-		// make map where key and value are both the group name since that what the tree.shared command wants
-		for (int i = 0; i < namesOfGroups.size(); i++) {
-			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
-			seqsPerGroup[namesOfGroups[i]] = 1;
-		}
-		
-		numGroups = namesOfGroups.size();
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "makeSim");
-		exit(1);
-	}
-}
-/************************************************************/
-void TreeMap::makeSim(ListVector* list) {
-	try {
-		//set names of groups
-		namesOfGroups.clear();
-		for(int i = 0; i < list->size(); i++) {
-			namesOfGroups.push_back(list->get(i));
-		}
-		
-		//set names of seqs to names of groups
-		namesOfSeqs = namesOfGroups;
-		
-		// make map where key and value are both the group name since that what the tree.shared command wants
-		for (int i = 0; i < namesOfGroups.size(); i++) {
-			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
-			seqsPerGroup[namesOfGroups[i]] = 1;
-		}
-		
-		numGroups = namesOfGroups.size();
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "makeSim");
-		exit(1);
-	}
-}
-/************************************************************/
-int TreeMap::getCopy(TreeMap& copy){
-	try {
-         
-        namesOfGroups = copy.getNamesOfGroups();
-		numGroups = copy.getNumGroups();
-        namesOfSeqs = copy.namesOfSeqs;
-        seqsPerGroup = copy.seqsPerGroup;
-        treemap = copy.treemap;
-        
-        return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "getCopy");
-		exit(1);
-	}
-}
-/************************************************************/
-vector<string> TreeMap::getNamesSeqs(){
-	try {
-        
-		vector<string> names;
-		
-        for(it = treemap.begin(); it != treemap.end(); it++){
-            names.push_back(it->first);
-		}
-		
-		return names;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "getNamesSeqs");
-		exit(1);
-	}
-}
-/************************************************************/
-vector<string> TreeMap::getNamesSeqs(vector<string> picked){
-	try {
-		
-		vector<string> names;
-		
-		for(it = treemap.begin(); it != treemap.end(); it++){
-			//if you are belong to one the the groups in the picked vector add you
-			if (m->inUsersGroups(it->second.groupname, picked)) {
-				names.push_back(it->first);
-			}
-		}
-		
-		return names;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TreeMap", "getNamesSeqs");
-		exit(1);
-	}
-}
-
-/************************************************************/
-