//**********************************************************************************************************************
//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-HClusterCommand::HClusterCommand(string option){
+HClusterCommand::HClusterCommand(string option) {
try{
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"};
+ string Array[] = {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","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;
}
globaldata->newRead();
+ //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("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->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; }
+ }
+ }
+
+ //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 = ""; }
+
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a hcluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+ if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
length = temp.length();
convert(temp, precision);
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
+ hard = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
convert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
+ cutoff += (5 / (precision * 10.0));
method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "nearest"; }
+ if (method == "not found") { method = "furthest"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
- else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
showabund = validParameter.validFile(parameters, "showabund", false);
if (showabund == "not found") { showabund = "T"; }
sort = validParameter.validFile(parameters, "sorted", false);
if (sort == "not found") { sort = "F"; }
- sorted = isTrue(sort);
+ sorted = m->isTrue(sort);
timing = validParameter.validFile(parameters, "timing", false);
if (timing == "not found") { timing = "F"; }
if (abort == false) {
-
- fileroot = getRootName(distfile);
- tag = "fn"; //until we figure out average and nearest methods
+ if (outputDir == "") { outputDir += m->hasPath(distfile); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
+
+ if (method == "furthest") { tag = "fn"; }
+ else if (method == "nearest") { tag = "nn"; }
+ else { tag = "an"; }
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".list", listFile);
+ m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+ m->openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ m->openOutputFile(fileroot+ tag + ".list", listFile);
+
+ outputNames.push_back(fileroot+ tag + ".sabund");
+ outputNames.push_back(fileroot+ tag + ".rabund");
+ outputNames.push_back(fileroot+ tag + ".list");
}
}
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "HClusterCommand");
+ m->errorOut(e, "HClusterCommand", "HClusterCommand");
exit(1);
}
}
void HClusterCommand::help(){
try {
- mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
- mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
- mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
- mothurOut("The hcluster command should be in the following format: \n");
- mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- mothurOut("The acceptable hcluster methods is furthest, but we hope to add nearest and average in the future.\n\n");
+ m->mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
+ m->mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
+ m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
+ m->mothurOut("The hcluster command should be in the following format: \n");
+ m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+ m->mothurOut("The acceptable hcluster methods are furthest, nearest and average.\n\n");
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "help");
+ m->errorOut(e, "HClusterCommand", "help");
exit(1);
}
}
time_t estart = time(NULL);
if (!sorted) {
- read = new ReadCluster(distfile, cutoff);
+ read = new ReadCluster(distfile, cutoff, outputDir, true);
read->setFormat(format);
read->read(globaldata->nameMap);
+
+ if (m->control_pressed) {
+ delete read;
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
distfile = read->getOutputFile();
list = read->getListVector();
}else {
list = new ListVector(globaldata->nameMap->getListVector());
}
-
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
+
+ if (m->control_pressed) {
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); m->mothurOutEndLine();
estart = time(NULL);
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
}else{
- mothurOut("Error: no list vector!"); mothurOutEndLine(); return 0;
+ m->mothurOut("Error: no list vector!"); m->mothurOutEndLine(); return 0;
}
float previousDist = 0.00000;
print_start = true;
start = time(NULL);
-
- ifstream in;
- openInputFile(distfile, in);
- string firstName, secondName;
- float distance;
-
- cluster = new HCluster(rabund, list);
+
+ cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
vector<seqDist> seqs; seqs.resize(1); // to start loop
- exitedBreak = false; //lets you know if there is a distance stored in next
-
+
+ if (m->control_pressed) {
+ delete cluster;
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+
while (seqs.size() != 0){
- seqs = getSeqs(in);
- random_shuffle(seqs.begin(), seqs.end());
+ seqs = cluster->getSeqs();
- if (seqs.size() == 0) { break; } //there are no more distances
-
- for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
+ if (m->control_pressed) {
+ delete cluster;
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
- if (print_start && isTrue(timing)) {
- mothurOut("Clustering (" + tag + ") dist " + toString(distance) + "/"
- + toString(roundDist(distance, precision))
- + "\t(precision: " + toString(precision) + ")");
- cout.flush();
- print_start = false;
- }
+ for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
- //cout << "before cluster update" << endl;
if (seqs[i].seq1 != seqs[i].seq2) {
cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
- float rndDist = roundDist(seqs[i].dist, precision);
- //cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;
-
+ if (m->control_pressed) {
+ delete cluster;
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(seqs[i].dist, precision);
+ }else{
+ rndDist = m->roundDist(seqs[i].dist, precision);
+ }
+
if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
printData("unique");
else if((rndDist != rndPreviousDist)){
printData(toString(rndPreviousDist, length-1));
}
-
+
previousDist = seqs[i].dist;
rndPreviousDist = rndDist;
oldRAbund = *rabund;
}
}
}
-
- in.close();
- if (print_start && isTrue(timing)) {
- //mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
- //+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
- cout.flush();
- print_start = false;
+ if (m->control_pressed) {
+ delete cluster;
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
}
-
+
if(previousDist <= 0.0000){
printData("unique");
}
sabundFile.close();
rabundFile.close();
listFile.close();
-
delete cluster;
- //if (isTrue(timing)) {
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine();
- //}
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "execute");
+ m->errorOut(e, "HClusterCommand", "execute");
exit(1);
}
}
void HClusterCommand::printData(string label){
try {
- if (isTrue(timing)) {
- mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
- + "\tclusters. Updates: " + toString(loops)); mothurOutEndLine();
+ if (m->isTrue(timing)) {
+ m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
+ + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
}
print_start = true;
loops = 0;
start = time(NULL);
oldRAbund.setLabel(label);
- if (isTrue(showabund)) {
+ if (m->isTrue(showabund)) {
oldRAbund.getSAbundVector().print(cout);
}
oldRAbund.print(rabundFile);
oldList.print(listFile);
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "printData");
+ m->errorOut(e, "HClusterCommand", "printData");
exit(1);
}
}
//**********************************************************************************************************************
-vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
- try {
- string firstName, secondName;
- float distance, prevDistance;
- vector<seqDist> 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) {
-
- filehandle >> firstName >> secondName >> distance;
-//cout << firstName << '\t' << secondName << '\t' << distance << endl;
- gobble(filehandle);
-
- //save first one
- if (prevDistance == -1) { prevDistance = distance; }
- //cout << prevDistance << endl;
-//if (globaldata->nameMap == NULL) { cout << "null" << endl; }
- map<string,int>::iterator itA = globaldata->nameMap->find(firstName);
- map<string,int>::iterator itB = globaldata->nameMap->find(secondName);
-
- if(itA == globaldata->nameMap->end()){
- cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
- }
- if(itB == globaldata->nameMap->end()){
- cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
- }
- //cout << "here" << endl;
- //using cutoff
- if (distance > cutoff) { break; }
-
- if (distance != -1) { //-1 means skip me
-
- //are the distances the same
- if (distance == prevDistance) { //save in vector
- seqDist temp;
- temp.seq1 = itA->second;
- temp.seq2 = itB->second;
- temp.dist = distance;
- sameSeqs.push_back(temp);
- exitedBreak = false;
- //what about precision??
-
- }else{
- next.seq1 = itA->second;
- next.seq2 = itB->second;
- next.dist = distance;
- exitedBreak = true;
- break;
- }
-
- }
- }
-
- return sameSeqs;
- }
- catch(exception& e) {
- errorOut(e, "HClusterCommand", "getSeqs");
- exit(1);
- }
-
-
-}
-
-//**********************************************************************************************************************
projects / mothur.git / blobdiff