*/
#include "mgclustercommand.h"
-#include "readcluster.h"
//**********************************************************************************************************************
MGClusterCommand::MGClusterCommand(string option){
else {
//valid paramters for this command
- string Array[] = {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge"};
+ string Array[] = {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("blast");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["blast"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+
//check for required parameters
blastfile = validParameter.validFile(parameters, "blast", true);
if (blastfile == "not open") { abort = true; }
else if (blastfile == "not found") { blastfile = ""; }
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(blastfile); //if user entered a file with a path then preserve it
+ }
+
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
nameMap->readMap();
}else{ nameMap= new NameAssignment(); }
- string fileroot = getRootName(blastfile);
+ string fileroot = outputDir + getRootName(getSimpleName(blastfile));
string tag = "";
time_t start;
float previousDist = 0.00000;
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();
delete read;
//create cluster
- 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();
+ if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix, cutoff, method); }
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){
- cluster->update();
+ cluster->update(cutoff);
float dist = distMatrix->getSmallDist();
float rndDist = roundDist(dist, precision);
delete cluster;
}else { //use hcluster to cluster
- tag = "fn";
//get distmatrix and overlap
overlapFile = read->getOverlapFile();
distFile = read->getDistFile();
sortHclusterFiles(distFile, overlapFile);
//create cluster
- hcluster = new HCluster(rabund, list);
+ hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
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
-
- ifstream inHcluster;
- openInputFile(distFile, inHcluster);
+ 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();
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
}
}
}
- inHcluster.close();
+ //inHcluster.close();
if(previousDist <= 0.0000){
oldList.setLabel("unique");
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