#include "treereader.h"
#include "readtree.h"
+#include "groupmap.h"
/***********************************************************************/
-
-TreeReader::TreeReader(string tf) : treefile(tf) {
+TreeReader::TreeReader(string tf, string cf) : treefile(tf), countfile(cf) {
try {
m = MothurOut::getInstance();
+ ct = new CountTable();
+ ct->readTable(cf, true);
+
+ //if no groupinfo in count file we need to add it
+ if (!ct->hasGroupInfo()) {
+ ct->addGroup("Group1");
+ vector<string> namesOfSeqs = ct->getNamesOfSeqs();
+ for (int i = 0; i < namesOfSeqs.size(); i++) {
+ ct->setAbund(namesOfSeqs[i], "Group1", ct->getNumSeqs(namesOfSeqs[i]));
+ }
+ }
namefile = "";
groupfile = "";
readTrees();
}
}
/***********************************************************************/
-
-TreeReader::TreeReader(string tf, string gf) : treefile(tf), groupfile(gf) {
- try {
- m = MothurOut::getInstance();
- namefile = "";
- readTrees();
- }
- catch(exception& e) {
- m->errorOut(e, "TreeReader", "TreeReader");
- exit(1);
- }
-}
-/***********************************************************************/
TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf), groupfile(gf), namefile(nf) {
try {
m = MothurOut::getInstance();
+ countfile = "";
+ ct = new CountTable();
+ if (namefile != "") { ct->createTable(namefile, groupfile, true); }
+ else {
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ set<string> nameMap;
+ map<string, string> groupMap;
+ set<string> gps;
+ for (int i = 0; i < m->Treenames.size(); i++) { nameMap.insert(m->Treenames[i]); }
+ if (groupfile == "") { gps.insert("Group1"); for (int i = 0; i < m->Treenames.size(); i++) { groupMap[m->Treenames[i]] = "Group1"; } }
+ else {
+ GroupMap g(groupfile);
+ g.readMap();
+ vector<string> seqs = g.getNamesSeqs();
+ for (int i = 0; i < seqs.size(); i++) {
+ string group = g.getGroup(seqs[i]);
+ groupMap[seqs[i]] = group;
+ gps.insert(group);
+ }
+ }
+ ct->createTable(nameMap, groupMap, gps);
+ }
+
readTrees();
}
catch(exception& e) {
bool TreeReader::readTrees() {
try {
- tmap = new TreeMap();
- if (groupfile != "") { tmap->readMap(groupfile); }
- else{ //fake out by putting everyone in one group
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
- }
-
- int numUniquesInName = 0;
- if (namefile != "") { numUniquesInName = readNamesFile(); }
+ int numUniquesInName = ct->getNumUniqueSeqs();
+ //if (namefile != "") { numUniquesInName = readNamesFile(); }
ReadTree* read = new ReadNewickTree(treefile);
- int readOk = read->read(tmap);
+ int readOk = read->read(ct);
if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete read; m->control_pressed=true; return 0; }
- read->AssembleTrees(names);
+ read->AssembleTrees();
trees = read->getTrees();
delete read;
//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
int numNamesInTree;
if (namefile != "") {
- if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ if (numUniquesInName == m->Treenames.size()) { numNamesInTree = ct->getNumSeqs(); }
else { numNamesInTree = m->Treenames.size(); }
}else { numNamesInTree = m->Treenames.size(); }
//output any names that are in group file but not in tree
- if (numNamesInTree < tmap->getNumSeqs()) {
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+ if (numNamesInTree < ct->getNumSeqs()) {
+ vector<string> namesSeqsCt = ct->getNamesOfSeqs();
+ for (int i = 0; i < namesSeqsCt.size(); i++) {
//is that name in the tree?
int count = 0;
for (int j = 0; j < m->Treenames.size(); j++) {
- if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
+ if (namesSeqsCt[i] == m->Treenames[j]) { break; } //found it
count++;
}
//then you did not find it so report it
if (count == m->Treenames.size()) {
- //if it is in your namefile then don't remove
- map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-
- if (it == nameMap.end()) {
- m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
+ m->mothurOut(namesSeqsCt[i] + " is in your name or group file and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+ ct->remove(namesSeqsCt[i]);
}
}
}
exit(1);
}
}
-/*****************************************************************/
-int TreeReader::readNamesFile() {
- try {
- nameMap.clear();
- names.clear();
- int numUniquesInName = 0;
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string first, second;
- map<string, string>::iterator itNames;
-
- while(!in.eof()) {
- in >> first >> second; m->gobble(in);
-
- numUniquesInName++;
-
- itNames = nameMap.find(first);
- if (itNames == nameMap.end()) {
- names[first] = second;
-
- //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
- vector<string> dupNames;
- m->splitAtComma(second, dupNames);
-
- for (int i = 0; i < dupNames.size(); i++) {
- nameMap[dupNames[i]] = first;
- if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); nameMap.clear(); names.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return numUniquesInName;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeReader", "readNamesFile");
- exit(1);
- }
-}
/***********************************************************************/
projects / mothur.git / blobdiff