--- /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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