/************************************************************/
TreeMap::TreeMap(string filename) {
+ m = MothurOut::getInstance();
+ ofstream out2;
+ m->openOutputFileAppend(filename, out2);
+ out2 << endl; out2.close();
groupFileName = filename;
m->openInputFile(filename, fileHandle);
}
/************************************************************/
TreeMap::~TreeMap(){}
-
/************************************************************/
-void TreeMap::readMap() {
- string seqName, seqGroup;
-
- while(fileHandle){
- fileHandle >> seqName; //read from first column
- fileHandle >> seqGroup; //read from second column
+int TreeMap::readMap(string gf) {
+ try {
+ ofstream out2;
+ m->openOutputFileAppend(gf, out2);
+ out2 << endl; out2.close();
+
+ groupFileName = gf;
+ m->openInputFile(gf, fileHandle);
+
+ string seqName, seqGroup;
+ int error = 0;
- 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]++;
- }
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+ fileHandle.close();
+
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeMap", "readMap");
+ exit(1);
+ }
+}
- m->gobble(fileHandle);
- }
- fileHandle.close();
+/************************************************************/
+int TreeMap::readMap() {
+ try {
+ string seqName, seqGroup;
+ int error = 0;
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+ fileHandle.close();
+
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeMap", "readMap");
+ exit(1);
+ }
}
/************************************************************/
void TreeMap::addSeq(string seqName, string seqGroup) {
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::makeSim(GroupMap* groupmap) {
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
try {
//set names of groups
- namesOfGroups = groupmap->namesOfGroups;
+ namesOfGroups = ThisnamesOfGroups;
//set names of seqs to names of groups
- namesOfSeqs = groupmap->namesOfGroups;
+ 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++) {
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