*/
#include "mgclustercommand.h"
-#include "readcluster.h"
//**********************************************************************************************************************
MGClusterCommand::MGClusterCommand(string option){
start = time(NULL);
oldList = *list;
+ if (method == "furthest") { tag = "fn"; }
+ else if (method == "nearest") { tag = "nn"; }
+ else { tag = "an"; }
+
+ //open output files
+ openOutputFile(fileroot+ tag + ".list", listFile);
+ openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+
if (!hclusterWanted) {
//get distmatrix and overlap
SparseMatrix* distMatrix = read->getDistMatrix();
if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, distMatrix); }
else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, distMatrix); }
else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix); }
- tag = cluster->getTag();
cluster->setMapWanted(true);
- //open output files
- openOutputFile(fileroot+ tag + ".list", listFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
-
//cluster using cluster classes
while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
sortHclusterFiles(distFile, overlapFile);
//create cluster
- hcluster = new HCluster(rabund, list);
+ hcluster = new HCluster(rabund, list, method);
hcluster->setMapWanted(true);
- //open output files
- openOutputFile(fileroot+ tag + ".list", listFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
-
- vector<DistNode> seqs; seqs.resize(1); // to start loop
- exitedBreak = false; //lets you know if there is a distance stored in next
-
+ vector<seqDist> seqs; seqs.resize(1); // to start loop
ifstream inHcluster;
openInputFile(distFile, inHcluster);
while (seqs.size() != 0){
- seqs = getSeqs(inHcluster);
- random_shuffle(seqs.begin(), seqs.end());
+ seqs = hcluster->getSeqs(inHcluster, nameMap, cutoff);
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
while (!done) {
//get next overlap
- DistNode overlapNode;
+ seqDist overlapNode;
if (!hclusterWanted) {
if (count < overlapMatrix.size()) { //do we have another node in the matrix
overlapNode = overlapMatrix[count];
void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
try {
//sort distFile
- ReadCluster* readCluster = new ReadCluster(unsortedDist, cutoff);
- readCluster->setFormat("column");
- readCluster->read(nameMap);
- string sortedDistFile = readCluster->getOutputFile();
- ListVector* extralist = readCluster->getListVector(); //we get this so we can delete it and not have a memory leak
-
+ string sortedDistFile = sortFile(unsortedDist);
remove(unsortedDist.c_str()); //delete unsorted file
distFile = sortedDistFile;
- delete extralist;
- delete readCluster;
//sort overlap file
- readCluster = new ReadCluster(unsortedOverlap, cutoff);
- readCluster->setFormat("column");
- readCluster->read(nameMap);
- string sortedOverlapFile = readCluster->getOutputFile();
- extralist = readCluster->getListVector(); //we get this so we can delete it and not have a memory leak
-
+ string sortedOverlapFile = sortFile(unsortedOverlap);
remove(unsortedOverlap.c_str()); //delete unsorted file
overlapFile = sortedOverlapFile;
- delete extralist;
- delete readCluster;
}
catch(exception& e) {
errorOut(e, "MGClusterCommand", "sortHclusterFiles");
exit(1);
}
}
-//**********************************************************************************************************************
-vector<DistNode> MGClusterCommand::getSeqs(ifstream& filehandle){
- try {
- string firstName, secondName;
- float distance, prevDistance;
- vector<DistNode> sameSeqs;
- prevDistance = -1;
-
- //if you are not at the beginning of the file
- if (exitedBreak) {
- sameSeqs.push_back(next);
- prevDistance = next.dist;
- exitedBreak = false;
- }
-
- //get entry
- while (!filehandle.eof()) {
-
- filehandle >> firstName >> secondName >> distance; gobble(filehandle);
-
- //save first one
- if (prevDistance == -1) { prevDistance = distance; }
-
- map<string,int>::iterator itA = nameMap->find(firstName);
- map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
-
- //using cutoff
- if (distance > cutoff) { break; }
-
- if (distance != -1) { //-1 means skip me
-
- //are the distances the same
- if (distance == prevDistance) { //save in vector
- DistNode temp(itA->second, itB->second, distance);
- sameSeqs.push_back(temp);
- exitedBreak = false;
- }else{
- next.seq1 = itA->second;
- next.seq2 = itB->second;
- next.dist = distance;
- exitedBreak = true;
- break;
- }
- }
- }
-
- return sameSeqs;
- }
- catch(exception& e) {
- errorOut(e, "MGClusterCommand", "getSeqs");
- exit(1);
- }
-}
+
//**********************************************************************************************************************
projects / mothur.git / blobdiff