/************************************************************/
GroupMap::GroupMap(string filename) {
+ m = MothurOut::getInstance();
groupFileName = filename;
- openInputFile(filename, fileHandle);
+ m->openInputFile(filename, fileHandle);
index = 0;
}
/************************************************************/
- GroupMap::~GroupMap(){};
+ GroupMap::~GroupMap(){}
/************************************************************/
-void GroupMap::readMap() {
+int GroupMap::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);
+
+ 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);
+ }
+ fileHandle.close();
+ m->setAllGroups(namesOfGroups);
+ return error;
+}
+/************************************************************/
+int GroupMap::readDesignMap() {
+ 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
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
setNamesOfGroups(seqGroup);
-
- groupmap[seqName] = seqGroup; //store data in map
-
- gobble(fileHandle);
+
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group 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);
}
fileHandle.close();
+ m->setAllGroups(namesOfGroups);
+ return error;
+}
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+ groupFileName = filename;
+ m->openInputFile(filename, fileHandle);
+ index = 0;
+ 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);
+
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group 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);
+ }
+ fileHandle.close();
+ m->setAllGroups(namesOfGroups);
+ return error;
}
/************************************************************/
int GroupMap::getNumGroups() { return namesOfGroups.size(); }
}
/************************************************************/
+
void GroupMap::setGroup(string sequenceName, string groupN) {
- groupmap[sequenceName] = groupN;
+ setNamesOfGroups(groupN);
+
+ 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
+ }
}
+
/************************************************************/
void GroupMap::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
- groupIndex[seqGroup] = index;
- index++;
+ 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
+ seqsPerGroup[seqGroup] = 0;
+ groupIndex[seqGroup] = index;
+ index++;
+ }
+}
+/************************************************************/
+bool GroupMap::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, "GroupMap", "isValidGroup");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::getNumSeqs(string group) {
+ try {
+
+ map<string, int>::iterator itNum;
+
+ itNum = seqsPerGroup.find(group);
+
+ if (itNum == seqsPerGroup.end()) { return 0; }
+
+ return seqsPerGroup[group];
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNumSeqs");
+ exit(1);
+ }
+}
+
+/************************************************************/
+vector<string> GroupMap::getNamesSeqs(){
+ try {
+
+ vector<string> names;
+
+ for (it = groupmap.begin(); it != groupmap.end(); it++) {
+ names.push_back(it->first);
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNamesSeqs");
+ exit(1);
+ }
+}
+/************************************************************/
+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