/************************************************************/
GroupMap::~GroupMap(){}
-
/************************************************************/
int GroupMap::readMap() {
- string seqName, seqGroup;
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ m->setAllGroups(namesOfGroups);
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readMap");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::readDesignMap() {
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
- 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);
-
- it = groupmap.find(seqName);
-
- if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
- else {
- groupmap[seqName] = seqGroup; //store data in map
- seqsPerGroup[seqGroup]++; //increment number of seqs in that group
- }
- m->gobble(fileHandle);
- }
+ }
+
+ m->setAllGroups(namesOfGroups);
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readDesignMap");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::readMap(string filename) {
+ try {
+ groupFileName = filename;
+ m->openInputFile(filename, fileHandle);
+ index = 0;
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ m->setAllGroups(namesOfGroups);
return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readMap");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+ try {
+ groupFileName = filename;
+ m->openInputFile(filename, fileHandle);
+ index = 0;
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ m->setAllGroups(namesOfGroups);
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readDesignMap");
+ exit(1);
+ }
}
/************************************************************/
int GroupMap::getNumGroups() { return namesOfGroups.size(); }
if (it != groupmap.end()) { //sequence name was in group file
return it->second;
}else {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
return "not found";
}
}
/************************************************************/
void GroupMap::setGroup(string sequenceName, string groupN) {
- groupmap[sequenceName] = groupN;
+ setNamesOfGroups(groupN);
+ m->checkName(sequenceName);
+ it = groupmap.find(sequenceName);
+
+ if (it != groupmap.end()) { m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[sequenceName] = groupN; //store data in map
+ seqsPerGroup[groupN]++; //increment number of seqs in that group
+ }
}
/************************************************************/
}
}
/************************************************************/
+int GroupMap::getCopy(GroupMap* g) {
+ try {
+ vector<string> names = g->getNamesSeqs();
+ for (int i = 0; i < names.size(); i++) {
+ if (m->control_pressed) { break; }
+ string group = g->getGroup(names[i]);
+ setGroup(names[i], group);
+ }
+ return names.size();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getCopy");
+ exit(1);
+ }
+}
+/************************************************************/
int GroupMap::getNumSeqs(string group) {
try {
exit(1);
}
}
-
+/************************************************************/
+int GroupMap::renameSeq(string oldName, string newName) {
+ try {
+
+ map<string, string>::iterator itName;
+
+ itName = groupmap.find(oldName);
+
+ if (itName == groupmap.end()) {
+ m->mothurOut("[ERROR]: cannot find " + toString(oldName) + " in group file");
+ m->control_pressed = true;
+ return 0;
+ }else {
+ string group = itName->second;
+ groupmap.erase(itName);
+ groupmap[newName] = group;
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "renameSeq");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::print(ofstream& out) {
+ try {
+
+ for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+ out << itName->first << '\t' << itName->second << endl;
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "print");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::print(ofstream& out, vector<string> userGroups) {
+ try {
+
+ for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+ if (m->inUsersGroups(itName->second, userGroups)) {
+ out << itName->first << '\t' << itName->second << endl;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "print");
+ exit(1);
+ }
+}
/************************************************************/
vector<string> GroupMap::getNamesSeqs(){
try {
}
}
/************************************************************/
+vector<string> GroupMap::getNamesSeqs(vector<string> picked){
+ try {
+
+ vector<string> names;
+
+ for (it = groupmap.begin(); it != groupmap.end(); it++) {
+ //if you are belong to one the the groups in the picked vector add you
+ if (m->inUsersGroups(it->second, picked)) {
+ names.push_back(it->first);
+ }
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNamesSeqs");
+ exit(1);
+ }
+}
+
+/************************************************************/
projects / mothur.git / blobdiff