/************************************************************/
TreeMap::TreeMap(string filename) {
+ m = MothurOut::getInstance();
groupFileName = filename;
- openInputFile(filename, fileHandle);
+ m->openInputFile(filename, fileHandle);
}
/************************************************************/
- TreeMap::~TreeMap(){};
+ 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;
+}
/************************************************************/
-void TreeMap::readMap() {
+int TreeMap::readMap() {
string seqName, seqGroup;
-
+ int error = 0;
+
while(fileHandle){
- fileHandle >> seqName; //read from first column
+ fileHandle >> seqName; m->gobble(fileHandle); //read from first column
fileHandle >> seqGroup; //read from second column
- namesOfSeqs.push_back(seqName);
- setNamesOfGroups(seqGroup);
-
- treemap[seqName].groupname = seqGroup; //store data in map
+ if (m->control_pressed) { fileHandle.close(); return 1; }
- 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]++;
+ 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]++;
+ }
}
-
- gobble(fileHandle);
+
+ 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);
}
/************************************************************/
return false;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "TreeMap", "isValidGroup");
exit(1);
}
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "TreeMap", "print");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/************************************************************/
+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);
}
}
/************************************************************/
+
projects / mothur.git / blobdiff