+++ /dev/null
-/*
- * 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);
- }
-}
-
-/************************************************************/
-
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